Contacts of the strand formed by residues 60 - 68 (chain A) in PDB entry 2KWI
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 GLU 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLN* 5.0 9.4 + - - -
12A LEU* 4.8 5.2 - - - +
13A ALA* 4.6 13.1 - - + +
56A VAL* 3.1 2.7 - - - -
57A LEU* 3.0 40.2 + - + +
58A ASP 3.8 0.4 - - - -
59A GLY* 1.3 77.1 - - - +
61A GLU* 1.3 61.1 + - - +
62A VAL* 3.1 31.9 - - + +
174A ARG* 5.6 5.4 + - - -
177A ARG* 5.8 6.2 + - - -
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Residues in contact with GLU 61 (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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13A ALA* 4.7 8.9 - - - +
54A LYS* 2.6 47.7 + - + +
55A VAL 3.6 4.7 - - - +
56A VAL* 4.1 18.8 - - + +
59A GLY 3.8 3.0 + - - +
60A GLU* 1.3 70.7 - - - +
62A VAL* 1.3 61.0 + - - +
63A GLN* 4.2 3.3 + - - +
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Residues in contact with VAL 62 (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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12A LEU 4.0 1.1 - - - +
13A ALA* 3.2 35.7 - - - +
15A HIS* 3.5 25.4 - - + +
53A LYS 3.7 0.5 - - - +
54A LYS* 3.8 3.5 - - - +
55A VAL* 2.6 49.0 + - + +
57A LEU* 3.7 21.5 - - + -
60A GLU* 3.1 35.7 - - + +
61A GLU* 1.3 75.3 - - - +
63A GLN* 1.3 61.5 + - - +
173A MET* 5.4 0.9 - - - -
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Residues in contact with GLN 63 (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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13A ALA 3.0 11.4 + - - +
14A LEU* 3.5 21.9 - - + +
15A HIS* 3.0 27.0 + - - +
52A ARG* 5.0 26.3 + - + +
53A LYS 3.8 7.0 - - - +
54A LYS* 5.0 16.5 + - + +
61A GLU 4.2 3.6 + - - +
62A VAL* 1.3 77.6 - - - +
64A ILE* 1.3 60.7 + - - +
65A ASP 4.0 0.2 - - - -
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Residues in contact with ILE 64 (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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15A HIS* 3.5 18.4 - - + +
17A VAL* 3.7 18.6 - - + -
34A PHE* 4.2 10.3 - - + -
52A ARG* 3.5 7.6 - - - +
53A LYS* 3.3 48.3 + - + +
55A VAL* 5.0 4.9 - - + +
62A VAL 4.1 0.4 + - - -
63A GLN* 1.3 72.3 - - - +
65A ASP* 1.3 62.0 + - - +
66A ILE* 3.6 29.8 + - + +
169A PHE* 4.5 13.7 - - + +
173A MET* 3.6 34.8 - - + -
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Residues in contact with ASP 65 (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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14A LEU* 5.0 3.6 - - + -
15A HIS 2.7 16.6 + - - +
16A LYS* 2.7 34.5 + - + +
17A VAL* 3.0 25.6 + - - +
52A ARG* 3.3 31.0 - - - +
63A GLN* 4.0 0.8 + - + -
64A ILE* 1.3 70.2 - - - +
66A ILE* 1.3 65.7 + - - +
67A LEU* 5.5 0.9 - - - +
430B TRP* 3.3 19.7 - - - -
433B GLN* 5.7 2.8 + - - +
434B ARG* 2.8 22.9 + - - +
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Residues in contact with ILE 66 (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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17A VAL* 3.5 22.0 - - + +
19A MET* 5.2 9.4 - - + -
31A THR* 3.5 30.7 - - + -
34A PHE* 5.9 1.1 - - + -
35A MET* 5.7 1.8 - - + -
50A SER* 3.1 21.5 - - - -
51A TYR 3.8 18.5 + - - +
53A LYS* 5.4 3.8 - - + +
64A ILE* 3.6 48.1 + - + +
65A ASP* 1.3 80.4 + - - +
67A LEU* 1.3 76.0 + - - +
68A ASP* 4.6 2.0 - - + +
169A PHE* 4.1 17.7 - - + -
430B TRP* 5.4 0.2 - - - -
433B GLN* 5.3 0.9 + - - -
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Residues in contact with LEU 67 (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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17A VAL 3.4 6.8 + - - +
18A ILE* 4.1 3.3 - - + -
19A MET* 3.4 24.3 + - - +
48A ALA* 3.7 26.2 - - + +
50A SER* 3.4 12.1 - - - +
65A ASP* 4.3 1.1 + - - +
66A ILE* 1.3 81.1 - - - +
68A ASP* 1.3 60.5 + - - +
69A THR* 3.4 23.1 + - + +
78A ILE* 6.0 0.7 - - + -
82A TYR* 3.4 38.6 - - + -
430B TRP* 3.6 36.8 - - + -
433B GLN* 3.9 19.3 - - + -
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Residues in contact with ASP 68 (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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19A MET* 4.6 2.9 - - + +
27A LYS* 2.5 54.2 + - - +
28A SER* 2.5 30.3 + - - -
31A THR* 5.1 7.0 - - + +
46A THR* 2.9 46.0 + - + +
47A LYS 3.6 5.9 - - - +
48A ALA* 4.6 1.2 + - - -
49A ASP 4.7 0.2 - - - +
50A SER* 2.8 18.7 + - - +
66A ILE* 4.3 4.1 - - + +
67A LEU* 1.3 69.2 - - - +
69A THR* 1.3 58.4 + - - +
501A MG 3.5 1.6 - - - -
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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