Contacts of the helix formed by residues 89 - 106 (chain B) in PDB entry 4HI7
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 ASP 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 4.7 0.2 + - - -
87B PRO* 3.3 3.9 - - + +
88B LYS* 1.3 77.5 - - - +
90B LEU* 1.3 61.2 + - - +
91B VAL* 3.3 9.5 + - - +
92B LYS* 2.9 50.4 + - + +
93B ARG* 2.8 28.1 + - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.8 21.7 - - + +
77A SER* 3.7 29.6 - - - +
78A LYS* 3.7 47.1 - - + +
93A ARG* 6.3 0.9 - - - +
88B LYS 3.2 11.6 + - - +
89B ASP* 1.3 75.3 + - - +
91B VAL* 1.3 59.0 + - + +
93B ARG* 3.8 10.9 - - + +
94B ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA* 3.7 32.8 - - + -
64A ASN 4.7 12.0 - - - +
65A ILE* 5.0 3.8 - - + +
74A TYR* 3.8 21.8 - - + +
78A LYS* 5.8 4.3 - - - +
89B ASP* 3.3 8.3 + - - +
90B LEU* 1.3 73.7 - - + +
92B LYS* 1.3 68.1 + - + +
94B ALA* 3.2 8.8 + - - +
95B LEU* 3.1 20.6 + - - +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO* 3.8 22.7 - - + -
89B ASP* 2.9 28.9 + - + +
91B VAL* 1.3 77.2 - - + +
93B ARG* 1.3 65.4 + - - +
95B LEU* 3.2 9.7 + - + +
96B VAL* 3.2 24.3 + - - +
153B ALA 5.2 2.7 - - - +
154B GLY* 6.0 3.2 - - - -
155B ASN 5.9 2.8 - - - +
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 4.2 24.0 - - - +
77B SER* 4.1 12.1 + - - +
86B TYR* 3.1 70.4 + - + +
87B PRO* 2.8 30.5 + - - +
88B LYS* 3.5 28.8 - - - +
89B ASP 2.8 15.1 + - - +
90B LEU* 3.8 12.6 - - - +
92B LYS* 1.3 76.9 - - - +
94B ALA* 1.3 59.3 + - - +
96B VAL* 3.1 5.7 + - - +
97B ASP* 2.8 35.4 + - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.7 36.2 - - + +
70A ALA* 3.6 8.4 - - - +
74A TYR* 4.3 12.6 - - + -
90B LEU 2.9 18.2 + - - +
91B VAL* 3.4 7.0 - - - +
92B LYS 3.2 0.2 - - - -
93B ARG* 1.3 77.0 - - - +
95B LEU* 1.3 56.2 + - - +
97B ASP* 4.3 9.0 - - - -
98B ASN* 2.8 30.1 + - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 6.0 2.9 - - - +
91B VAL 3.1 12.6 + - - +
92B LYS* 3.6 11.4 - - + +
93B ARG 3.2 0.2 - - - -
94B ALA* 1.3 74.1 - - - +
96B VAL* 1.3 66.1 + - - +
98B ASN* 3.3 12.1 + - - +
99B ARG* 3.0 56.0 + - - +
149B GLN* 5.2 3.6 - - - +
152B VAL 4.8 0.7 - - - +
153B ALA* 3.7 34.8 - - + +
154B GLY* 4.1 4.3 - - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 3.7 25.4 - - + -
87B PRO* 4.0 14.8 - - + -
92B LYS 3.2 13.2 + - - +
93B ARG 3.1 7.2 + - - +
95B LEU* 1.3 74.5 - - - +
97B ASP* 1.3 65.7 + - - +
99B ARG* 3.2 3.8 + - - +
100B MET* 3.0 24.2 + - + +
153B ALA* 3.8 24.5 - - + +
158B THR* 3.9 21.1 - - + +
159B ILE* 3.9 18.4 - - + -
160B ALA* 4.0 13.0 - - + +
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 4.0 12.8 - - + +
73A ALA* 4.4 18.5 - - - +
86A TYR* 5.0 3.4 + - - -
101A TYR* 4.2 9.0 + - - -
86B TYR* 2.7 35.0 + - - -
93B ARG* 2.8 30.9 + - - +
94B ALA* 3.7 6.8 - - - +
96B VAL* 1.3 72.7 - - - +
98B ASN* 1.3 53.2 + - - +
100B MET* 3.0 9.4 + - - +
101B TYR* 2.8 49.9 + - + -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 4.3 11.5 + - - +
66A ALA* 3.3 42.2 + - - +
67A ASP* 3.6 16.1 + - - +
70A ALA* 3.7 6.7 - - - +
94B ALA 2.8 22.2 + - - +
95B LEU* 3.5 14.1 - - - +
97B ASP* 1.3 70.4 - - - +
99B ARG* 1.3 80.5 + - - +
101B TYR* 3.3 2.0 + - - +
102B PHE* 2.9 29.1 + - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 3.8 8.7 + - - -
95B LEU* 3.0 36.5 + - + +
96B VAL 3.2 0.2 + - - -
98B ASN* 1.3 99.1 + - - +
100B MET* 1.3 57.7 + - - +
102B PHE* 3.4 5.8 - - - +
103B GLU* 3.0 25.8 + - - +
145B PHE* 3.4 65.4 + - - +
147B LYS* 4.7 7.9 - - - +
152B VAL* 2.8 30.2 + - - +
153B ALA* 3.9 7.4 - - + -
160B ALA* 3.7 21.3 - - + -
164B LEU* 4.1 12.0 - - + +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.3 25.1 - - - +
69B HIS* 3.6 38.1 + - + +
72B MET* 4.1 13.9 - - - -
73B ALA* 4.9 1.3 - - + -
86B TYR* 4.4 4.0 - - + +
96B VAL* 3.0 16.9 + - + +
97B ASP* 3.0 19.5 + - - +
99B ARG* 1.3 72.7 - - - +
101B TYR* 1.3 61.3 + - - +
103B GLU* 3.2 6.8 + - - +
104B SER* 2.9 27.4 + - - -
159B ILE* 3.7 39.7 - - + +
160B ALA* 3.8 17.9 - - + -
163B SER* 4.2 3.4 - - - -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.3 34.8 - - - +
69A HIS* 3.3 36.1 - + + +
70A ALA 4.3 6.7 - - - -
97A ASP* 4.0 4.7 + - - -
100A MET* 3.3 29.9 - - + +
101A TYR* 3.3 60.3 - + - -
104A SER* 3.8 14.9 + - - -
301A GSH 5.1 2.9 + - - -
97B ASP* 2.8 43.1 + - + +
98B ASN 3.9 0.4 - - - +
100B MET* 1.3 68.3 - - - +
102B PHE* 1.3 65.7 + - - +
104B SER* 3.3 4.5 + - - -
105B GLY* 3.2 18.5 + - - -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 3.6 25.1 - - - +
67A ASP* 4.5 2.3 + - - -
301A GSH 5.9 1.6 - - - -
98B ASN* 2.9 18.7 + - - +
99B ARG* 3.4 11.7 - - - +
101B TYR* 1.3 77.3 - - - +
103B GLU* 1.3 63.9 + - - +
106B VAL* 3.0 61.8 + - + +
107B VAL* 3.4 24.8 + - + -
138B ALA* 4.3 2.2 - - - -
141B PHE* 3.5 35.7 - + + -
142B VAL* 3.7 16.4 - - + -
145B PHE* 3.7 25.1 - + + -
164B LEU* 4.0 6.3 - - + -
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Residues in contact with GLU 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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13B PRO* 5.6 0.5 - - - +
14B PRO* 6.1 1.2 - - - +
69B HIS* 2.7 31.1 + - - -
99B ARG 3.0 13.9 + - - +
100B MET* 3.2 8.9 + - - +
102B PHE* 1.3 76.1 - - - +
104B SER* 1.3 59.3 + - - +
105B GLY 3.3 0.3 + - - -
107B VAL* 3.9 10.3 - - + -
108B PHE* 2.7 43.2 + - - +
163B SER* 3.3 29.7 - - - +
164B LEU* 3.6 16.4 - - + -
166B SER* 4.4 2.6 + - - -
167B SER* 2.7 38.2 + - - +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.4 17.4 + - - +
104A SER* 2.8 26.4 + - - -
105A GLY* 3.8 6.1 + - - -
69B HIS* 3.9 15.5 - - - -
100B MET 2.9 14.0 + - - -
101B TYR 3.4 6.7 - - - -
102B PHE 3.2 0.2 - - - -
103B GLU* 1.3 83.8 + - - +
105B GLY* 1.3 57.3 + - - +
108B PHE* 3.5 8.3 - - - +
109B ALA* 3.1 24.4 + - - +
301B GSH 4.5 7.7 + - - -
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 4.0 10.3 + - - -
109A ALA* 3.6 23.5 - - - +
101B TYR 3.2 8.6 + - - -
104B SER* 1.3 79.6 - - - +
106B VAL* 1.3 61.5 + - - +
107B VAL 3.3 1.1 - - - -
109B ALA* 3.4 3.3 + - - +
110B ASN* 2.8 32.4 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 5.4 2.2 - - - +
113A ARG* 6.3 4.3 - - - -
301A GSH 6.2 2.5 - - - +
101B TYR 4.7 0.2 + - - -
102B PHE* 3.0 51.4 + - + +
105B GLY* 1.3 72.3 - - - -
107B VAL* 1.3 60.9 + - - +
110B ASN* 3.5 24.2 + - - +
111B ALA* 3.6 8.0 + - - +
134B ALA 4.8 1.8 - - - +
137B GLU* 6.1 1.1 - - + -
138B ALA* 4.5 10.4 - - + +
141B PHE* 4.1 19.3 - - + -
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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) + - + + + + + -
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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