Contacts of the strand formed by residues 74 - 81 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 2.8 31.6 + - - +
141A GLU* 4.2 2.5 - - - +
144A PHE* 3.0 33.1 - - + -
145A GLU* 3.8 39.9 + - + +
558A KAN 4.6 2.2 + - - -
50B ASP* 3.8 24.0 + - + +
51B ILE* 3.6 19.7 + - - +
67B GLU* 3.1 26.1 + - - -
68B TRP 3.2 8.7 + - - +
69B THR* 4.7 2.9 - - - -
73B TRP* 1.3 79.8 - - - +
75B VAL* 1.3 72.0 + - - +
76B GLU* 5.2 2.4 + - - +
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Residues in contact with VAL 75 (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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15B ILE* 4.2 0.4 - - + -
19B ILE* 3.2 22.9 - - + -
50B ASP* 5.4 0.2 - - - -
51B ILE* 3.5 29.6 - - + -
67B GLU* 3.3 4.2 - - - +
68B TRP* 3.0 66.7 + - + +
73B TRP* 3.1 31.9 - - + -
74B LYS* 1.3 77.2 + - - +
76B GLU* 1.3 67.5 + - - +
77B VAL* 3.6 8.3 - - + -
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Residues in contact with GLU 76 (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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145A GLU* 4.8 3.8 - - - +
558A KAN 3.2 32.0 + - - -
37B TYR* 4.2 9.7 + - - -
50B ASP* 4.9 3.0 - - - +
51B ILE 2.9 14.0 + - - +
52B GLU* 3.5 14.8 - - + +
53B MET* 2.8 30.0 + - - +
65B SER* 4.7 0.2 - - - +
66B HIS 3.6 2.9 - - - -
67B GLU* 3.3 36.9 - - + +
74B LYS* 5.2 1.9 + - - +
75B VAL* 1.3 80.3 - - - +
77B VAL* 1.3 62.1 + - - +
78B ASN* 3.4 24.7 + - - +
557B APC 5.4 1.0 + - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PHE* 4.8 3.6 - - + -
19B ILE* 4.3 11.2 - - + -
23B ILE* 4.0 17.0 - - + -
53B MET* 3.7 20.9 - - + -
54B MET* 4.6 2.0 - - - +
55B CYS* 5.0 2.0 - - + -
65B SER* 2.5 30.8 + - - -
66B HIS* 2.9 16.6 + - + +
68B TRP* 3.7 16.8 - - + -
75B VAL* 3.6 21.5 - - + -
76B GLU* 1.3 76.9 - - - +
78B ASN* 1.3 61.1 + - - +
79B PHE* 3.7 31.5 - - + -
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Residues in contact with ASN 78 (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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37B TYR* 2.7 30.1 + - - -
53B MET 3.2 11.7 + - - +
54B MET* 3.3 1.5 - - - +
55B CYS 2.5 35.2 + - - +
64B PHE 4.0 3.4 - - - +
65B SER* 3.5 14.1 + - - -
76B GLU* 3.4 19.6 + - - +
77B VAL* 1.3 83.6 + - - +
79B PHE* 1.3 60.4 + - - +
80B TYR* 3.4 34.7 + - + +
102B GLN* 4.6 0.9 - - - +
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Residues in contact with PHE 79 (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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253A PHE* 4.5 6.5 - + - -
23B ILE* 4.2 18.6 - - + -
27B TYR* 4.0 19.7 - + - -
55B CYS* 3.3 23.1 - - + -
57B MET* 3.2 25.6 - - - -
62B ALA* 4.8 0.7 - - + -
63B GLU* 3.4 5.2 - - - +
64B PHE* 3.0 80.0 + + + +
65B SER* 4.4 1.1 - - - -
66B HIS* 3.8 14.1 - + - -
77B VAL* 3.7 32.5 - - + -
78B ASN* 1.3 78.2 - - - +
80B TYR* 1.3 66.8 + - - +
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Residues in contact with TYR 80 (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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54B MET* 4.5 13.7 - - + -
55B CYS 2.9 12.2 + - - +
56B VAL* 3.1 5.2 - - - -
57B MET* 2.5 32.5 + - - -
62B ALA* 3.5 14.3 - - - +
63B GLU* 4.5 21.1 - - + -
78B ASN* 3.4 43.4 + - + +
79B PHE* 1.3 79.0 - - - +
81B SER* 1.3 58.1 + - - +
84B ILE* 4.8 3.6 - - + -
85B LEU* 3.4 51.4 - - + +
88B TYR* 4.5 22.2 - + + -
102B GLN* 4.0 13.1 + - - -
103B PHE* 5.7 0.2 - + - -
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Residues in contact with SER 81 (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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57B MET 3.1 9.2 - - - -
58B SER 5.1 0.7 - - - -
59B THR 2.8 27.1 - - - -
60B GLU* 3.2 12.0 + - - -
62B ALA* 3.1 9.3 + - - +
80B TYR* 1.3 75.0 - - - +
82B GLU* 1.3 66.7 + - - +
83B GLU* 3.0 5.9 + - - +
84B ILE* 2.8 44.0 + - - +
85B LEU 3.1 9.7 + - - -
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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