Contacts of the strand formed by residues 287 - 292 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X LEU* 3.1 38.3 + - - -
100X LYS* 3.1 34.3 - - + +
277X MET* 3.1 25.0 - - - +
280X MET* 3.6 31.0 - - - -
283X ALA* 4.7 0.7 - - - -
285X LYS 4.0 6.5 - - - +
286X THR* 1.3 71.9 - - - +
288X ILE* 1.3 62.9 + - - +
463X LEU* 5.9 1.8 - - - +
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Residues in contact with ILE 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X ILE* 4.9 2.7 - - + -
87X MET 3.1 8.7 - - - +
88X PHE* 3.1 50.9 - - + -
89X LEU 4.4 0.7 - - - +
99X PHE* 3.6 27.4 - - + -
100X LYS 3.0 5.3 + - - +
101X ILE* 3.1 29.2 - - + +
102X LEU* 2.9 25.3 + - - +
277X MET* 3.4 2.7 - - - +
286X THR* 4.8 1.8 - - + -
287X CYS* 1.3 80.9 - - - +
289X THR* 1.3 62.7 + - - +
290X ILE* 5.2 0.4 - - + -
309X PHE* 3.7 29.8 - - + -
313X THR* 4.7 1.6 - - - +
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Residues in contact with THR 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X LEU 3.9 0.3 - - - +
86X ILE* 3.1 6.0 - - - +
87X MET* 2.8 56.6 + - + +
102X LEU* 3.3 18.8 - - + +
273X SER* 4.0 13.3 + - - +
274X PHE* 5.1 1.1 - - - -
277X MET* 3.0 36.5 - - - +
288X ILE* 1.3 74.2 + - - +
290X ILE* 1.3 63.8 + - - +
291X LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 290 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X LEU 3.8 4.3 - - - +
86X ILE* 4.4 12.8 - - + +
101X ILE* 3.4 25.1 - - + -
102X LEU 2.7 12.0 + - - +
103X GLY* 3.5 7.3 - - - -
104X ALA 3.2 17.9 + - - +
288X ILE* 4.8 1.1 - - + +
289X THR* 1.3 76.1 - - - +
291X LEU* 1.3 78.9 + - - +
292X VAL* 3.9 23.6 - - + -
308X LYS* 6.5 0.7 - - + -
309X PHE* 3.4 44.6 - - + -
338X MET* 5.0 0.9 - - - -
423X LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 291 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X VAL* 5.8 0.2 - - + -
49X ILE* 4.0 27.4 - - + -
84X GLY* 3.5 4.0 - - - -
85X LEU* 2.8 57.6 + - + +
87X MET* 5.5 0.9 - - + -
103X GLY 5.2 0.2 - - - -
104X ALA* 3.2 16.6 - - + +
106X ILE* 3.9 21.4 - - + +
270X ALA* 3.9 33.2 - - + +
273X SER* 4.4 1.8 - - - +
274X PHE* 5.1 3.6 - - + -
289X THR* 4.1 18.2 - - + -
290X ILE* 1.3 91.6 - - - +
292X VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 292 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X LYS 4.8 0.4 - - - -
84X GLY* 4.7 7.4 - - - -
85X LEU 5.6 0.2 - - - +
104X ALA 3.2 8.8 + - - +
105X HIS* 2.9 7.3 - - + -
106X ILE* 2.7 33.0 + - - +
290X ILE* 3.9 20.6 - - + -
291X LEU* 1.3 78.2 - - - +
293X ASP* 1.3 63.9 + - - +
295X GLU* 5.9 0.7 - - + -
303X THR 3.6 9.6 - - - +
304X GLY* 4.2 16.4 - - - +
306X GLN* 3.9 24.2 - - - +
308X LYS* 6.2 0.7 - - + -
419X 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