Contacts of the strand formed by residues 4 - 13 (chain A) in PDB entry 2K8M
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 3.7 5.6 - - - +
3A LEU* 1.3 80.8 - - - +
5A LYS* 1.3 68.4 + - - +
27A ALA 3.1 11.0 - - - -
28A GLU* 3.4 16.9 + - - +
122A ASP* 3.7 3.3 - - - +
123A LEU* 2.9 23.7 + - - +
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Residues in contact with LYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY* 1.3 81.0 - - - +
6A LEU* 1.3 60.9 + - - +
7A GLN* 3.6 17.8 + - - +
26A ALA* 3.4 3.5 - - - +
27A ALA* 3.2 30.8 + - + -
28A GLU* 4.8 3.9 - - + +
120A TRP* 3.3 46.9 + - - +
121A ARG 3.6 4.5 - - - +
122A ASP* 4.5 10.5 - - + +
123A LEU* 3.9 3.5 - - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 1.3 73.4 - - - +
7A GLN* 1.3 67.1 + - - +
8A TYR* 3.4 14.1 - - + -
23A ILE* 4.0 35.9 - - + -
25A GLN 3.4 17.3 - - - +
26A ALA* 3.8 16.2 - - + -
42A VAL* 5.7 7.4 - - + -
87A MET* 4.8 7.0 - - + -
104A PHE* 3.7 34.1 - - + -
120A TRP* 4.2 0.2 - - - -
121A ARG* 2.8 34.7 + - + +
123A LEU* 3.6 22.0 - - + +
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 3.6 27.6 + - - +
6A LEU* 1.3 72.6 - - - +
8A TYR* 1.3 53.2 + - - +
23A ILE* 3.7 1.9 - - - +
24A ILE* 2.7 50.5 + - + +
25A GLN* 2.9 47.6 + - + +
27A ALA* 5.1 3.0 - - - +
119A GLU 3.6 5.2 - - - -
120A TRP* 3.2 38.9 - - + +
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Residues in contact with TYR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.4 18.2 - - + -
7A GLN* 1.3 75.4 - - - +
9A SER* 1.3 62.0 + - - +
10A LEU* 3.7 44.1 - - + +
21A VAL* 5.3 1.8 - - + -
22A GLY 3.6 11.9 - - - +
23A ILE* 3.7 21.1 - - + +
24A ILE* 4.0 6.6 - - - +
85A LEU* 6.2 0.7 - - + -
104A PHE* 3.6 31.0 - + - -
106A VAL* 4.9 7.0 - - + +
117A THR* 3.9 1.8 - - + +
118A GLU* 3.5 2.6 - - - +
119A GLU* 2.6 69.5 + - + +
120A TRP* 5.4 0.5 - - - -
121A ARG* 3.3 32.0 + - + +
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Residues in contact with SER 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 1.3 75.8 - - - +
10A LEU* 1.3 63.6 + - - +
11A ASP* 4.1 4.6 + - - +
20A LEU 3.8 1.7 - - - +
22A GLY* 2.9 33.9 + - - +
24A ILE* 4.0 16.5 - - - +
68A ASN* 5.5 0.3 + - - -
116A VAL* 6.1 0.2 - - - -
117A THR 3.6 4.0 - - - -
118A GLU* 3.1 33.0 + - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 3.7 36.8 - - + +
9A SER* 1.3 74.6 - - - +
11A ASP* 1.3 61.1 + - - +
19A LEU* 6.2 3.4 - - + -
20A LEU 3.5 4.0 - - - +
21A VAL* 3.6 41.3 - - + -
22A GLY 4.3 0.4 - - - +
85A LEU* 5.4 5.8 - - + -
106A VAL* 5.2 8.3 - - + -
108A MET* 5.0 21.1 - - + -
111A VAL* 5.6 1.1 - - + -
116A VAL* 3.2 8.1 - - - +
117A THR* 2.7 65.3 + - + +
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER 4.5 4.0 - - - +
10A LEU* 1.3 74.8 - - - +
12A TYR* 1.3 63.9 + - - +
13A ASP* 5.4 1.9 - - - +
19A LEU* 3.6 5.0 - - - +
20A LEU* 2.7 66.7 + - - +
115A HIS 4.3 2.2 - - - +
116A VAL* 3.7 21.3 - - + -
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Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 1.3 80.5 - - - +
13A ASP* 1.3 65.0 + - - +
14A PHE* 3.7 38.9 + + + -
18A GLN 4.0 3.6 - - - -
19A LEU* 3.7 20.6 - - + -
77A TYR* 5.9 4.0 - - + -
113A PHE* 3.1 52.9 - + + -
114A GLY 3.7 15.7 + - - -
115A HIS* 3.5 17.9 + + - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 4.2 2.9 + - - +
12A TYR* 1.3 76.1 - - - +
14A PHE* 1.3 60.2 + - - +
15A GLN* 2.7 60.5 + - - +
16A ASN* 3.0 29.9 + - - +
17A ASN* 3.5 6.1 + - - +
18A GLN* 3.0 42.2 + - - +
20A LEU* 6.0 0.3 - - - +
77A TYR* 6.1 1.2 - - - +
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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