Contacts of the helix formed by residues 90 - 115 (chain A) in PDB entry 4KNF
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 PRO 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.2 7.9 - - + -
79A MET* 3.5 42.6 - - + +
82A VAL* 3.8 23.6 - - + -
83A TRP* 4.8 2.9 - - + +
88A ASP 3.3 6.7 - - - +
89A THR* 1.4 78.2 - - - +
91A THR* 1.3 59.3 + - - +
92A VAL 3.4 2.0 + - - -
93A PHE* 3.5 2.2 + - + -
94A ARG* 2.9 30.2 + - - +
221A ASN* 3.7 22.0 - - - +
22E ASP* 3.6 15.0 - - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 2.9 26.4 + - - +
90A PRO* 1.3 71.8 - - - +
92A VAL* 1.3 60.8 + - + +
94A ARG* 3.2 8.6 + - - +
95A TYR* 2.9 46.2 + - + -
139A PHE* 4.2 13.5 - - + -
142A GLU* 3.7 39.7 + - + +
143A ALA* 4.6 2.7 - - + +
208A TYR* 4.5 5.7 + - - -
22E ASP* 3.2 5.5 + - - -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 1.3 73.1 - - + +
93A PHE* 1.3 52.6 + - - +
95A TYR* 3.3 1.0 + - - +
96A ILE* 2.7 51.8 + - + +
139A PHE* 4.2 17.9 - - + -
143A ALA* 6.1 0.9 - - + -
22E ASP* 2.8 25.2 + - - +
23E LEU* 3.4 41.1 - - + +
25E ILE* 4.0 37.5 - - + +
31E VAL* 4.9 0.7 - - + -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 4.0 13.4 - + + +
78A TYR* 3.7 39.5 - + + -
79A MET* 3.6 21.5 - - + +
82A VAL* 3.9 16.8 - - + -
90A PRO* 3.8 2.9 - - + +
91A THR 3.4 0.2 - - - -
92A VAL* 1.3 75.5 - - - +
94A ARG* 1.3 56.4 + - - +
96A ILE* 3.8 2.9 - - + +
97A ASN* 2.9 31.7 + - - +
21E GLY 3.8 14.1 - - - -
22E ASP* 3.1 22.3 + - - +
23E LEU* 3.6 39.5 - - + -
34E TRP* 3.6 37.5 - + - -
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.5 12.3 - - - -
76A TYR* 3.1 21.8 + - - -
79A MET* 3.5 20.9 - - - -
90A PRO* 2.9 15.9 + - - +
91A THR* 3.2 13.0 + - - +
93A PHE* 1.3 76.1 - - - +
95A TYR* 1.3 59.9 + - + +
97A ASN* 3.4 4.7 - - - +
98A TRP* 3.0 69.7 + - + +
221A ASN* 2.8 33.7 + - - -
224A TYR* 3.5 25.0 - - + +
225A ASN* 3.0 29.7 + - - -
228A ASP* 3.3 7.5 + - - -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 2.9 31.6 + - + +
92A VAL 4.2 1.6 - - - +
94A ARG* 1.3 74.3 - - + +
96A ILE* 1.3 58.8 + - + +
98A TRP* 3.6 31.1 - + - +
99A LEU* 2.8 36.2 + - - +
135A LEU* 3.4 41.0 - - + +
138A GLY* 3.2 17.7 - - - -
139A PHE* 3.4 40.6 - + + -
142A GLU* 2.5 38.5 + - + -
224A TYR* 5.4 0.2 - + - -
301A RET 3.6 12.6 - - + +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 3.5 7.2 - - - +
92A VAL* 2.7 44.6 + - + +
93A PHE* 3.8 5.6 - - - +
95A TYR* 1.3 71.7 - - - +
97A ASN* 1.3 63.5 + - - +
99A LEU* 3.2 13.9 + - + +
100A LEU* 2.9 29.2 + - + +
23E LEU* 4.1 11.9 - - + -
25E ILE* 5.4 3.8 - - + -
31E VAL* 3.9 27.4 - - + -
34E TRP* 3.3 34.8 - - + +
35E LEU* 4.0 13.9 - - + -
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.5 4.7 - - - +
72A ALA* 3.4 33.6 + - - +
75A HIS* 3.3 38.3 + - + +
76A TYR* 4.4 5.5 - - - -
79A MET* 4.2 13.1 - - + +
93A PHE 2.9 19.0 + - - +
94A ARG* 3.4 6.2 + - - +
96A ILE* 1.3 75.6 - - - +
98A TRP* 1.3 61.1 + - - +
100A LEU* 3.0 5.4 + - - +
101A THR* 2.8 32.3 + - - +
228A ASP* 4.6 4.9 + - - -
232A LYS* 4.5 9.3 - - - +
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Residues in contact with TRP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.0 40.6 + - + +
95A TYR* 3.4 49.1 + + - +
97A ASN* 1.3 78.6 - - - +
99A LEU* 1.3 57.9 + - - +
101A THR* 3.6 3.1 - - - -
102A VAL* 2.9 38.5 + - + +
135A LEU* 3.6 23.1 - - + +
200A TYR* 3.4 28.7 - + - -
224A TYR* 3.6 38.1 - + + -
228A ASP* 2.9 25.2 + - - -
232A LYS* 4.0 3.4 - - - -
301A RET 3.4 36.1 - - + -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR 2.8 23.0 + - - +
96A ILE* 3.3 14.1 - - + +
98A TRP* 1.3 74.0 - - - +
100A LEU* 1.3 56.6 + - + +
103A PRO* 3.0 27.3 - - + +
132A LEU* 3.8 29.8 - - + -
135A LEU* 3.7 11.5 - - + +
35E LEU* 4.4 29.4 - - + -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.0 17.6 - - + +
75A HIS* 3.4 34.5 - - + +
96A ILE* 2.9 27.6 + - + +
97A ASN* 3.7 4.5 - - - +
99A LEU* 1.3 79.2 - - + +
101A THR* 1.3 60.9 + - - +
103A PRO* 3.9 6.6 - - - +
104A LEU* 3.8 18.8 + - - +
34E TRP* 4.7 1.3 - - + +
35E LEU* 3.6 38.4 - - + +
38E ALA* 3.9 17.0 - - + -
39E GLY* 4.9 6.3 - - - +
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Residues in contact with THR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.6 41.9 - - + +
71A ILE* 4.2 13.7 - - + -
97A ASN* 2.8 31.0 + - - +
98A TRP* 3.6 4.3 - - - -
100A LEU* 1.3 73.5 - - - +
102A VAL* 1.3 66.9 + - - +
103A PRO 3.2 2.5 - - - -
104A LEU* 2.9 9.0 + - - +
105A LEU* 2.9 21.6 + - - +
232A LYS* 3.1 31.1 + - - -
301A RET 3.4 2.6 - - - +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 2.9 29.8 + - + +
101A THR* 1.3 71.8 - - - +
103A PRO* 1.3 66.7 - - + +
105A LEU* 3.2 7.9 + - - +
106A VAL* 2.8 29.5 + - + +
131A SER* 3.8 30.5 - - - +
134A MET* 6.1 0.9 - - - -
135A LEU* 4.1 13.7 - - + -
197A TRP* 3.9 21.1 - - + -
301A RET 3.6 40.2 - - + -
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Residues in contact with PRO 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP 3.6 0.9 - - - +
99A LEU* 3.0 34.8 - - + +
100A LEU 3.9 4.9 - - - +
101A THR 3.5 2.7 - - - -
102A VAL* 1.3 95.3 - - + +
104A LEU* 1.3 51.6 + - + +
106A VAL* 3.2 4.3 + - + +
107A VAL* 2.8 38.8 + - + +
124A PHE* 4.5 2.2 - - + -
128A LEU* 3.8 31.4 - - + -
131A SER* 5.6 0.7 - - - +
132A LEU* 5.3 5.2 - - + -
135A LEU* 5.5 0.9 - - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.6 26.0 - - + +
67A LEU* 4.0 25.8 - - + -
68A ILE* 3.7 18.6 - - + -
71A ILE* 3.8 28.7 - - + -
100A LEU 3.8 13.2 - - - +
101A THR* 2.9 10.1 + - - +
103A PRO* 1.3 77.1 - - + +
105A LEU* 1.3 59.9 + - - +
107A VAL* 3.0 16.4 + - + +
108A GLU 3.0 23.4 + - - -
42E ALA* 5.6 2.2 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.7 15.8 - - + +
101A THR 2.9 11.7 + - - +
102A VAL* 3.7 9.9 - - - +
104A LEU* 1.3 75.0 - - - +
106A VAL* 1.3 58.3 + - - +
108A GLU* 3.1 28.3 + - - +
109A PHE* 3.0 46.5 + - + -
192A ILE* 6.0 0.9 - - + -
197A TRP* 4.2 16.6 - - + +
231A ASN* 4.0 19.7 - - + +
232A LYS* 5.4 2.5 - - + -
235A PHE* 3.7 24.5 - - + -
301A RET 3.8 28.0 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 2.8 32.6 + - + +
103A PRO* 3.5 10.8 - - + +
105A LEU* 1.3 71.9 - - - +
107A VAL* 1.3 66.0 + - - +
109A PHE* 3.1 12.7 + - + +
110A TYR* 2.9 21.0 + - - +
124A PHE* 3.7 23.6 - - + +
127A LEU* 3.7 34.0 - - + +
128A LEU* 4.2 7.0 - - + +
131A SER* 4.6 2.5 - - - +
162A MET* 4.3 20.0 - - + -
197A TRP* 4.8 4.3 - - + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 5.0 10.8 - - + -
103A PRO* 2.8 26.4 + - + +
104A LEU* 3.3 19.7 - - + +
106A VAL* 1.3 72.5 - - - +
108A GLU* 1.3 62.1 + - - +
110A TYR* 3.1 9.4 + - + +
111A LEU* 3.0 35.8 + - + +
124A PHE* 3.7 25.1 - - + -
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER* 3.3 31.8 - - - +
64A VAL* 4.1 9.8 - - + +
65A SER* 3.0 26.5 + - - -
68A ILE* 4.1 9.0 - - - +
104A LEU 3.0 10.5 + - - +
105A LEU* 3.4 30.8 - - + +
107A VAL* 1.3 75.2 - - - +
109A PHE* 1.3 66.6 - - + +
111A LEU* 3.3 13.8 + - + +
112A ILE* 3.1 34.8 + - + +
235A PHE* 4.4 10.4 - - + -
239A ILE* 4.0 12.4 - - + +
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.0 34.2 + - + -
106A VAL* 3.4 17.3 - - + +
108A GLU* 1.3 77.8 - - + +
110A TYR* 1.3 56.2 + - - +
112A ILE* 3.5 5.3 + - + +
113A LEU* 2.9 38.4 + - + +
127A LEU* 4.9 13.5 - - + -
162A MET* 5.6 0.2 - - + -
189A MET* 3.5 33.9 - - + +
192A ILE* 3.9 20.2 - - + -
193A ILE* 3.5 33.4 - - + -
197A TRP* 4.2 19.5 - + - -
235A PHE* 3.9 28.9 - + - -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL 2.9 6.7 + - - -
107A VAL* 3.1 13.4 + - + +
109A PHE* 1.3 75.0 - - - +
111A LEU* 1.3 74.6 + - + +
113A LEU* 3.3 9.3 + - - +
114A ALA* 2.8 42.7 + - + +
120A ALA* 3.2 42.8 - - + +
121A ALA* 3.9 11.1 - - + +
124A PHE* 3.7 35.0 - + + +
127A LEU* 5.9 1.0 - - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 4.3 26.2 - - + -
61A SER* 4.7 18.8 - - - +
64A VAL* 5.2 4.5 - - + -
107A VAL* 3.0 27.7 + - + +
108A GLU* 3.3 15.9 + - + +
110A TYR* 1.3 94.1 - - + +
112A ILE* 1.3 63.8 + - + +
114A ALA* 3.3 19.1 - - + +
115A ALA* 3.7 5.4 + - - +
240E TRP* 6.0 5.4 - - + -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TRP* 5.6 5.4 - - + -
108A GLU* 3.1 25.2 + - + +
109A PHE* 3.7 9.4 - - + +
111A LEU* 1.3 75.8 - - + +
113A LEU* 1.3 64.0 + - - +
115A ALA* 3.1 22.6 + - - +
116A CYS* 3.7 6.4 - - - -
182A VAL* 4.6 4.4 - - + +
185A ALA* 3.9 30.5 - - + +
186A TYR* 3.6 35.4 - - + +
189A MET* 3.8 20.6 - - + -
235A PHE* 5.0 3.1 - - + -
239A ILE* 4.5 13.5 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE 2.9 28.7 + - - +
110A TYR* 3.6 7.4 - - - +
112A ILE* 1.3 73.0 - - - +
114A ALA* 1.3 57.4 + - - +
116A CYS* 3.0 7.8 + - + -
117A THR* 2.9 42.7 + - + +
120A ALA* 3.9 9.9 - - + +
123A LEU* 3.7 37.0 - - + -
124A PHE 5.8 0.2 - - - +
127A LEU* 4.4 8.7 - - + -
166A LEU* 3.8 22.2 - - + -
171A GLY* 5.9 3.1 - - - +
186A TYR* 4.2 16.6 - - + -
189A MET* 3.9 21.8 - - + -
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 2.8 29.6 + - + +
111A LEU* 3.3 18.4 - - + +
112A ILE 3.1 0.4 - - - -
113A LEU* 1.3 72.0 - - - +
115A ALA* 1.3 60.8 + - - +
116A CYS 3.2 1.3 + - - -
117A THR 3.8 9.6 + - - +
120A ALA* 3.8 14.4 - - + -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 6.6 0.2 - - - -
111A LEU 3.7 4.2 + - - +
112A ILE* 3.1 13.2 + - - +
114A ALA* 1.3 77.3 - - - +
116A CYS* 1.3 59.4 + - - +
176A SER* 5.7 0.3 - - - -
178A ALA* 4.1 19.3 - - + +
182A VAL* 3.8 29.6 - - + +
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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