Contacts of the strand formed by residues 287 - 292 (chain A) 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 CYS 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.1 38.1 + - - -
100A LYS* 3.1 34.5 - - + +
277A MET* 3.1 26.0 - - - +
280A MET* 3.7 31.4 - - + -
283A ALA* 4.7 1.1 - - - -
285A LYS 4.0 5.6 - - - +
286A THR* 1.3 71.9 - - - +
288A ILE* 1.3 61.6 + - - +
463A LEU* 6.2 0.7 - - - -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 4.9 2.7 - - + -
87A MET 3.1 9.0 - - - +
88A PHE* 3.0 51.1 - - + -
89A LEU 4.4 0.4 - - - +
99A PHE* 3.6 27.6 - - + -
100A LYS 3.0 6.8 + - - +
101A ILE* 3.1 28.1 - - + +
102A LEU* 2.8 25.5 + - - +
277A MET* 3.3 3.8 - - - -
286A THR* 4.8 2.0 - - + -
287A CYS* 1.3 80.9 - - - +
289A THR* 1.3 61.0 + - - +
290A ILE* 5.2 0.7 - - + -
309A PHE* 3.7 28.9 - - + -
313A THR* 4.7 1.6 - - - +
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Residues in contact with THR 289 (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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85A LEU* 4.0 0.3 - - - +
86A ILE* 3.1 6.2 - - - +
87A MET* 2.8 57.4 + - + -
102A LEU* 3.3 19.0 - - + +
273A SER* 4.1 13.3 + - - +
274A PHE* 5.1 0.9 - - - -
277A MET* 3.0 37.2 - - - +
288A ILE* 1.3 72.8 - - - +
290A ILE* 1.3 63.5 + - - +
291A LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 290 (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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85A LEU 3.8 4.7 - - - +
86A ILE* 4.3 14.4 - - + +
101A ILE* 3.4 28.7 - - + -
102A LEU 2.7 11.8 + - - +
103A GLY* 3.5 6.9 - - - -
104A ALA 3.2 17.2 + - - -
288A ILE* 4.8 0.9 - - + +
289A THR* 1.3 77.4 - - - +
291A LEU* 1.3 78.3 + - - +
292A VAL* 3.9 23.6 - - + -
308A LYS* 6.5 0.4 - - + -
309A PHE* 3.4 38.8 - - + -
338A MET* 4.9 0.9 - - - -
423A LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 291 (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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49A ILE* 4.0 27.1 - - + -
84A GLY* 3.5 4.2 - - - -
85A LEU* 2.8 57.7 + - + +
87A MET* 5.5 0.7 - - + -
103A GLY 5.2 0.2 - - - -
104A ALA* 3.1 17.3 - - + +
106A ILE* 3.9 22.1 - - + +
270A ALA* 3.9 32.5 - - + +
273A SER* 4.4 1.8 - - - +
274A PHE* 5.1 4.0 - - + -
289A THR* 4.1 18.4 - - + -
290A ILE* 1.3 92.0 - - - +
292A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 292 (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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83A LYS 4.8 0.9 - - - -
84A GLY* 4.8 7.4 - - - -
85A LEU 5.6 0.7 - - - +
104A ALA 3.2 8.5 + - - +
105A HIS* 2.9 7.5 - - + -
106A ILE* 2.7 36.4 + - - +
290A ILE* 3.9 20.6 - - + -
291A LEU* 1.3 78.8 - - - +
293A ASP* 1.3 64.4 + - - +
295A GLU* 5.9 0.7 - - + -
303A THR 3.6 8.5 - - - +
304A GLY* 4.2 15.7 - - - +
306A GLN* 4.0 24.2 - - - +
308A LYS* 6.3 0.7 - - + -
419A ILE* 4.3 22.0 - - + -
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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