Contacts of the strand formed by residues 74 - 77 (chain B) in PDB entry 1GGT
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 LEU 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.1 24.0 - - + +
53B PHE 4.6 0.2 - - - -
54B LYS* 4.0 30.5 - - + +
60B ASN* 3.9 34.1 - - + +
61B LYS* 4.2 7.6 - - + +
73B LYS* 1.3 75.5 - - - +
75B ILE* 1.3 75.3 + - - +
76B VAL* 4.5 5.4 - - + -
82B PHE* 4.0 25.6 - - + -
179B ASP 3.8 3.6 + - - -
180B THR* 3.5 30.1 - - + +
181B TYR* 3.0 24.4 + - - -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LYS* 4.0 13.4 + - - +
64B HIS* 4.5 0.9 - - - +
66B THR* 3.1 42.8 + - + +
69B TYR* 3.5 26.5 - - + -
71B ASN* 3.5 39.9 - - + +
73B LYS 3.7 3.3 + - - +
74B LEU* 1.3 87.6 - - - +
76B VAL* 1.3 67.2 + - - +
181B TYR* 3.6 15.0 - - + -
183B LEU* 3.5 24.7 - - + -
235B LEU* 4.0 10.3 - - + -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASN* 5.7 0.4 - - + -
64B HIS* 3.0 47.1 - - + +
66B THR* 4.4 1.3 - - - -
74B LEU* 4.5 9.6 - - + -
75B ILE* 1.3 78.1 - - - +
77B ARG* 1.3 66.5 + - - +
80B GLN 5.0 0.2 - - - +
82B PHE* 4.0 33.2 - - + -
148B SER* 5.4 1.6 - - - +
180B THR* 4.1 11.4 - - + -
181B TYR 2.9 15.4 + - - +
182B ILE* 3.2 22.5 - - + -
183B LEU* 3.1 23.4 + - - +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B HIS* 2.7 42.8 + - - +
65B HIS* 2.9 22.8 + - - -
66B THR* 4.2 12.3 - - + +
69B TYR* 4.3 12.9 + - - -
76B VAL* 1.3 78.1 - - - +
78B ARG* 1.3 68.6 + - - +
80B GLN* 3.3 20.1 + - - +
148B SER* 4.0 2.1 + - - -
182B ILE* 4.4 1.1 - - - -
183B LEU* 3.6 12.9 - - + +
184B PHE 3.2 23.4 + - - +
185B ASN* 3.3 22.9 - - + +
186B PRO* 4.2 2.2 - - - +
187B TRP* 3.2 39.5 - - - -
205B VAL* 4.6 5.0 - - - +
206B LEU* 4.2 10.5 - - - +
230B PHE* 5.3 0.6 - - - -
326B ARG 5.9 0.4 + - - -
329B GLY* 3.9 19.8 - - - -
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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