Contacts of the strand formed by residues 82 - 90 (chain B) in PDB entry 3KNB
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 GLY 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LYS* 4.4 5.8 - - - -
81B ALA* 1.3 76.8 - - - +
83B VAL* 1.3 66.1 + - - -
84B TYR* 3.5 8.8 - - - -
100B ALA* 3.2 4.2 - - - -
101B VAL 2.9 33.1 + - - -
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Residues in contact with VAL 83 (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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9A GLU 5.4 0.7 - - - +
10A ALA* 4.0 21.8 - - + -
11A LEU 4.9 7.6 - - - +
12A PRO* 5.7 0.2 - - + -
49B LYS* 3.6 22.3 - - - +
50B GLY 4.3 4.0 + - - -
82B GLY* 1.3 74.8 - - - -
84B TYR* 1.3 65.4 + - - +
85B VAL* 4.5 8.1 - - + +
98B ALA* 3.8 26.9 - - + -
99B ALA 3.5 2.9 - - - -
100B ALA* 4.4 7.2 - - + -
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Residues in contact with TYR 84 (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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33B LEU* 3.9 16.2 - - + -
47B TRP* 4.1 10.0 - - + -
48B GLU 3.6 2.9 - - - +
49B LYS* 3.6 28.5 - - + +
54B LEU* 3.8 22.0 - - + -
60B LEU* 5.5 3.6 - - + -
71B LEU* 3.5 24.9 - - + -
73B LEU* 4.1 10.2 - - + +
80B ASP* 2.6 45.1 + - - +
82B GLY 3.5 13.9 - - - -
83B VAL* 1.3 74.2 - - - +
85B VAL* 1.3 63.7 + - - +
86B CYS 4.1 0.4 + - - -
97B ALA 4.0 0.3 - - - +
98B ALA* 3.2 4.0 - - - +
99B ALA 2.7 36.2 + - - +
101B VAL* 3.6 25.1 - - + -
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Residues in contact with VAL 85 (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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12A PRO* 4.0 32.3 - - + -
13A SER 5.5 0.4 - - - +
14A ASP 5.9 0.7 - - - +
46B VAL 3.7 0.2 - - - +
47B TRP* 3.3 7.8 - - - -
48B GLU* 2.8 65.9 + - + +
49B LYS* 6.0 0.4 - - - -
50B GLY 6.1 1.8 - - - +
51B GLY 6.3 0.7 - - - +
83B VAL* 4.5 8.3 - - + +
84B TYR* 1.3 77.2 - - - +
86B CYS* 1.3 72.5 + - - +
87B ARG* 4.6 1.1 - - + +
96B TYR* 4.3 12.8 - - + -
97B ALA 3.6 6.1 - - - +
98B ALA* 4.1 12.8 - - + -
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Residues in contact with CYS 86 (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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16B PHE* 4.1 20.3 - - + -
20B PRO* 4.9 0.9 - - + -
35B CYS* 4.2 7.6 - - - -
37B VAL* 4.8 0.9 - - - -
45B VAL* 3.3 32.1 - - - -
46B VAL 3.8 2.7 - - - -
47B TRP* 3.7 35.8 - - + -
85B VAL* 1.3 74.2 - - - +
87B ARG* 1.3 61.0 + - - +
88B ALA* 5.4 0.2 - - - -
95B ALA 3.7 0.9 - - - +
96B TYR* 3.4 5.5 - - - -
97B ALA* 2.7 44.1 + - + +
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Residues in contact with ARG 87 (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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16A SER* 5.2 3.8 - - - -
98A ARG* 2.8 30.9 - - - +
44B VAL 3.6 1.6 - - - +
45B VAL* 3.3 3.3 - - - -
46B VAL* 2.8 48.3 + - + +
48B GLU* 4.8 18.1 + - - +
85B VAL* 3.9 4.2 + - + +
86B CYS* 1.3 75.4 - - - +
88B ALA* 1.3 67.1 + - - +
89B ARG* 5.3 5.8 - - + +
94B GLU* 3.3 11.5 + - - +
95B ALA 3.5 3.4 - - - -
96B TYR* 3.2 43.1 + - + -
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Residues in contact with ALA 88 (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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14B PRO* 3.7 13.9 - - + +
16B PHE* 5.1 4.5 - - + -
37B VAL* 3.8 31.4 - - + -
43B PRO* 4.0 4.0 - - + -
44B VAL 3.3 5.6 - - - +
45B VAL* 4.2 7.6 - - + +
86B CYS 4.2 0.4 - - - -
87B ARG* 1.3 75.5 - - - +
89B ARG* 1.3 60.6 + - - +
94B GLU* 3.1 8.1 - - - +
95B ALA* 2.8 37.6 + - + +
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Residues in contact with ARG 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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14B PRO* 4.0 2.9 - - - -
43B PRO* 3.3 3.3 - - - +
44B VAL* 2.9 41.7 + - + +
87B ARG* 5.3 7.2 - - + +
88B ALA* 1.3 76.5 - - - +
90B ASN* 1.3 61.9 + - - +
93B GLY 3.6 4.5 - - - -
94B GLU* 4.1 18.2 - - + +
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Residues in contact with ASN 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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12B SER 3.0 24.5 + - - -
14B PRO* 3.2 23.9 - - - +
39B GLY* 3.9 3.2 - - - -
40B GLU 3.4 8.9 + - - +
41B PRO* 2.9 35.0 + - + +
42B PRO 4.7 1.3 - - - +
43B PRO* 4.1 5.6 - - + +
89B ARG* 1.3 78.0 - - - +
91B ALA* 1.3 66.1 + - - +
92B ALA* 3.0 16.3 + - - +
93B GLY* 3.0 17.4 + - - +
94B GLU* 5.4 0.7 - - - +
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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