Contacts of the strand formed by residues 74 - 81 (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 LYS 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER 5.2 0.6 + - - +
50A ASP* 3.9 24.4 - - + +
51A ILE* 3.5 19.9 + - - +
67A GLU* 2.8 33.7 + - - -
68A TRP 3.2 17.0 - - - +
69A THR* 4.3 3.8 - - - -
73A TRP* 1.3 78.2 - - - +
75A VAL* 1.4 67.1 + - - +
76A GLU* 5.2 0.2 - - - -
140B VAL* 3.5 20.6 - - + +
141B GLU* 3.0 15.5 + - - +
144B PHE* 3.6 27.8 - - + -
145B GLU* 3.0 40.3 + - + +
559B KAN 3.1 2.4 + - - -
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Residues in contact with VAL 75 (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 ILE* 3.6 26.5 - - + -
50A ASP* 4.5 1.6 - - - -
51A ILE* 3.4 30.3 - - + +
53A MET* 5.0 0.4 - - - -
66A HIS 4.4 1.1 - - - -
67A GLU* 3.1 4.0 - - - +
68A TRP* 2.7 59.2 + - + +
73A TRP* 2.9 37.5 - - + -
74A LYS* 1.4 76.3 - - - +
76A GLU* 1.3 74.0 + - - +
77A VAL* 4.2 8.3 - - + -
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Residues in contact with GLU 76 (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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37A TYR* 3.9 6.2 + - - -
50A ASP* 4.5 4.0 - - - +
51A ILE 2.8 12.9 + - - +
52A GLU* 3.2 16.3 - - - +
53A MET* 2.6 34.2 + - - +
65A SER* 5.0 1.1 + - - +
66A HIS 3.6 3.4 - - - -
67A GLU* 3.2 23.3 - - + +
75A VAL* 1.3 76.9 - - - +
77A VAL* 1.3 60.4 + - - +
78A ASN* 3.5 29.9 + - - +
145B GLU* 4.5 2.9 - - - +
559B KAN 2.7 43.1 + - - +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.1 23.8 - - + -
23A ILE* 4.6 7.4 - - + -
53A MET* 3.4 19.1 - - + +
55A CYS* 4.5 8.1 - - + -
65A SER* 3.0 3.3 - - - -
66A HIS* 2.6 41.9 + - + +
68A TRP* 4.2 10.1 - - + -
75A VAL* 4.2 14.4 - - + -
76A GLU* 1.3 80.8 - - - +
78A ASN* 1.3 67.0 + - - +
79A PHE* 3.3 35.5 - - + -
253B PHE* 5.1 1.8 - - + -
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Residues in contact with ASN 78 (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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37A TYR* 2.3 34.1 + - - -
53A MET 2.9 9.6 + - - +
54A MET* 3.1 4.0 - - - +
55A CYS 2.5 34.3 + - - +
64A PHE 3.8 2.7 - - - +
65A SER* 2.8 28.1 + - - -
76A GLU* 3.5 21.8 + - - +
77A VAL* 1.3 74.8 - - - +
79A PHE* 1.3 57.4 + - - +
80A TYR* 3.6 31.1 + - + +
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Residues in contact with PHE 79 (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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23A ILE* 4.1 15.7 - - + -
27A TYR* 3.9 17.7 - + - -
55A CYS* 3.2 26.9 - - + +
57A MET* 3.4 28.7 - - + -
62A ALA 4.6 0.7 - - - -
63A GLU* 3.5 1.6 - - - +
64A PHE* 2.6 72.5 + + + +
65A SER* 4.1 0.4 - - - -
66A HIS* 3.3 29.6 - + - -
77A VAL* 3.3 35.4 - - + -
78A ASN* 1.3 74.6 - - - +
80A TYR* 1.3 71.2 + - - +
253B PHE* 4.7 4.5 - + - -
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Residues in contact with TYR 80 (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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54A MET* 4.2 12.3 - - + +
55A CYS 2.9 13.1 + - - -
56A VAL* 3.5 3.5 - - - -
57A MET* 2.6 38.1 + - - +
62A ALA 3.3 8.5 - - - +
63A GLU* 4.2 15.7 - - + -
64A PHE 5.7 0.4 - - - -
78A ASN* 3.6 34.8 + - + +
79A PHE* 1.3 82.2 - - - +
81A SER* 1.3 68.9 + - - +
84A ILE* 4.1 17.0 - - + -
85A LEU* 3.4 48.7 - - + +
88A TYR* 4.2 17.7 - + + -
102A GLN* 4.1 13.6 + - - -
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Residues in contact with SER 81 (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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56A VAL* 4.5 0.6 - - - +
57A MET 3.7 7.2 - - - -
58A SER 5.4 0.6 + - - -
59A THR 3.6 20.0 - - - -
60A GLU* 4.4 6.3 - - - +
61A GLU 4.1 3.5 + - - -
62A ALA 2.9 11.9 + - - -
80A TYR* 1.3 81.0 - - - +
82A GLU* 1.3 66.6 + - - +
83A GLU* 3.1 16.0 + - - +
84A ILE* 3.2 32.8 - - - +
85A LEU* 3.3 17.2 + - - +
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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