Contacts of the strand formed by residues 62 - 65 (chain A) in PDB entry 2D8M
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 HIS 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.8 17.6 - - + +
27A VAL 3.0 18.0 + - - +
28A VAL* 3.6 5.5 - - + -
29A VAL* 3.5 11.6 + - - +
56A TRP* 3.8 10.0 - - - -
61A THR* 1.3 111.6 + - - +
63A LEU* 1.3 61.4 + - - +
64A ILE* 5.6 0.4 - - + -
82A ARG* 3.3 51.3 + - + +
84A VAL* 4.4 11.9 - - + -
88A TRP* 4.4 19.5 - + + -
101A SER* 4.3 20.2 + - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.7 20.4 - - + +
31A SER* 3.6 26.7 - - - +
56A TRP* 3.6 18.4 - - + -
62A HIS* 1.3 75.5 - - - +
64A ILE* 1.3 68.7 + - - +
65A CYS* 4.6 5.4 - - + +
72A LYS* 3.5 29.6 - - + +
73A TYR* 4.6 2.9 - - - -
76A VAL* 3.5 20.0 - - + -
82A ARG 3.0 11.8 + - - +
83A ILE* 4.0 20.0 - - + -
84A VAL* 2.9 30.0 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.8 30.7 - - + -
29A VAL 2.9 27.7 + - - +
30A LEU* 4.5 4.0 - - + -
31A SER* 3.2 19.8 + - - -
33A PHE* 3.3 28.5 - - + -
41A LEU* 4.0 10.8 - - + -
45A ALA* 6.3 0.4 - - + -
63A LEU* 1.3 75.3 - - - +
65A CYS* 1.3 59.3 + - - +
84A VAL* 4.0 4.0 - - + -
85A ARG 4.2 9.0 - - - +
86A LYS* 3.9 17.9 - - + -
88A TRP* 4.2 12.1 - - + -
89A VAL* 3.5 26.7 - - + -
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Residues in contact with CYS 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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31A SER* 4.1 9.0 - - - -
33A PHE* 4.0 3.7 - - - -
63A LEU* 3.5 7.1 + - + +
64A ILE* 1.3 75.1 - - - +
66A ALA* 1.3 63.1 + - - +
67A PHE 2.8 34.8 - - - -
68A ALA* 4.6 1.1 - - - -
70A THR* 3.4 16.8 - - - -
73A TYR* 4.8 7.6 - - + -
83A ILE* 4.7 8.5 - - + -
84A VAL 3.3 8.6 + - - +
85A ARG* 4.0 5.7 + - - +
86A LYS* 3.6 20.3 + - - +
106A MET* 3.7 25.5 - - - +
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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