Contacts of the strand formed by residues 287 - 292 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I LEU* 3.2 38.9 + - - -
100I LYS* 3.1 34.1 - - + +
277I MET* 3.1 24.7 - - - +
280I MET* 3.6 31.6 - - + -
283I ALA* 4.7 1.1 - - - -
285I LYS 4.0 4.9 - - - +
286I THR* 1.3 72.2 - - - +
288I ILE* 1.3 62.5 + - - +
463I LEU* 6.2 0.7 - - - -
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Residues in contact with ILE 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ILE* 4.9 2.9 - - + -
87I MET 3.1 9.0 - - - +
88I PHE* 3.0 50.7 - - + -
89I LEU 4.4 0.2 - - - +
99I PHE* 3.6 28.0 - - + -
100I LYS 3.0 6.3 + - - +
101I ILE* 3.1 28.5 - - + +
102I LEU* 2.8 25.7 + - - +
277I MET* 3.4 3.6 - - - -
286I THR* 4.8 2.5 - - + -
287I CYS* 1.3 81.2 - - - +
289I THR* 1.3 60.8 + - - +
290I ILE* 5.2 1.1 - - + -
309I PHE* 3.7 29.2 - - + -
313I THR* 4.7 1.1 - - - +
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Residues in contact with THR 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I LEU 4.0 0.3 - - - +
86I ILE* 3.1 5.9 - - - +
87I MET* 2.8 57.0 + - + +
102I LEU* 3.3 18.1 - - + +
273I SER* 4.0 14.2 + - - +
274I PHE* 5.1 0.7 - - - -
277I MET* 3.0 37.9 - - - +
288I ILE* 1.3 71.9 + - - +
290I ILE* 1.3 63.7 + - - +
291I LEU* 4.1 25.1 - - + -
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Residues in contact with ILE 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I LEU 3.8 4.3 - - - +
86I ILE* 4.3 14.6 - - + +
101I ILE* 3.5 24.0 - - + -
102I LEU 2.7 11.6 + - - +
103I GLY* 3.5 6.7 - - - -
104I ALA 3.1 18.0 + - - -
288I ILE* 4.7 1.3 - - + +
289I THR* 1.3 76.0 - - - +
291I LEU* 1.3 78.7 + - - +
292I VAL* 4.0 23.8 - - + +
308I LYS* 6.6 0.2 - - + -
309I PHE* 3.4 44.0 - - + -
338I MET* 4.9 0.9 - - - -
423I LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I ILE* 4.0 28.0 - - + -
84I GLY* 3.5 3.6 - - - -
85I LEU* 2.8 58.4 + - + +
87I MET* 5.5 0.7 - - + -
104I ALA* 3.2 16.8 - - + +
106I ILE* 3.9 21.8 - - + +
270I ALA* 3.8 32.5 - - + +
273I SER* 4.4 1.6 - - - +
274I PHE* 5.1 4.0 - - + -
289I THR* 4.1 19.3 - - + -
290I ILE* 1.3 85.3 - - - +
292I VAL* 1.3 62.8 + - - +
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Residues in contact with VAL 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I LYS 4.8 0.7 - - - -
84I GLY* 4.8 7.9 - - - -
85I LEU 5.6 0.7 - - - +
104I ALA 3.2 8.6 + - - +
105I HIS* 2.9 8.0 - - + -
106I ILE* 2.7 35.0 + - - +
290I ILE* 4.0 20.9 - - + -
291I LEU* 1.3 77.7 - - - +
293I ASP* 1.3 65.0 + - - +
295I GLU* 5.9 0.4 - - + -
303I THR 3.6 9.4 - - - +
304I GLY* 4.1 16.2 - - - +
306I GLN* 3.9 25.1 - - - +
308I LYS* 6.3 0.7 - - + -
419I ILE* 4.3 21.8 - - + -
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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