Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 2A3W
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 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A TYR* 3.0 4.5 - - - -
75A ILE 2.8 35.2 + - - +
76A GLY 3.1 14.7 + - - -
77A ARG* 1.3 82.3 - - + +
79A LYS* 1.3 60.3 + - - +
119A LEU* 3.3 9.9 - - + +
120A ARG* 3.7 45.6 + - + +
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Residues in contact with LYS 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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66A GLU* 4.1 11.0 - - - +
72A SER* 4.3 0.9 - - - +
73A LEU 3.3 7.6 - - - +
74A TYR* 3.5 44.7 + - + +
77A ARG 4.0 0.6 + - - +
78A HIS* 1.3 77.0 - - - +
80A VAL* 1.3 68.3 + - - +
81A THR* 3.5 23.1 - - - +
119A LEU* 4.0 3.5 - - - +
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Residues in contact with VAL 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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71A TYR 4.1 0.2 - - - +
72A SER* 3.2 5.2 - - - -
73A LEU* 2.9 46.1 + - + +
79A LYS* 1.3 79.7 - - - +
81A THR* 1.3 65.1 + - - +
105A ALA* 4.0 26.0 - - + -
107A PHE* 5.4 3.8 - - + -
117A LYS* 3.6 24.7 - - + -
118A GLY 3.5 24.9 - - - +
119A LEU* 3.8 17.7 - - + -
12E PRO 5.1 1.6 - - - +
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Residues in contact with THR 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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66A GLU* 4.2 3.7 + - + -
70A GLU* 4.2 30.1 - - + +
71A TYR 3.3 10.3 - - - +
72A SER* 2.5 26.2 + - - +
79A LYS* 3.5 17.8 - - - -
80A VAL* 1.3 75.9 - - - +
82A SER* 1.3 64.4 + - - +
83A LYS* 5.6 1.6 - - + +
107A PHE* 5.7 0.4 - - - -
117A LYS* 3.0 25.1 + - - +
42E ASP* 4.3 0.5 - - - +
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Residues in contact with SER 82 (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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69A GLY 4.0 0.2 - - - +
70A GLU* 3.5 2.4 - - - -
71A TYR* 2.8 33.5 + - - +
81A THR* 1.3 76.6 + - - +
83A LYS* 1.3 65.5 + - - +
107A PHE* 4.4 14.3 - - - -
114A LEU* 3.9 22.4 - - - +
115A VAL 2.8 26.5 + - - -
117A LYS* 3.5 14.4 + - - +
42E ASP* 3.4 6.4 + - - -
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Residues in contact with LYS 83 (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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69A GLY 3.2 5.8 - - - +
70A GLU* 3.6 38.6 + - + -
81A THR* 5.6 2.0 - - + +
82A SER* 1.3 76.9 - - - +
84A VAL* 1.3 62.5 + - - +
114A LEU* 3.7 16.1 - - - +
115A VAL* 5.2 1.6 + - - +
40E TYR* 5.2 1.7 + - - -
42E ASP* 2.9 46.0 + - + +
44E SER* 4.9 6.9 + - - -
88E PHE* 4.2 18.8 - - + -
89E PRO* 3.6 19.7 - - + +
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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