Contacts of the helix formed by residues 90 - 111 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP* 3.4 10.5 - - - +
33B PHE* 4.3 8.3 - - + -
79B MET* 3.3 50.5 - - + +
82B VAL* 4.1 13.2 - - + -
83B TRP* 4.7 2.7 - - + +
88B ASP 3.7 8.1 - - - +
89B THR* 1.3 87.1 - - + +
91B THR* 1.3 57.5 + - - +
92B VAL 3.4 2.9 - - - -
93B PHE* 3.5 8.4 + - + -
94B ARG* 2.8 31.3 + - - +
221B ASN* 3.8 14.6 - - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 3.0 4.7 + - - -
89B THR* 3.0 29.7 + - - +
90B PRO* 1.3 71.9 - - - +
92B VAL* 1.3 55.0 + - + +
94B ARG* 3.3 5.6 - - - +
95B TYR* 2.8 52.8 + - + -
139B PHE* 4.0 14.4 - - + -
142B GLU* 3.8 40.8 + - + +
143B ALA* 4.6 2.9 - - + +
208B TYR* 4.7 1.6 + - - -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 2.9 22.5 + - - +
23A LEU* 3.4 37.7 - - + +
25A ILE* 4.1 37.0 - - + +
31A VAL* 4.9 2.9 - - + -
91B THR* 1.3 69.7 - - - +
93B PHE* 1.3 58.6 + - - +
95B TYR* 4.1 0.4 - - - +
96B ILE* 2.7 53.4 + - + +
139B PHE* 4.1 18.8 - - + -
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 3.9 5.8 - - - -
22A ASP* 3.1 21.0 + - - -
23A LEU* 3.5 44.2 - - + -
34A TRP* 3.6 31.0 - + - -
75B HIS* 4.0 11.2 - + + +
78B TYR* 3.7 40.2 - + + -
79B MET* 3.8 16.6 - - + +
82B VAL* 3.8 27.6 - - + -
90B PRO* 3.5 8.3 + - + +
91B THR 3.4 0.2 - - - -
92B VAL* 1.3 73.6 - - - +
94B ARG* 1.3 56.7 + - - +
96B ILE* 3.9 3.1 - - - +
97B ASN* 2.9 33.6 + - - +
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.6 6.3 - - - -
76B TYR* 3.4 15.0 + - - -
79B MET* 2.6 38.9 - - + +
89B THR* 5.8 1.8 - - + +
90B PRO* 2.8 18.5 + - - +
91B THR* 3.3 9.0 - - - +
93B PHE* 1.3 76.5 - - - +
95B TYR* 1.3 61.2 + - + +
97B ASN* 3.3 4.6 + - - +
98B TRP* 2.9 67.6 + - + +
221B ASN* 2.5 37.2 + - - +
224B TYR* 3.4 30.9 - - + +
225B ASN* 2.9 28.5 + - - -
228B ASP* 3.9 3.2 + - - -
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 2.8 34.9 + - + +
92B VAL 4.1 2.0 - - - +
94B ARG* 1.3 75.5 - - + +
96B ILE* 1.3 56.7 + - + +
98B TRP* 3.0 33.6 + + - +
99B LEU* 2.6 36.9 + - - +
135B LEU* 3.4 23.6 - - + +
138B GLY* 3.3 16.8 - - - -
139B PHE* 3.3 54.7 - + + -
142B GLU* 2.5 41.8 + - + +
224B TYR* 3.9 3.6 + - - -
301B RET 3.9 7.3 - - + +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.3 7.2 - - + -
25A ILE* 5.8 3.4 - - + -
31A VAL* 4.1 19.3 - - + -
34A TRP* 3.4 37.0 - - + +
35A LEU* 3.8 25.4 - - + -
75B HIS* 3.7 5.6 - - + +
92B VAL* 2.7 40.0 + - + +
93B PHE* 3.9 4.0 - - - +
95B TYR* 1.3 72.7 - - + +
97B ASN* 1.3 62.9 + - - +
99B LEU* 3.2 15.9 + - + +
100B LEU* 3.0 25.8 + - + +
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.9 0.3 - - - +
72B ALA* 3.5 25.6 + - - +
75B HIS* 3.4 39.6 + - + +
76B TYR* 4.2 14.8 - - - -
79B MET* 5.1 3.4 - - - +
93B PHE 2.9 19.4 + - - +
94B ARG* 3.4 6.2 + - - +
96B ILE* 1.3 76.2 - - - +
98B TRP* 1.3 63.4 + - - +
100B LEU* 3.2 2.8 + - - +
101B THR* 2.9 44.9 + - - +
228B ASP* 4.4 7.5 + - - -
232B LYS* 4.6 3.4 - - - +
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Residues in contact with TRP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ARG* 2.9 39.0 + - + +
95B TYR* 3.0 42.8 + + - +
97B ASN* 1.3 78.3 - - - +
99B LEU* 1.3 59.0 + - - +
101B THR* 3.5 3.1 - - - -
102B VAL* 2.8 37.8 + - + +
135B LEU* 3.7 32.8 - - + -
200B TYR* 3.4 26.0 - + - -
224B TYR* 3.7 32.8 - + + -
228B ASP* 2.9 26.2 + - - -
232B LYS* 4.2 4.3 - - - -
301B RET 3.3 38.9 - - + +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.9 32.5 - - + -
95B TYR 2.6 17.2 + - - +
96B ILE* 3.4 21.5 - - + +
98B TRP* 1.3 72.8 - - - +
100B LEU* 1.3 58.6 + - + +
103B PRO* 3.0 26.9 - - + +
132B LEU* 4.2 25.4 - - + -
135B LEU* 4.1 16.2 - - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 4.6 1.1 - - + +
35A LEU* 4.0 34.8 - - + +
38A ALA* 3.8 20.2 - - + -
39A GLY* 5.0 4.9 - - - +
71B ILE* 3.9 18.4 - - + +
75B HIS* 3.3 35.4 - - + +
96B ILE* 3.0 23.1 + - + +
97B ASN 3.7 3.1 - - - +
99B LEU* 1.3 77.7 - - + +
101B THR* 1.3 62.4 + - - +
103B PRO* 3.6 8.0 - - - +
104B LEU* 3.7 18.7 - - - +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.8 34.1 - - + +
71B ILE* 4.1 14.6 - - + -
72B ALA* 4.5 0.4 - - + +
97B ASN* 2.9 36.6 + - - +
98B TRP* 3.5 4.9 - - - -
100B LEU* 1.3 77.4 - - - +
102B VAL* 1.3 61.1 + - - +
103B PRO 3.3 2.0 - - - -
104B LEU* 2.9 26.8 + - - +
105B LEU* 3.1 10.6 + - - +
232B LYS* 2.9 28.6 + - - +
301B RET 3.3 3.3 - - - +
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Residues in contact with VAL 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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98B TRP 2.8 25.6 + - - +
101B THR* 1.3 73.9 + - - +
103B PRO* 1.4 63.2 - - + +
105B LEU* 3.2 10.0 + - - +
106B VAL* 3.1 20.3 + - + +
131B SER* 3.6 31.2 - - - +
134B MET* 6.1 1.3 - - + -
135B LEU* 3.8 20.6 - - + -
197B TRP* 4.2 16.8 - - + -
301B RET 3.5 44.2 - - + -
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Residues in contact with PRO 103 (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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98B TRP 3.7 0.4 - - - +
99B LEU* 3.0 31.4 - - + +
100B LEU 3.6 6.1 - - - +
101B THR 3.4 3.8 - - - -
102B VAL* 1.4 94.5 - - + +
104B LEU* 1.3 58.9 + - + +
106B VAL* 3.3 6.4 + - + +
107B VAL* 2.9 34.3 + - + +
124B PHE* 4.4 2.5 - - + -
128B LEU* 4.2 26.9 - - + -
131B SER* 5.8 0.4 - - - +
132B LEU* 6.1 2.7 - - + -
135B LEU* 5.7 0.7 - - + -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 5.7 1.6 - - + -
64B VAL* 3.5 21.1 - - + +
67B LEU* 4.2 25.6 - - + -
68B ILE* 3.7 24.9 - - + -
71B ILE* 3.9 27.4 - - + -
100B LEU 3.7 13.7 - - - +
101B THR* 2.9 8.7 + - - +
103B PRO* 1.3 78.9 - - + +
105B LEU* 1.3 64.8 + - - +
107B VAL* 3.4 16.9 - - + +
108B GLU* 3.2 15.6 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.7 21.0 - - + +
101B THR 3.1 10.0 + - - +
102B VAL* 3.2 10.1 + - - +
104B LEU* 1.3 72.4 - - - +
106B VAL* 1.3 65.2 + - + +
108B GLU* 2.9 28.5 + - - +
109B PHE* 3.6 11.0 + - + -
189B MET* 4.9 0.2 - - - +
192B ILE* 6.1 1.1 - - + -
193B ILE* 5.0 6.3 - - + -
197B TRP* 3.9 22.7 - - + +
231B ASN 4.9 10.3 - - - +
232B LYS* 5.6 2.2 - - + -
235B PHE* 3.2 42.6 - - + -
301B RET 3.7 32.5 - - + -
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Residues in contact with VAL 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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102B VAL* 3.1 16.5 + - + +
103B PRO* 3.3 8.7 + - + +
105B LEU* 1.3 71.0 - - - +
107B VAL* 1.3 67.1 + - - +
109B PHE* 2.9 27.0 + - + +
110B TYR 3.3 3.3 + - - -
124B PHE* 3.6 28.0 - - + +
127B LEU* 3.5 32.5 - - + +
128B LEU* 4.1 4.9 - - + +
131B SER* 4.4 16.4 - - - +
162B MET* 4.2 23.6 - - + -
197B TRP* 5.1 3.6 - - + -
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Residues in contact with VAL 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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64B VAL* 5.0 10.3 - - + -
103B PRO* 2.9 24.3 + - + +
104B LEU* 3.4 22.7 - - + +
105B LEU 3.3 0.2 - - - -
106B VAL* 1.3 74.6 - - - +
108B GLU* 1.3 55.9 + - - +
110B TYR* 3.0 13.8 + - + +
111B LEU* 2.9 41.3 + - + +
124B PHE* 3.5 27.8 - - + -
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Residues in contact with GLU 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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61B SER* 2.8 45.0 + - - +
64B VAL* 3.8 12.4 - - + +
65B SER* 3.5 20.2 + - - -
68B ILE* 4.3 2.9 - - - +
104B LEU 3.2 7.2 + - - +
105B LEU* 2.9 24.7 + - - +
107B VAL* 1.3 75.7 - - - +
109B PHE* 1.3 60.5 + - - +
111B LEU* 3.5 13.3 + - + +
112B ILE* 3.5 16.3 + - - +
189B MET* 3.6 18.5 - - + +
235B PHE* 3.2 22.9 - - + -
239B ILE* 4.4 12.7 - - + +
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.9 12.6 - - + -
106B VAL* 2.9 16.5 + - + +
108B GLU* 1.3 75.0 - - - +
110B TYR* 1.3 60.5 + - - +
112B ILE* 2.7 36.0 + - + +
124B PHE* 6.5 0.2 - - - -
127B LEU* 4.3 22.9 - - + -
162B MET* 6.5 1.3 - - + -
166B LEU* 4.1 22.2 - - + -
186B TYR* 4.1 22.2 - + - -
189B MET* 3.0 62.6 - - + -
193B ILE* 3.8 26.0 - - + -
235B PHE* 5.1 2.7 - + - -
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Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASN* 5.5 3.8 + - - -
106B VAL 3.3 2.4 + - - -
107B VAL* 3.0 18.1 + - + +
109B PHE* 1.3 78.3 - - - +
111B LEU* 1.3 71.2 + - + +
112B ILE 3.1 5.2 + - - -
120B ALA* 3.7 40.5 - - + +
121B ALA* 4.2 15.8 - - + +
124B PHE* 4.0 33.9 - + + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TRP* 5.0 10.3 - - + -
60B THR* 3.7 32.8 - - + -
61B SER* 3.9 25.8 - - - +
64B VAL* 4.2 15.5 - - + -
107B VAL* 2.9 22.6 + - + +
108B GLU* 3.5 16.2 - - - +
109B PHE 3.1 0.2 - - - -
110B TYR* 1.3 85.6 - - + +
112B ILE* 1.3 63.0 + - + +
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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
------------------------------------------------------------
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