Contacts of the strand formed by residues 88 - 98 (chain B) in PDB entry 4ICK
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 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B LEU* 4.0 18.2 + - - +
82B TYR 3.8 5.6 - - - +
83B VAL* 4.2 15.4 - - + -
86B ASN 3.9 6.7 - - - +
87B LYS* 1.3 87.0 - - + +
89B LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 89 (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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3B LEU* 3.8 36.3 - - + +
81B ASN* 3.4 5.4 - - - +
82B TYR* 2.7 72.3 + - + +
84B ALA* 3.7 22.8 + - - +
85B ARG* 6.1 1.5 - - - +
87B LYS* 3.7 31.9 - - - +
88B PRO* 1.3 78.3 - - - +
90B THR* 1.3 64.9 + - - +
91B VAL* 5.4 2.5 - - + -
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Residues in contact with THR 90 (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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129A LYS* 5.0 4.7 + - - -
3B LEU* 3.1 14.5 + - - +
4B ARG* 3.8 27.5 + - + +
5B ALA* 2.9 25.5 + - - +
79B GLU* 3.3 31.4 - - + +
80B LEU 3.2 4.0 - - - -
81B ASN* 3.1 16.5 + - - +
89B LYS* 1.3 73.8 + - - +
91B VAL* 1.3 70.1 + - - +
92B ILE* 4.2 7.4 - - + -
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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
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3B LEU* 6.4 1.1 - - + -
5B ALA* 3.2 21.8 - - + +
6B CYS* 4.4 1.6 - - - +
42B LYS* 4.0 19.3 - - + +
78B ARG 3.7 0.7 - - - +
79B GLU* 3.4 1.7 - - - -
80B LEU* 2.7 45.7 + - + +
82B TYR* 4.2 25.1 - - + +
89B LYS* 5.4 2.5 - - + -
90B THR* 1.3 81.1 - - - +
92B ILE* 1.3 69.3 + - - +
93B TYR* 3.6 38.4 - - + +
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Residues in contact with ILE 92 (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 ARG* 4.0 22.0 - - - +
5B ALA 3.0 12.5 + - - +
6B CYS* 3.3 11.4 - - - +
7B GLY 3.0 25.5 + - - +
51B ASP* 4.6 2.5 - - - +
77B LYS* 3.8 26.2 - - + -
78B ARG 3.5 2.0 - - - +
79B GLU* 3.0 46.4 - - + +
90B THR* 4.2 4.9 - - + -
91B VAL* 1.3 74.8 - - - +
93B TYR* 1.3 63.0 + - - +
94B TRP* 3.5 31.9 - - + -
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Residues in contact with TYR 93 (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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7B GLY* 3.4 22.2 - - - -
8B LEU 3.8 8.3 - - - -
9B ILE* 3.8 24.2 - - + -
39B THR* 4.1 0.9 - - - +
40B PRO* 3.5 31.0 + - + +
41B PRO 4.0 18.8 - - - -
42B LYS* 3.4 25.0 - - + +
76B PHE* 4.7 1.3 - - - -
77B LYS* 3.3 7.6 - - - +
78B ARG* 2.8 37.6 + - + +
80B LEU* 3.8 26.2 - - + -
91B VAL* 3.6 20.9 - - + +
92B ILE* 1.3 73.4 - - - +
94B TRP* 1.3 64.8 + - - +
131B MET* 3.7 26.4 - - + -
134B ALA* 5.2 0.4 - - + -
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Residues in contact with TRP 94 (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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140A GLN* 5.4 2.5 - - - -
6B CYS* 4.2 2.0 - - + -
7B GLY 3.3 15.1 + - - -
8B LEU* 3.4 17.8 - - + -
9B ILE* 2.8 27.0 + - - +
51B ASP* 3.7 29.2 - - + -
52B LEU* 3.6 51.9 - - + +
55B ALA* 3.9 4.3 - - + -
72B ILE* 4.6 14.6 - - + -
73B ILE 5.6 0.4 - - - -
76B PHE* 3.6 23.3 - - - +
77B LYS* 3.5 25.1 - - + +
92B ILE* 3.5 27.4 - - + -
93B TYR* 1.3 79.1 - - - +
95B LEU* 1.3 63.7 + - - +
202B MG 3.2 23.2 - - - -
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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
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9B ILE* 3.6 33.9 - - + +
11B PHE* 3.9 15.3 - - + -
26B PHE* 4.6 2.5 - - + -
72B ILE* 3.7 6.8 - - - +
73B ILE* 2.9 37.6 + - + -
76B PHE* 3.7 28.9 + - + -
94B TRP* 1.3 74.6 - - - +
96B ALA* 1.3 61.9 + - - +
138B GLY* 3.8 21.8 - - - +
141B PHE* 3.6 31.9 - - + -
142B LEU* 3.8 17.5 - - + -
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Residues in contact with ALA 96 (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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8B LEU* 4.0 29.2 - - + -
9B ILE 3.0 8.5 + - - +
10B ILE* 3.3 16.5 - - + +
11B PHE* 3.0 27.6 + - - -
70B LEU* 4.2 8.3 - - + -
71B THR 3.2 12.1 - - - +
72B ILE* 4.2 9.0 - - + -
73B ILE* 4.4 0.4 - - - -
94B TRP 4.1 0.2 + - - -
95B LEU* 1.3 76.1 - - - +
97B GLU* 1.3 61.0 + - - +
98B VAL 4.0 0.2 + - - -
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Residues in contact with GLU 97 (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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11B PHE* 3.4 38.9 - - + +
12B ARG* 4.7 2.0 - - - -
13B ARG* 3.2 43.4 + - - +
70B LEU* 3.5 3.3 - - - -
71B THR* 2.9 38.7 + - - +
73B ILE* 4.3 12.4 - - + +
96B ALA* 1.3 72.1 - - - +
98B VAL* 1.3 77.4 + - - +
99B LYS 3.6 0.2 + - - -
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Residues in contact with VAL 98 (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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10B ILE* 3.7 28.3 - - + -
11B PHE 3.0 9.0 + - - +
12B ARG* 3.7 28.7 - - + -
65B ILE* 4.2 6.7 - - + -
69B GLN 3.4 7.4 - - - +
70B LEU* 4.1 11.2 - - + -
96B ALA 4.0 0.2 + - - -
97B GLU* 1.3 85.3 - - - +
99B LYS* 1.3 65.6 + - - +
100B ASP 3.3 25.2 - - - +
101B TYR* 4.3 2.3 + - - +
103B VAL* 3.9 20.9 - - + -
116B TRP* 4.0 7.0 - - + -
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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
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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