Contacts of the strand formed by residues 51 - 57 (chain A) in PDB entry 1KNY
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 ILE 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A MET* 5.7 0.7 - - + -
12A ARG* 3.9 26.0 - - + +
15A ILE* 3.5 42.8 - - + -
16A VAL* 4.1 15.3 - - + -
19A ILE* 5.1 0.9 - - + -
36A VAL* 5.0 0.2 - - + -
40A LEU* 4.4 12.3 - - + -
49A SER 5.3 0.4 - - - +
50A ASP* 1.3 86.2 + - - +
52A GLU* 1.3 64.2 + - - +
53A MET* 3.9 22.4 - - + -
73A TRP* 4.9 4.3 - - + -
74A LYS 3.5 7.7 + - - +
75A VAL* 3.4 20.1 - - + +
76A GLU 2.8 26.7 + - - +
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Residues in contact with GLU 52 (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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36A VAL* 3.8 4.7 - - - +
37A TYR* 3.3 63.3 + - + +
38A GLY* 3.6 6.4 - - - -
39A SER 4.3 0.3 + - - -
40A LEU* 5.0 1.2 + - - +
50A ASP* 2.6 26.7 - - - +
51A ILE* 1.3 74.8 - - - +
53A MET* 1.3 70.3 + - - +
76A GLU* 3.2 18.8 - - - +
556A APC 2.7 27.9 + - - +
603A MG 2.0 31.9 - - - -
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Residues in contact with MET 53 (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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16A VAL* 4.2 30.3 - - + +
19A ILE* 4.1 28.5 - - + -
20A LYS* 4.7 1.6 - - + +
23A ILE* 4.3 17.0 - - + -
34A ILE* 3.6 29.8 - - + -
35A GLY 3.3 10.5 - - - +
36A VAL* 4.3 7.4 - - + -
37A TYR* 3.1 14.9 - - - -
51A ILE* 3.9 16.2 - - + -
52A GLU* 1.3 83.4 - - - +
54A MET* 1.3 61.6 + - - +
76A GLU 2.6 13.0 + - - +
77A VAL* 3.4 12.4 - - + -
78A ASN* 2.9 24.0 + - - -
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Residues in contact with MET 54 (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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34A ILE* 3.5 2.4 - - - +
35A GLY* 2.7 40.8 + - - +
37A TYR* 3.2 44.6 - - + -
53A MET* 1.3 77.7 - - - +
55A CYS* 1.3 64.1 + - - +
56A VAL* 5.5 0.8 - - + +
78A ASN* 3.1 9.0 - - + +
80A TYR* 4.2 13.7 - - + -
85A LEU* 4.4 21.5 - - + -
102A GLN* 4.0 18.6 - - + +
103A PHE* 4.9 6.7 - - - -
106A ILE* 3.4 36.3 - - + -
116A LEU* 5.0 7.1 - - + +
119A VAL* 5.4 0.9 - - - -
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Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.0 14.1 - - + -
31A VAL* 4.2 3.1 - - - -
33A ALA 3.7 11.7 - - - +
34A ILE* 4.1 12.3 - - + -
54A MET* 1.3 76.2 - - - +
56A VAL* 1.4 60.0 + - - +
57A MET* 2.9 37.9 - - - -
77A VAL* 4.5 7.2 - - + -
78A ASN 2.5 10.7 + - - +
79A PHE* 3.2 25.0 - - + -
80A TYR* 2.9 35.3 + - - +
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Residues in contact with VAL 56 (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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31A VAL* 3.5 0.9 - - - -
32A LYS* 2.5 56.3 + - + +
33A ALA* 2.9 25.4 + - + +
54A MET* 5.5 1.8 - - + -
55A CYS* 1.4 72.8 - - - +
57A MET* 1.3 57.1 + - - +
80A TYR 3.5 2.5 - - - +
82A GLU* 3.9 36.3 - - + +
85A LEU* 3.5 31.2 - - + -
115A TYR* 4.6 9.6 - - + -
116A LEU* 4.9 11.9 - - + -
119A VAL* 5.0 5.2 - - + -
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Residues in contact with MET 57 (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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27A TYR* 4.1 18.6 - - + -
30A ASP* 3.2 13.7 - - - +
31A VAL* 3.7 22.7 - - + -
32A LYS* 3.3 10.2 - - - +
55A CYS* 2.9 34.5 - - - -
56A VAL* 1.3 74.2 - - - +
58A SER* 1.3 63.8 + - - +
59A THR* 4.1 21.5 - - + +
62A ALA* 4.3 5.6 - - + -
64A PHE* 4.4 12.3 - - + -
79A PHE* 3.4 23.1 - - + -
80A TYR 2.6 30.4 + - - +
81A SER* 3.7 1.2 - - - -
82A GLU 3.4 19.8 + - - -
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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