Contacts of the helix formed by residues 101 - 121 (chain B) in PDB entry 2PS2
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 HIS 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B GLY* 4.8 10.8 + - - -
71B GLY* 4.9 1.6 - - - -
98B LEU* 3.5 26.1 - - + +
99B LEU 3.0 24.0 - - - -
100B GLY* 1.3 72.8 - - - +
102B GLU* 1.3 68.4 + - - +
103B ASP* 3.1 16.2 + - - +
104B ALA* 3.0 15.5 + - + +
105B LYS* 3.1 14.1 + - + +
62C ALA* 3.7 27.2 + - + +
63C SER* 4.5 0.4 - - - -
64C HIS* 3.3 33.5 + + - -
67C GLY* 5.5 1.1 - - - -
101C HIS* 5.3 13.9 - + - -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLY* 3.6 19.3 - - - +
101B HIS* 1.3 82.1 + - - +
103B ASP* 1.3 58.4 + - - +
105B LYS* 3.8 7.9 + - + -
106B THR* 2.7 34.1 + - - -
249B THR* 4.8 6.2 - - - +
250B ASN* 3.0 38.2 + - + +
271B SER 3.5 1.8 - - - +
272B LYS* 3.4 23.0 - - - +
273B ALA 3.5 20.0 - - - +
274B GLY* 3.5 12.3 - - - +
278B ARG* 4.5 9.6 + - - +
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 2.6 33.7 + - - +
55B PRO* 5.9 0.2 - - + -
61B ILE* 6.3 1.1 - - + -
62B ALA 4.5 3.4 - - - +
63B SER* 2.5 42.1 + - - +
64B HIS 4.1 2.3 + - - +
67B GLY* 4.9 2.3 - - - +
68B VAL* 3.6 24.1 + - + +
101B HIS* 3.5 19.1 + - - +
102B GLU* 1.3 81.2 + - - +
104B ALA* 1.3 66.9 + - - +
106B THR* 3.8 3.9 - - - -
271B SER* 3.3 17.3 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLY 4.5 1.1 - - - +
68B VAL* 3.5 31.9 - - - +
71B GLY* 3.8 15.0 - - - -
72B ILE* 3.5 19.9 - - - +
75B MET* 3.7 18.2 - - + +
101B HIS* 3.0 12.9 + - + +
103B ASP* 1.3 84.3 + - - +
105B LYS* 1.3 63.7 + - - +
106B THR 3.6 0.2 + - - -
107B ALA* 4.3 2.9 + - - +
108B ILE* 4.2 6.1 - - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 3.4 27.8 - - + -
91B ASN* 5.5 2.7 - - - +
94B MET* 3.6 26.5 - - + +
95B ASP* 2.8 24.8 + - - +
98B LEU 2.9 25.0 + - - -
99B LEU* 4.4 0.6 - - - +
100B GLY* 2.8 34.7 + - - +
101B HIS* 3.1 8.8 + - - +
102B GLU* 3.3 9.0 + - + +
104B ALA* 1.3 76.5 - - - +
106B THR* 1.3 64.6 + - - +
108B ILE* 3.3 5.5 + - - +
109B ASP* 3.1 21.8 + - - +
274B GLY* 4.0 9.6 - - - +
278B ARG* 3.7 19.0 - - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU 3.5 18.4 - - - +
53B SER* 4.4 0.4 - - - -
102B GLU 2.7 21.2 + - - -
103B ASP 3.8 8.1 - - - -
104B ALA 3.3 0.8 - - - -
105B LYS* 1.3 74.7 - - - +
107B ALA* 1.3 64.6 + - - +
109B ASP* 3.2 2.1 + - - +
110B VAL* 3.0 26.0 + - + +
270B ILE* 4.0 19.3 - - + +
271B SER* 3.1 35.7 + - - -
274B GLY 3.2 18.6 + - - -
275B GLY* 4.1 1.8 - - - -
297B GLU* 4.9 0.2 - - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 4.5 2.5 - - + +
39B VAL* 3.6 27.8 - - + +
51B GLY* 3.4 21.2 + - - +
52B GLU* 3.8 22.0 + - - +
53B SER* 4.2 9.2 - - - +
72B ILE* 4.9 7.2 - - + -
104B ALA 4.3 1.6 + - - +
105B LYS 3.5 0.4 - - - -
106B THR* 1.3 79.2 - - - +
108B ILE* 1.3 62.1 + - - +
111B ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.7 0.7 - - + -
9B ILE* 3.8 22.0 - - + -
39B VAL* 3.6 30.3 - - + -
41B ILE* 3.6 15.6 - - + +
72B ILE* 4.4 13.9 - - + -
76B ALA* 5.7 1.3 - - + -
79B LEU* 3.7 26.0 - - + -
90B ILE* 4.7 2.7 - - + -
94B MET* 3.4 31.6 - - + -
104B ALA 4.2 9.2 - - - +
105B LYS 3.3 0.6 + - - +
106B THR 3.2 0.6 - - - -
107B ALA* 1.3 75.6 - - - +
109B ASP* 1.3 67.3 + - - +
111B ALA* 3.2 4.7 + - - +
112B CYS* 3.0 28.4 + - - -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL* 4.5 2.6 - - - +
90B ILE* 5.5 3.2 - - - +
91B ASN* 2.8 23.3 + - - +
94B MET* 4.8 2.6 - - - -
105B LYS 3.1 10.6 + - - +
106B THR 3.7 6.7 - - - +
108B ILE* 1.3 81.2 - - - +
110B VAL* 1.3 62.6 + - - +
112B CYS* 3.0 18.1 + - - +
113B TRP* 3.0 19.0 + - - -
274B GLY 4.0 10.8 - - - +
275B GLY* 4.2 1.6 - - - -
276B LEU 2.7 29.1 + - - -
277B THR* 2.5 32.0 + - - -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TRP 3.6 4.7 - - - +
51B GLY* 3.8 14.4 - - - -
52B GLU 4.8 3.4 - - - +
106B THR* 3.0 30.2 + - + +
109B ASP* 1.3 76.3 - - - +
111B ALA* 1.3 63.5 + - - +
113B TRP* 3.2 8.4 + - - +
114B ASP* 3.0 19.8 + - - +
270B ILE* 4.3 1.8 - - + -
276B LEU* 4.3 28.7 - - + +
303B ILE 5.2 2.9 - - - +
307B ALA* 4.2 23.1 - - + -
354B LEU* 3.6 24.9 - - + +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 4.1 4.0 - - + +
41B ILE* 3.7 20.6 - - + -
49B GLY* 3.5 21.1 - - - +
50B TRP 3.4 18.3 + - - +
51B GLY 3.9 0.7 - - - +
107B ALA 3.1 19.4 + - - +
108B ILE 3.6 4.3 - - - +
110B VAL* 1.3 76.0 - - - +
112B CYS* 1.3 63.2 + - - +
114B ASP* 3.2 4.4 + - - +
115B ILE* 3.0 27.0 + - - +
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.4 5.6 - - - -
41B ILE* 3.8 15.9 - - - -
84B PRO* 3.5 39.2 - - - +
87B VAL* 4.7 6.7 - - + -
90B ILE* 4.2 24.0 - - + -
108B ILE* 3.0 17.3 + - - -
109B ASP* 3.0 12.4 + - - +
111B ALA* 1.3 78.4 - - - +
113B TRP* 1.3 56.6 + - - +
115B ILE* 3.2 9.3 + - - +
116B PHE* 2.8 29.3 + - - +
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL* 3.7 28.8 - - + +
109B ASP* 3.0 36.7 + - - -
110B VAL 3.5 7.4 - - - +
112B CYS* 1.3 72.7 - - - +
114B ASP* 1.3 61.2 + - - +
116B PHE* 3.4 26.9 - + - +
117B GLY 2.9 25.1 + - - -
124B VAL* 3.6 28.8 - - + +
127B LEU* 3.8 34.8 - - + -
128B LEU* 3.4 31.0 - - + -
276B LEU* 3.5 27.4 - - + -
277B THR* 2.8 30.1 + - - +
280B ARG* 4.2 13.5 - - - -
354B LEU* 5.2 0.2 - - + -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY* 3.3 9.6 - - - -
50B TRP* 2.9 29.3 + - - +
110B VAL 3.0 13.0 + - - +
111B ALA 3.4 9.0 - - - +
112B CYS 3.2 0.2 - - - -
113B TRP* 1.3 77.3 - - - +
115B ILE* 1.3 62.4 + - - +
117B GLY 3.3 0.3 + - - -
118B LYS* 2.9 47.2 + - - +
124B VAL* 4.4 0.4 - - - +
353B GLY* 3.6 4.3 - - - -
354B LEU* 2.8 46.8 + - + +
355B GLY 4.4 1.0 + - - -
356B ILE* 4.7 5.8 + - - +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.2 10.3 - - + -
41B ILE* 3.4 46.4 - - + +
43B THR* 3.6 31.4 - - + -
47B ILE* 4.1 15.7 - - + +
48B GLU 3.9 3.4 - - - -
49B GLY* 3.5 15.3 - - - +
84B PRO* 3.9 21.1 - - + -
85B ARG* 5.3 0.2 - - + -
111B ALA 3.0 14.5 + - - +
112B CYS* 3.5 6.7 - - - +
114B ASP* 1.3 76.1 - - - +
116B PHE* 1.3 55.2 + - - +
118B LYS* 3.0 3.1 + - - +
119B SER* 2.7 33.6 + - - -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO 4.9 0.4 - - - +
85B ARG* 3.7 49.4 - - + -
87B VAL* 4.3 9.0 - - + -
112B CYS 2.8 20.7 + - - +
113B TRP* 3.4 35.7 - + - +
115B ILE* 1.3 72.5 - - - +
117B GLY* 1.3 62.1 + - - +
119B SER* 2.6 24.8 + - - -
120B VAL* 3.3 19.9 + - + +
127B LEU* 3.7 33.2 - - + -
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TRP 2.9 18.2 + - - -
114B ASP 3.8 1.1 - - - -
116B PHE* 1.3 74.0 - - - +
118B LYS* 1.3 57.0 + - - +
120B VAL 3.5 0.2 + - - -
121B GLY* 3.0 9.7 + - - -
122B LEU 2.9 44.3 + - - +
124B VAL* 5.0 2.0 - - - -
127B LEU* 3.6 13.6 - - - +
353B GLY* 3.5 9.9 + - - -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.9 18.4 - - + -
48B GLU* 2.7 34.0 + - - +
50B TRP* 4.8 7.1 - - - +
114B ASP* 2.9 37.3 + - - +
115B ILE 3.5 6.1 - - - +
117B GLY* 1.3 75.7 - - - +
119B SER* 1.3 63.5 + - - +
120B VAL 3.3 0.7 + - - -
121B GLY* 3.3 10.0 + - - -
352B PRO* 4.2 15.7 - - + +
353B GLY* 4.3 8.5 - - - +
355B GLY 6.1 0.7 - - - +
356B ILE 4.9 11.5 + - - -
357B MET* 5.6 6.6 - - - -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.0 24.7 - - - -
47B ILE* 4.1 14.1 - - - +
85B ARG* 3.6 19.7 - - - +
115B ILE 2.7 16.2 + - - -
116B PHE* 2.6 22.0 + - - -
118B LYS* 1.3 74.4 - - - +
120B VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ARG* 5.4 5.4 - - - +
116B PHE* 3.5 24.0 - - + +
117B GLY 3.8 3.1 - - - +
119B SER* 1.3 90.0 + - - +
121B GLY* 1.3 62.6 + - - +
122B LEU* 4.0 23.3 - - + +
127B LEU* 3.8 24.5 - - + -
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY 3.0 6.9 + - - -
118B LYS 3.3 9.8 + - - -
119B SER 4.0 0.2 + - - -
120B VAL* 1.3 79.1 - - - +
122B LEU* 1.3 65.4 + - - +
123B PRO* 4.5 1.6 - - - +
352B PRO* 3.9 22.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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