Contacts of the strand formed by residues 84 - 87 (chain U) in PDB entry 2GLJ
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 GLY 84 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46U THR* 4.1 5.7 + - - -
79U ASN* 3.6 8.0 - - - +
80U ASN* 2.9 42.2 + - - +
82U GLY 3.4 0.4 - - - -
83U LYS* 1.3 82.2 - - - +
85U LEU* 1.3 62.5 + - - +
106U ILE* 5.0 0.2 - - - -
291U LEU 3.5 9.6 - - - -
292U VAL* 4.7 6.7 - - - -
293U ASP 5.6 0.2 - - - -
303U THR* 4.4 3.1 - - - +
308U LYS* 5.0 0.9 - - - -
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Residues in contact with LEU 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U THR* 4.3 11.9 + - - +
49U ILE* 3.4 33.9 - - + -
50U LYS* 3.4 31.2 - - - +
77U TYR* 4.0 16.2 - - + -
78U ALA 3.6 13.0 - - - +
84U GLY* 1.3 76.0 - - - +
86U ILE* 1.3 81.9 + - - +
87U MET* 4.2 13.5 - - + -
106U ILE* 6.0 0.7 - - + -
289U THR 3.9 0.5 - - - +
290U ILE* 3.7 1.1 - - - +
291U LEU* 2.8 54.6 + - + +
292U VAL* 5.6 0.8 - - - +
308U LYS* 5.1 1.5 - - - +
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Residues in contact with ILE 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77U TYR* 3.3 3.3 - - - +
78U ALA* 2.9 52.0 + - + +
85U LEU* 1.3 78.7 - - - +
87U MET* 1.3 67.7 + - - +
88U PHE* 3.6 31.8 - - + -
288U ILE* 4.8 2.9 - - + -
289U THR 3.1 14.6 - - - +
290U ILE* 4.3 11.0 - - + -
308U LYS* 3.7 17.7 - - + -
309U PHE* 3.6 41.3 - - + +
312U ASN* 4.5 5.2 - - - +
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Residues in contact with MET 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U ILE* 5.4 0.2 - - + -
53U GLU* 3.2 39.0 - - - +
57U TYR* 4.1 13.7 - - + -
76U VAL 3.5 3.4 - - - -
77U TYR* 4.3 7.4 - - + -
85U LEU* 4.2 24.0 - - + -
86U ILE* 1.3 77.2 - - - +
88U PHE* 1.3 65.0 + - - +
274U PHE* 3.3 30.3 - - + -
277U MET* 3.2 18.1 - - + +
288U ILE* 3.1 9.5 - - - +
289U THR* 2.7 62.0 + - + +
291U LEU* 5.5 1.3 - - + -
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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