Contacts of the strand formed by residues 287 - 292 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D LEU* 3.2 38.9 + - - -
100D LYS* 3.1 34.3 - - + +
277D MET* 3.1 26.1 - - - +
280D MET* 3.6 31.0 - - + -
283D ALA* 4.7 0.9 - - - -
285D LYS 4.0 5.2 - - - +
286D THR* 1.3 72.8 - - - +
288D ILE* 1.3 62.2 + - - +
463D LEU* 6.0 1.3 - - - +
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Residues in contact with ILE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ILE* 4.9 2.5 - - + -
87D MET 3.1 9.6 - - - +
88D PHE* 3.1 49.4 - - + -
89D LEU 4.4 0.4 - - - +
99D PHE* 3.6 30.7 - - + -
100D LYS 3.0 6.7 + - - +
101D ILE* 3.1 28.2 - - + +
102D LEU* 2.9 24.8 + - - +
277D MET* 3.3 3.8 - - - -
286D THR* 4.8 2.0 - - + -
287D CYS* 1.3 79.8 - - - +
289D THR* 1.3 61.2 + - - +
290D ILE* 5.2 0.4 - - + -
309D PHE* 3.8 29.4 - - + -
313D THR* 4.7 1.3 - - + +
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Residues in contact with THR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU 4.0 0.3 - - - +
86D ILE* 3.1 5.8 - - - +
87D MET* 2.8 57.7 + - + +
102D LEU* 3.3 18.7 - - + +
273D SER* 4.1 14.0 + - - +
274D PHE* 5.1 0.9 - - - -
277D MET* 3.0 37.3 - - - +
288D ILE* 1.3 73.8 + - - +
290D ILE* 1.3 65.0 + - - +
291D LEU* 4.2 23.1 - - + -
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU 3.8 3.8 - - - +
86D ILE* 4.3 13.2 - - + +
101D ILE* 3.5 24.2 - - + -
102D LEU 2.7 12.0 + - - +
103D GLY* 3.5 6.7 - - - -
104D ALA 3.1 16.8 + - - -
288D ILE* 4.8 1.3 - - + +
289D THR* 1.3 75.5 - - - +
291D LEU* 1.3 79.7 + - - +
292D VAL* 4.0 23.1 - - + +
308D LYS* 6.6 0.4 - - + -
309D PHE* 3.3 45.1 - - + -
338D MET* 4.9 0.7 - - - -
423D LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 4.0 27.1 - - + -
84D GLY* 3.5 4.2 - - - -
85D LEU* 2.8 56.4 + - + +
87D MET* 5.5 1.1 - - + -
103D GLY 5.2 0.2 - - - -
104D ALA* 3.1 17.0 - - + +
106D ILE* 3.9 21.8 - - + +
270D ALA* 3.9 31.9 - - + +
273D SER* 4.4 1.6 - - - +
274D PHE* 5.1 4.0 - - + -
289D THR* 4.2 18.2 - - + -
290D ILE* 1.3 91.1 - - - +
292D VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LYS 4.8 0.7 - - - -
84D GLY* 4.8 7.9 - - - -
85D LEU 5.6 0.7 - - - +
104D ALA 3.1 8.6 + - - +
105D HIS* 2.9 7.4 - - + -
106D ILE* 2.7 36.1 + - - +
290D ILE* 4.0 20.9 - - + -
291D LEU* 1.3 77.5 - - - +
293D ASP* 1.3 63.3 + - - +
295D GLU* 5.9 0.4 - - + -
303D THR 3.6 9.4 - - - +
304D GLY* 4.2 16.4 - - - +
306D GLN* 3.9 24.7 - - - +
308D LYS* 6.3 0.9 - - + -
419D ILE* 4.3 22.2 - - + -
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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