Contacts of the strand formed by residues 62 - 68 (chain F) in PDB entry 2WTK
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 62 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F LEU* 3.9 16.2 - - + -
56F GLY 3.8 4.3 - - - -
57F GLU* 3.8 31.0 - - + +
61F GLY* 1.3 71.9 - - - -
63F VAL* 1.3 60.6 + - - +
64F LYS* 5.4 9.4 - - + -
79F ILE* 3.0 44.4 + - + +
81F LYS* 5.2 16.3 - - - +
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Residues in contact with VAL 63 (chain F).
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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4F ANP 3.7 67.1 - - + +
54F LEU* 3.4 5.8 - - - +
55F LEU* 2.8 37.3 + - + -
56F GLY 2.7 17.2 + - - +
61F GLY 4.5 0.2 - - - +
62F LYS* 1.3 75.1 - - - +
64F LYS* 1.3 61.6 + - - +
76F ALA* 4.6 4.5 - - + -
77F VAL 3.5 11.2 - - - +
78F LYS* 4.0 26.0 - - + +
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F MET* 4.4 19.1 - - + +
52F GLY 3.7 17.3 - - - +
53F ASP 3.5 6.1 - - - +
54F LEU* 4.2 20.2 - - + +
55F LEU* 4.2 4.0 - - - -
62F LYS* 4.1 10.5 + - - -
63F VAL* 1.3 77.0 - - - +
65F GLU* 1.3 67.4 + - - +
76F ALA* 3.8 2.1 - - - +
77F VAL* 2.9 33.7 + - - +
79F ILE* 3.7 27.8 - - + +
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Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F MET* 3.6 2.6 - - - +
52F GLY* 2.6 33.5 + - - -
53F ASP 3.0 15.3 + - - +
55F LEU* 3.8 26.3 - - + +
64F LYS* 1.3 75.7 - - - +
66F VAL* 1.3 74.6 + - - +
67F LEU* 4.9 0.5 - - - +
74F ARG* 2.5 47.4 + - - -
75F ARG 4.0 6.9 - - - +
76F ALA* 4.6 0.2 - - - +
131F TYR* 4.8 4.5 - - + -
336F THR* 3.4 33.4 + - + -
337F VAL* 4.0 12.0 - - + +
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ILE* 4.9 0.4 - - + -
49F TYR* 3.4 35.4 - - + +
50F LEU 3.1 25.1 - - - +
51F MET* 3.9 11.7 - - + -
64F LYS 3.7 0.6 + - - -
65F GLU* 1.3 88.4 - - - +
67F LEU* 1.3 61.8 + - - +
74F ARG* 4.1 0.5 - - - -
75F ARG* 3.0 54.7 + - + +
77F VAL* 3.4 31.0 - - + -
128F VAL* 4.7 0.4 - - + -
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Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E LEU 5.9 0.2 - - - +
251E GLN* 5.0 0.4 - - - +
285E THR* 4.2 4.9 - - + -
288E LEU* 4.3 13.9 - - + -
49F TYR* 3.4 4.2 - - - -
50F LEU* 2.9 55.9 + - + +
66F VAL* 1.3 77.0 - - - +
68F ASP* 1.3 89.0 + - - +
69F SER 3.3 1.6 + - - -
72F LEU* 3.7 39.3 - - + +
73F CYS 3.9 9.6 - - - +
74F ARG* 4.2 14.1 - - + +
337F VAL* 4.1 30.7 - - + -
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Residues in contact with ASP 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LYS* 2.9 41.4 + - - +
49F TYR* 3.8 19.9 + - + -
66F VAL* 5.0 0.4 - - - +
67F LEU* 1.3 74.9 - - - +
69F SER* 1.3 57.6 + - - +
70F GLU* 3.1 6.2 + - - -
71F THR* 3.0 39.1 + - - +
72F LEU* 2.9 28.8 + - - -
73F CYS* 3.1 21.3 + - + +
75F ARG* 4.1 9.8 + - - +
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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