Contacts of the strand formed by residues 466 - 472 (chain G) in PDB entry 6IY6
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 HIS 466 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255G GLN* 2.9 37.1 + - + +
258G ILE* 3.5 26.5 - - + +
259G CYS* 4.9 2.7 - - - -
292G GLU* 3.8 12.1 - - + -
293G MET 3.4 16.8 - - - +
294G ALA* 3.6 7.9 - - - -
295G PHE* 3.4 11.2 - - - -
430G GLN* 3.5 5.2 - - - +
431G ARG* 2.8 57.9 + - + +
433G HIS* 4.1 11.6 + - + +
459G PHE* 3.8 17.9 - + - -
464G PRO 2.9 24.0 + - - -
465G PRO* 1.3 73.1 - - - +
467G ALA* 1.3 52.3 + - - +
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Residues in contact with ALA 467 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292G GLU* 3.1 11.8 - - - +
293G MET* 2.9 30.7 + - - +
295G PHE* 3.7 7.5 - - + -
299G TYR* 4.5 7.0 - - + +
302G VAL* 3.8 25.1 - - + +
416G TYR* 3.9 4.5 - - + +
429G ALA 3.3 19.1 - - - +
430G GLN* 3.6 11.9 - - + -
431G ARG 4.3 0.7 - - - +
466G HIS* 1.3 72.3 - - - +
468G GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 468 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G ILE* 3.3 16.6 - - - -
292G GLU* 3.4 3.2 + - - -
302G VAL* 4.3 1.1 - - - -
306G ILE* 3.8 9.0 - - - -
416G TYR* 2.7 23.9 + - - -
428G GLY* 3.1 14.2 - - - -
429G ALA 3.2 6.4 + - - -
431G ARG* 3.3 12.5 - - - +
467G ALA* 1.3 77.4 - - - +
469G GLY* 1.3 56.4 + - - -
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Residues in contact with GLY 469 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G LEU 4.4 0.3 - - - +
291G ILE* 2.9 38.1 + - - +
306G ILE* 3.8 4.3 - - - +
426G LEU* 4.0 19.1 - - - +
428G GLY* 3.9 14.8 - - - -
468G GLY* 1.3 73.2 - - - -
470G GLY* 1.3 54.6 + - - -
602G PO4 3.4 13.2 + - - -
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Residues in contact with GLY 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289G LEU 3.4 9.4 - - - -
290G ASP* 3.5 18.6 - - - -
425G ILE 3.4 2.3 - - - +
426G LEU* 3.4 24.8 - - - +
427G SER 4.1 2.9 + - - +
469G GLY* 1.3 72.4 - - - -
471G ILE* 1.3 64.1 + - - -
602G PO4 3.4 12.0 + - - -
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Residues in contact with ILE 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G ILE* 5.6 0.2 - - + -
206G PHE* 4.3 10.3 - - + -
286G PHE* 5.0 1.3 - - - -
288G GLY* 3.3 5.4 - - - -
289G LEU* 2.8 69.5 + - + +
310G MET* 3.5 31.2 - - + -
313G ILE* 4.8 2.7 - - + -
425G ILE* 3.6 28.7 - - + +
426G LEU* 3.8 22.7 - - + -
470G GLY* 1.3 77.1 - - - +
472G GLY* 1.3 60.4 + - - +
473G LEU 3.6 0.2 + - - -
476G VAL* 3.9 15.9 - - + -
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Residues in contact with GLY 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286G PHE* 3.7 19.6 - - - -
287G VAL 3.7 8.5 - - - -
425G ILE* 4.0 6.9 + - - +
471G ILE* 1.3 69.5 - - - +
473G LEU* 1.3 56.3 + - - -
474G GLU* 3.2 3.8 - - - -
475G ARG* 2.8 19.2 + - - +
476G VAL* 2.8 35.3 + - - +
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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