Contacts of the strand formed by residues 63 - 66 (chain A) in PDB entry 2HRG
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 ILE 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.7 3.6 - - + -
10A ILE* 4.1 9.6 - - + -
48A VAL* 3.8 36.8 - - + -
61A THR* 4.6 2.0 - - - +
62A SER* 1.3 78.4 - - - +
64A HIS* 1.3 69.8 + - - +
65A TRP* 3.4 44.2 + - + -
78A GLY* 3.2 16.5 - - - -
95A TYR* 3.0 15.6 + - + +
108A TYR* 3.9 17.0 - - + -
109A HIS 3.6 11.2 - - - +
120A LEU* 3.9 29.8 - - + -
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER 4.2 0.8 + - - -
63A ILE* 1.3 73.0 - - - +
65A TRP* 1.3 74.3 + - - +
66A HIS* 3.3 13.3 + - - -
67A GLY 4.6 1.3 - - - -
68A PHE 5.4 1.3 - - - -
77A ASP* 2.7 36.1 + - - +
78A GLY* 4.1 0.6 - - - -
108A TYR* 3.2 7.6 - - - +
109A HIS* 2.9 57.0 + - + +
111A HIS* 3.5 29.3 - + + +
399A HIS* 3.2 26.6 - + + -
400A GLY 6.0 0.2 - - - -
1498A CU 3.7 2.2 - - - -
1499A CU 1.9 32.9 - - - -
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Residues in contact with TRP 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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8A LEU* 3.7 21.3 - - + -
36A ILE* 4.3 3.6 - - + -
46A LEU* 3.4 30.7 - - + -
48A VAL* 4.4 1.8 - - + -
63A ILE* 3.4 26.6 + - + -
64A HIS* 1.3 80.4 + - - +
66A HIS* 1.3 64.1 + - - +
67A GLY 3.2 3.6 + - - -
68A PHE* 3.3 40.7 + - + +
70A GLN* 3.6 14.2 + - - +
76A ALA 3.3 17.7 - - - -
77A ASP* 4.4 2.1 - - - +
95A TYR* 3.2 51.0 - + + +
97A PHE* 3.8 12.6 - + + -
107A TRP 3.6 4.5 - - - -
108A TYR* 3.6 33.0 - + + -
124A ILE* 4.0 8.3 - - + -
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Residues in contact with HIS 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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64A HIS* 3.3 12.8 + - + +
65A TRP* 1.3 69.7 - - - +
67A GLY* 1.3 63.1 + - - +
68A PHE 3.5 0.2 - - - -
106A PHE* 3.4 26.5 - - - +
107A TRP* 2.7 36.5 + - + +
109A HIS* 4.1 3.4 - - - +
240A ALA* 3.6 12.3 - - + -
242A ARG* 3.3 23.0 + - - -
397A HIS* 3.2 28.4 - + - -
423A ASP* 3.0 22.3 + - - -
424A VAL* 3.4 13.2 - - + +
451A HIS* 3.6 0.2 - - - -
1498A CU 1.9 34.3 - - - -
1499A CU 3.4 3.9 - - - -
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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