Contacts of the strand formed by residues 64 - 68 (chain A) in PDB entry 2WYG
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 PHE 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.1 19.3 - - + -
34A ILE 3.3 13.9 - - - +
35A ASN* 4.5 1.8 - - - +
41A PHE* 3.7 25.4 - + + -
59A LEU* 3.6 37.5 - - + -
61A ALA* 4.5 10.5 - - + -
62A LYS 4.8 3.4 - - - -
63A ARG* 1.3 86.6 - - - +
65A LYS* 1.3 78.5 + - - +
84A GLU* 5.9 0.2 - - - +
85A VAL* 3.9 23.8 + - + +
88A VAL* 4.5 11.2 - - + -
106A LEU* 3.8 32.5 - - + -
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Residues in contact with LYS 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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33A LEU* 3.4 5.5 - - - -
34A ILE* 3.0 41.8 + - + +
35A ASN 6.1 0.2 - - - +
38A ASN* 5.5 6.8 - - - +
63A ARG* 3.5 26.1 - - + +
64A PHE* 1.3 81.9 - - - +
66A VAL* 1.3 64.3 + - - +
82A VAL* 3.5 27.8 - - + +
83A HIS 3.6 8.7 - - - +
84A GLU* 3.2 41.3 + - + +
85A VAL* 4.8 0.9 - - - -
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Residues in contact with VAL 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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31A ALA* 3.7 28.9 - - + -
32A LEU 3.4 4.9 - - - +
33A LEU* 3.8 20.6 - - + -
34A ILE* 5.0 0.2 - - - -
52A ILE* 4.1 12.6 - - + -
64A PHE* 4.7 0.7 - - + -
65A LYS* 1.3 78.3 - - - +
67A ARG* 1.3 64.6 + - - +
68A VAL* 4.1 7.1 + - + -
81A ALA 3.7 1.6 - - - +
82A VAL* 3.6 3.0 - - - -
83A HIS* 2.8 43.5 + - + +
85A VAL* 4.0 6.7 - - + -
106A LEU* 3.9 17.5 - - + -
108A LEU* 3.9 22.2 - - + -
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Residues in contact with ARG 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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31A ALA* 3.5 4.5 - - - -
32A LEU* 2.7 66.7 + - + +
34A ILE* 4.3 25.3 - - + +
38A ASN* 4.9 11.9 + - - +
40A GLY 5.7 1.6 - - - +
65A LYS 4.2 0.4 - - - -
66A VAL* 1.3 73.8 - - - +
68A VAL* 1.3 67.6 + - - +
70A ASP* 3.4 33.0 + - + +
73A THR* 3.0 51.7 + - - +
81A ALA 3.5 12.1 - - - +
82A VAL* 4.4 15.5 - - + +
141A PHE* 6.2 0.4 - - - -
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Residues in contact with VAL 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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30A GLN 4.3 4.3 - - - -
31A ALA* 4.2 13.0 - - + -
46A ILE* 3.8 28.9 - - + -
66A VAL* 4.3 7.9 - - + +
67A ARG* 1.3 82.8 - - - +
69A GLY* 1.3 59.9 + - - +
70A ASP* 3.3 9.4 + - - +
81A ALA* 3.1 34.9 + - + +
83A HIS* 4.4 14.8 - - + +
108A LEU* 6.0 0.2 - - + -
112A ILE* 4.1 20.0 - - + -
115A ARG* 4.0 3.3 + - - +
118A VAL* 4.1 18.2 - - + -
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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