Contacts of the helix formed by residues 102 - 128 (chain L) in PDB entry 1VEQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 102 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L VAL* 3.8 17.0 - - + -
43L VAL 3.1 13.6 + - - +
44L GLY* 3.9 12.3 - - - +
45L PRO* 4.7 1.6 - - + -
46L ASN* 3.6 37.7 - - - +
47L PHE 4.6 0.2 - - - +
50L VAL* 3.2 37.5 - - + -
101L THR* 1.3 76.8 - - - +
103L GLN* 1.3 75.2 + - + +
105L HIS* 3.2 2.3 + - - +
106L LEU* 3.1 32.6 + - + +
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Residues in contact with GLN 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 4.5 18.8 - - - +
46L ASN* 4.8 4.5 + - - +
101L THR* 3.6 10.1 - - - +
102L VAL* 1.3 89.8 - - + +
104L ALA* 1.3 66.8 + - - +
106L LEU* 3.4 3.7 + - - +
107L ALA* 3.0 23.7 + - - +
155L HIS* 4.0 20.4 + - - +
156L LEU* 4.1 19.9 - - + +
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Residues in contact with ALA 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L VAL* 4.8 6.1 - - + -
100L ASP* 3.5 28.9 - - + +
101L THR* 2.9 24.6 + - - +
103L GLN* 1.3 78.6 - - - +
105L HIS* 1.3 62.9 + - - +
107L ALA* 3.5 4.3 - - - +
108L ALA* 3.0 21.6 + - - +
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Residues in contact with HIS 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L VAL* 3.9 20.3 - - + +
41L ASN* 3.2 28.4 + - + -
42L VAL* 3.7 23.1 - - + -
50L VAL* 6.5 0.4 - - + -
95L TYR* 2.6 40.2 + + - +
97L VAL* 3.1 29.6 - - + +
98L GLU 3.1 12.4 + - - -
100L ASP* 3.6 6.5 + - + -
101L THR 3.4 19.3 + - - -
102L VAL 3.2 6.0 + - - +
104L ALA* 1.3 78.0 - - - +
106L LEU* 1.3 56.4 + - + +
108L ALA* 2.8 3.4 + - - -
109L LEU* 2.5 37.8 + - + +
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Residues in contact with LEU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L VAL* 6.5 0.7 - - + -
50L VAL* 3.9 10.8 - - + -
53L MET* 4.1 16.6 - - + -
54L ILE* 6.2 0.9 - - + -
102L VAL* 3.1 36.4 + - + +
103L GLN* 3.8 5.6 - - - +
105L HIS* 1.3 79.1 - - + +
107L ALA* 1.3 57.9 + - - +
109L LEU* 4.1 9.6 - - + -
110L ASP* 2.8 26.5 + - - +
152L VAL* 3.1 41.0 - - + +
155L HIS* 3.4 37.2 - - + -
156L LEU* 4.0 12.6 - - + -
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Residues in contact with ALA 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L GLN 3.0 18.7 + - - +
104L ALA* 3.5 4.7 - - - +
106L LEU* 1.3 75.8 - - - +
108L ALA* 1.3 61.2 + - - +
110L ASP* 3.0 8.0 - - - +
111L LEU* 3.0 27.7 - - + +
156L LEU* 3.8 21.4 - - + +
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Residues in contact with ALA 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L TYR* 3.5 23.1 - - + +
97L VAL* 4.0 13.7 - - + -
104L ALA 3.0 12.1 + - - +
105L HIS 2.8 7.5 + - - +
107L ALA* 1.3 75.8 - - - +
109L LEU* 1.3 60.9 + - - +
111L LEU* 3.4 14.2 + - - +
112L VAL* 2.9 25.8 + - - +
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Residues in contact with LEU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 5.6 0.4 - - + -
34L THR* 4.7 9.0 - - + -
35L LEU* 3.9 29.2 - - + -
38L VAL* 4.2 31.6 - - + -
54L ILE* 5.4 2.9 - - + -
95L TYR* 4.1 7.4 - - + -
105L HIS 2.5 18.9 + - - +
106L LEU* 3.5 14.4 - - + +
108L ALA* 1.3 71.8 - - - +
110L ASP* 1.3 65.6 + - - +
112L VAL* 2.9 28.5 + - + +
113L TYR* 3.0 28.7 + - + -
148L PHE* 4.2 17.7 - - + -
152L VAL* 4.3 9.6 - - + -
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Residues in contact with ASP 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L LEU 2.8 14.3 + - - +
107L ALA* 3.0 16.8 - - - +
109L LEU* 1.3 77.8 - - - +
111L LEU* 1.3 67.3 + - + +
113L TYR* 3.3 2.8 + - - +
114L ASN* 2.9 27.6 + - - +
149L GLN* 3.4 8.9 + - - +
152L VAL* 4.2 8.7 - - + +
153L ARG* 2.7 47.8 + - - +
156L LEU* 4.6 10.4 - - + +
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L ALA* 3.0 20.9 - - + +
108L ALA* 3.4 12.1 + - - +
109L LEU 3.1 0.4 - - - -
110L ASP* 1.3 84.2 - - + +
112L VAL* 1.3 67.1 + - + +
114L ASN* 2.9 29.7 + - + +
115L GLY 3.1 5.2 + - - -
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Residues in contact with VAL 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ASP* 5.0 11.7 - - - +
31L LEU* 4.7 16.6 - - + -
34L THR* 5.3 8.7 - - + -
92L TRP* 5.7 6.5 - - + -
95L TYR* 4.4 13.7 - - + -
108L ALA 2.9 20.6 - - - +
109L LEU* 2.9 25.1 + - + +
111L LEU* 1.3 75.5 - - + +
113L TYR* 1.3 63.3 + - + +
115L GLY* 3.3 3.1 + - - -
116L VAL* 3.1 28.9 + - + +
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Residues in contact with TYR 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 3.4 30.2 - - + +
35L LEU* 3.5 17.3 - - + +
57L GLN* 3.2 27.4 + - - +
109L LEU* 3.0 27.1 + - + +
110L ASP 3.6 4.5 - - - +
112L VAL* 1.3 75.3 - - + +
114L ASN* 1.3 58.2 + - - +
116L VAL* 4.2 5.8 - - + -
117L ILE* 2.7 42.6 + - + +
145L LEU* 3.6 44.4 - - + -
148L PHE* 3.4 33.0 - + - -
149L GLN* 3.4 27.6 - - + +
152L VAL* 5.5 1.1 - - + -
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Residues in contact with ASN 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J PRO* 3.7 28.4 - - + +
110L ASP* 2.9 21.7 + - - +
111L LEU* 2.9 20.1 + - - +
113L TYR* 1.3 76.4 - - - +
115L GLY* 1.3 58.0 + - - +
117L ILE 3.9 0.2 - - - -
118L GLU* 2.9 35.0 + - - +
149L GLN* 3.0 12.0 + - - +
153L ARG* 3.1 15.9 + - - +
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Residues in contact with GLY 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L TRP* 4.3 14.3 - - - -
111L LEU 3.1 6.8 + - - -
112L VAL* 3.7 4.7 - - - -
113L TYR 3.2 0.2 - - - -
114L ASN* 1.3 80.3 - - - +
116L VAL* 1.3 60.2 + - - +
118L GLU* 4.1 7.2 - - - -
119L ASP* 3.2 30.5 + - - +
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Residues in contact with VAL 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L THR* 3.9 30.7 - - + +
28L TYR* 4.7 7.4 - - + -
31L LEU* 4.5 31.2 - - + -
92L TRP* 4.7 7.4 - - + -
112L VAL* 3.1 22.4 - - + +
113L TYR* 3.0 11.5 + - + +
115L GLY* 1.3 77.4 - - - +
117L ILE* 1.3 62.0 + - + +
119L ASP* 3.8 1.8 + - - +
120L THR* 2.7 39.2 + - - +
145L LEU* 4.7 15.5 - - + -
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Residues in contact with ILE 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 4.2 10.3 - - + -
7J PRO* 4.3 10.5 - - + +
113L TYR* 2.7 25.8 + - + +
114L ASN 4.0 1.6 - - - +
116L VAL* 1.3 73.8 - - + +
118L GLU* 1.3 58.0 + - - +
120L THR* 3.3 6.8 + - - -
121L ARG* 2.9 36.4 + - + +
142L ALA* 5.6 3.4 - - + +
145L LEU* 4.5 11.9 - - + -
146L GLU* 3.5 55.0 - - + +
149L GLN* 3.5 38.8 - - + +
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Residues in contact with GLU 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J PRO* 3.9 30.5 + - + +
8J GLY* 5.2 2.9 - - - -
114L ASN* 2.9 20.3 + - - +
115L GLY* 4.4 5.4 - - - +
117L ILE* 1.3 74.2 - - - +
119L ASP* 1.3 71.3 + - - +
120L THR 3.0 1.0 + - - -
121L ARG* 3.2 4.9 + - + +
122L LYS* 3.1 22.9 + - - +
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Residues in contact with ASP 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LYS* 3.3 34.5 + - + -
24L GLN* 4.7 7.4 - - - +
27L THR* 5.2 9.2 + - + +
91L THR* 5.0 4.1 + - - -
92L TRP* 5.0 11.0 - - - -
115L GLY* 3.2 23.9 + - - +
116L VAL* 4.2 3.6 - - - +
118L GLU* 1.3 84.0 - - - +
120L THR* 1.3 60.5 + - - +
122L LYS* 3.8 6.4 + - - +
123L SER* 3.1 26.6 + - - -
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Residues in contact with THR 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLN* 2.6 24.9 + - - +
28L TYR* 4.8 1.9 + - - +
116L VAL* 2.7 26.8 + - - +
117L ILE* 3.3 7.1 - - - -
118L GLU 3.0 0.6 + - - -
119L ASP* 1.3 75.3 - - - +
121L ARG* 1.3 68.7 + - + +
123L SER* 2.8 16.2 + - - -
124L ILE* 2.8 29.0 + - + +
138L LEU* 3.6 28.5 - - + +
141L HIS* 5.7 0.4 - - + -
142L ALA* 4.4 14.4 - - + +
145L LEU* 5.7 4.2 - - + +
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Residues in contact with ARG 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 3.5 19.2 - - - +
7J PRO 4.3 9.4 - - - +
8J GLY* 5.2 9.3 + - - -
9J LEU* 4.3 18.8 - - - +
71J ARG* 3.7 5.9 - - - +
131J ASP* 2.6 33.8 + - - +
132J LEU* 4.7 3.2 - - - +
133J VAL* 3.9 10.6 - - - +
117L ILE* 2.9 30.5 + - + +
118L GLU* 3.5 5.8 - - + +
120L THR* 1.3 72.9 - - + +
122L LYS* 1.3 63.9 + - - +
124L ILE* 2.9 25.3 + - - +
125L GLU* 3.0 15.0 + - - +
142L ALA* 5.8 0.7 - - + -
146L GLU* 2.9 39.4 + - - +
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Residues in contact with LYS 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L GLU 3.1 12.8 + - - +
119L ASP* 3.9 6.1 - - - +
121L ARG* 1.3 78.3 - - - +
123L SER* 1.3 64.0 + - - +
124L ILE 3.1 0.3 + - - -
125L GLU* 3.3 5.9 + - - +
126L LYS* 2.9 38.9 + - - +
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Residues in contact with SER 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 3.3 30.8 + - - +
23L LYS* 5.8 3.1 - - - +
24L GLN* 4.2 11.4 + - - -
119L ASP 3.1 13.9 + - - -
120L THR* 2.8 16.9 + - - -
122L LYS* 1.3 74.3 - - - +
124L ILE* 1.3 59.3 + - - +
126L LYS* 3.9 7.9 - - - +
127L LEU* 3.0 33.5 + - - +
138L LEU* 5.0 9.2 - - - -
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Residues in contact with ILE 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU* 4.6 13.0 - - + -
133J VAL* 5.0 6.5 - - + -
120L THR* 2.8 31.4 + - + +
121L ARG* 2.9 16.6 + - - +
123L SER* 1.3 76.2 - - - +
125L GLU* 1.3 58.9 + - - +
127L LEU* 2.7 34.8 + - - +
128L GLU 3.3 5.0 + - - -
135L GLN* 3.5 28.2 + - + +
138L LEU* 4.0 15.5 - - + +
139L ILE* 3.8 37.5 - - + +
142L ALA* 4.5 8.5 - - + -
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Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LEU* 4.6 19.9 - - + +
121L ARG 3.0 8.3 + - - +
122L LYS* 3.8 8.5 - - - +
124L ILE* 1.3 81.5 - - - +
126L LYS* 1.3 62.2 + - - +
127L LEU 3.2 0.7 + - - -
128L GLU* 3.4 25.6 + - - +
129L ASP* 4.6 6.6 - - - +
135L GLN* 5.1 2.0 - - - +
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Residues in contact with LYS 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 4.5 26.0 - - + +
122L LYS* 2.9 26.9 + - - +
123L SER* 3.9 7.0 - - - +
124L ILE 3.0 0.2 + - - -
125L GLU* 1.3 76.6 - - - +
127L LEU* 1.3 61.2 + - - +
128L GLU 3.8 0.2 + - - -
129L ASP* 4.1 9.3 + - - +
130L LEU* 3.6 19.1 + - + +
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Residues in contact with LEU 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L VAL* 3.9 29.8 - - + -
20L LEU* 4.1 10.5 - - + -
21L LEU* 5.0 7.2 - - + -
123L SER* 3.0 24.5 + - - +
124L ILE* 2.7 20.3 + - - +
126L LYS* 1.3 70.5 - - - +
128L GLU* 1.3 55.7 + - - +
129L ASP 2.9 5.8 - - - -
130L LEU* 2.8 39.6 + - + +
131L ASP 3.2 25.1 + - - +
134L SER* 3.2 29.6 - - - +
135L GLN* 4.2 9.9 - - + -
138L LEU* 4.5 11.2 - - + -
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Residues in contact with GLU 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J GLU* 4.0 14.5 - - - +
132J LEU* 4.8 14.6 - - - +
128K GLU* 4.0 19.4 - - - +
124L ILE 3.3 6.0 + - - +
125L GLU* 3.4 23.4 + - - +
127L LEU* 1.3 74.9 - - - +
129L ASP* 1.3 65.1 + - - +
130L LEU 5.2 0.2 - - - -
132L LEU* 4.5 22.1 - - + +
135L GLN* 3.3 30.5 + - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il