Contacts of the helix formed by residues 459 - 471 (chain B) in PDB entry 2GQ3
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 GLY 459 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432B MET* 3.7 15.3 - - - +
433B ASP 3.2 6.5 + - - -
434B GLU* 3.2 12.7 - - - +
457B ASN* 3.1 11.4 + - - -
458B THR* 1.3 66.3 - - - +
460B PHE* 1.3 65.0 + - - -
461B LEU 3.0 1.7 + - - -
462B ASP 3.5 0.9 + - - -
463B ARG* 3.1 17.3 + - - +
492B TYR* 3.4 2.0 - - - -
514B GLY* 5.5 1.3 - - - -
901B MLT 3.1 27.3 - - - +
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Residues in contact with PHE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B THR 2.8 7.6 + - - +
459B GLY* 1.3 71.6 - - - +
461B LEU* 1.3 92.3 + - + +
463B ARG* 3.4 4.7 - - - +
464B THR* 2.8 35.5 + - - -
489B ILE* 4.2 21.5 - - + +
492B TYR* 3.6 15.5 - - + -
493B GLU* 3.8 22.0 - - - +
514B GLY* 4.3 15.3 - - - -
515B MET 3.6 31.2 - - - -
517B THR* 5.7 2.7 - - + -
532B GLN* 6.1 0.2 - - - -
901B MLT 4.6 1.3 - - - -
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B GLY 3.0 0.2 + - - -
460B PHE* 1.3 111.2 - - + +
462B ASP* 1.3 68.9 + - - +
463B ARG 3.0 0.8 + - - -
464B THR 3.2 2.1 + - - -
465B GLY* 3.1 16.8 + - - -
515B MET* 4.9 4.7 - - + -
517B THR* 4.5 15.3 - - + -
631B MET* 6.4 0.2 - - + -
633B ASP* 4.6 3.1 - - - +
635B ALA* 3.5 16.1 - - + +
636B THR* 3.9 26.7 - - + -
639B ILE* 3.4 32.1 - - + +
901B MLT 3.1 25.2 + - + +
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Residues in contact with ASP 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASP* 3.3 4.0 - - - +
399B LYS* 2.8 30.8 + - - -
434B GLU* 2.9 21.8 - - + +
461B LEU* 1.3 76.9 - - - +
463B ARG* 1.3 57.7 + - - +
465B GLY 3.0 2.6 + - - -
466B ASP 2.9 17.0 + - - -
634B ARG 5.4 0.2 - - - -
635B ALA* 3.7 14.3 - - - +
638B ARG* 2.7 46.5 + - - +
901B MLT 3.1 12.2 + - - +
1001B MG 2.0 29.1 - - - -
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Residues in contact with ARG 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B GLU* 3.1 10.7 + - - -
435B GLU 3.9 4.3 - - - -
436B ARG* 3.6 41.8 - - - +
439B THR* 2.9 33.2 + - - +
440B VAL* 5.5 0.2 - - - +
459B GLY 3.1 18.3 + - - +
460B PHE 3.4 6.3 - - - +
461B LEU 3.0 0.4 - - - -
462B ASP* 1.3 74.8 - - - +
464B THR* 1.3 59.6 + - - +
466B ASP* 3.5 1.7 + - - +
467B GLU* 2.7 51.4 + - - +
488B TRP* 3.5 26.1 - - + -
492B TYR* 3.5 28.2 - - + +
578B LEU 4.2 10.9 + - - -
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Residues in contact with THR 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PHE* 2.8 24.1 + - - -
461B LEU* 3.2 0.4 + - - -
463B ARG* 1.3 73.6 - - - +
465B GLY* 1.3 62.3 + - - +
467B GLU* 3.2 2.3 + - - +
468B ILE* 3.0 39.9 + - + +
480B LYS 5.6 0.7 - - - +
483B MET* 3.8 34.6 - - + +
488B TRP* 3.6 20.4 - - + -
489B ILE* 3.9 9.4 - - - +
639B ILE* 3.7 27.1 - - + +
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Residues in contact with GLY 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B LEU 3.1 8.9 + - - -
462B ASP 3.0 8.1 + - - -
464B THR* 1.3 76.2 - - - +
466B ASP* 1.3 55.8 + - - +
468B ILE* 3.3 9.3 + - - +
469B HIS* 3.0 27.9 + - - +
638B ARG* 4.1 25.4 - - - -
639B ILE* 3.8 11.7 - - - +
642B GLN* 4.1 5.0 - - - +
707B ASN 4.5 0.3 - - - +
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Residues in contact with ASP 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 5.2 0.2 + - - -
401B HIS* 3.7 14.1 + - - -
435B GLU* 2.8 34.5 - - - +
436B ARG* 2.7 34.5 + - - +
437B ARG* 4.3 1.4 + - - +
462B ASP 2.9 13.1 + - - +
463B ARG* 3.7 7.6 - - - +
465B GLY* 1.3 68.8 - - - -
467B GLU* 1.3 60.6 + - - +
469B HIS* 4.4 1.8 - - - +
470B THR* 2.7 45.2 + - - -
638B ARG* 3.6 10.7 + - - +
707B ASN* 4.1 12.5 - - - +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B ARG* 3.4 20.0 + - - +
463B ARG* 2.7 52.5 + - - +
464B THR 3.2 11.2 + - - +
466B ASP* 1.3 75.5 - - - +
468B ILE* 1.3 64.9 + - + +
470B THR* 4.2 3.1 - - - -
471B SER* 3.5 23.6 + - - -
477B MET* 4.4 2.3 - - - +
483B MET* 5.5 0.4 - - - -
488B TRP* 3.6 33.1 - - + +
578B LEU 5.1 0.3 - - - +
580B THR 4.0 4.3 - - - +
581B ILE* 3.9 10.9 - - - +
582B PRO* 3.2 31.5 - - + +
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Residues in contact with ILE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B THR* 3.0 31.6 + - + +
465B GLY* 3.3 8.0 + - - +
467B GLU* 1.3 78.2 - - + +
469B HIS* 1.3 65.2 + - - +
471B SER 3.7 0.9 - - - -
472B MET* 3.0 23.0 + - + +
477B MET* 3.9 21.7 - - + +
480B LYS* 6.0 0.4 - - + -
483B MET* 4.1 23.8 - - + -
639B ILE* 4.0 27.4 - - + +
642B GLN* 3.6 29.8 - - + +
643B LEU* 4.1 10.8 - - + +
646B ASN* 4.1 9.2 - - + -
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Residues in contact with HIS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.7 28.9 + - + +
465B GLY 3.0 13.2 + - - +
466B ASP* 4.2 3.6 - - - +
468B ILE* 1.3 77.7 - - - +
470B THR* 1.3 62.6 + - - +
471B SER 3.1 0.9 + - - -
472B MET* 3.1 25.3 + - + +
642B GLN* 2.8 28.0 + - - +
702B GLY 4.1 1.1 - - - -
703B ALA* 3.2 28.8 + - - -
705B GLN 3.0 24.3 + - - -
706B PRO* 4.6 1.0 - - - +
707B ASN* 3.2 38.0 + - - +
708B GLY 3.4 7.0 + - - -
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Residues in contact with THR 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 2.8 35.6 + - - +
64B ILE* 3.3 29.5 - - + +
65B ASP* 4.2 1.7 - - - +
68B HIS* 4.6 0.2 - - - -
90B TYR* 3.8 12.3 + - + +
436B ARG* 3.6 34.2 - - - +
466B ASP* 2.7 44.4 + - - -
467B GLU 4.2 2.9 - - - -
468B ILE 3.3 0.2 - - - -
469B HIS* 1.3 73.4 - - - +
471B SER* 1.3 62.4 + - - +
472B MET 3.7 0.2 + - - -
707B ASN* 5.4 0.3 + - - -
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Residues in contact with SER 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B HIS* 4.2 10.1 + - - -
81B TYR* 4.5 2.3 + - - -
436B ARG* 4.5 2.9 + - - -
467B GLU* 3.5 9.8 + - - -
468B ILE 3.4 2.2 + - - -
469B HIS 3.2 0.2 - - - -
470B THR* 1.3 84.8 - - - +
472B MET* 1.3 63.7 + - - +
473B GLU 3.1 3.6 - - - -
474B ALA* 2.9 18.1 + - - +
475B GLY 4.2 0.2 + - - -
477B MET* 3.2 20.3 - - - +
581B ILE* 3.3 50.7 - - - +
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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