Contacts of the helix formed by residues 479 - 492 (chain A) in PDB entry 3GEB
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 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A ALA* 3.3 20.7 + - - -
477A LYS 3.2 4.3 + - - -
478A THR* 1.3 81.2 + - - +
480A LYS* 1.3 66.3 + - - -
481A GLU* 3.5 3.8 - - - -
482A SER 3.4 1.0 + - - -
483A CYS* 3.3 23.9 + - - -
505A GLU* 4.3 5.6 - - - -
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Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A TRP 5.0 0.2 + - - -
274A ASP* 3.2 29.6 + - - +
446A VAL* 3.2 42.7 + - + +
447A THR* 4.5 0.8 - - - +
448A THR* 4.0 22.2 - - + +
475A ALA* 3.9 9.0 - - + -
479A GLY* 1.3 69.8 - - - -
481A GLU* 1.3 59.7 + - - +
483A CYS* 3.1 3.8 + - - +
484A PHE* 2.8 50.3 + - + -
505A GLU* 3.1 47.1 + - + +
506A GLU* 4.0 19.7 + - + +
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A THR 5.6 0.7 - - - +
479A GLY* 5.3 1.3 - - - -
480A LYS* 1.3 79.7 - - - +
482A SER* 1.3 65.0 + - - +
484A PHE* 3.4 12.6 - - - +
485A GLU* 2.9 26.2 + - - +
509A GLY* 4.2 13.4 - - - -
512A LYS* 3.8 28.5 + - - +
513A HIS* 3.5 32.3 + - + +
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A THR* 2.9 45.4 + - - +
479A GLY 3.4 1.3 + - - -
480A LYS 3.2 0.6 - - - -
481A GLU* 1.3 84.5 - - - +
483A CYS* 1.3 64.0 + - - +
485A GLU* 3.4 5.3 + - - +
486A ARG* 3.0 23.3 + - - +
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Residues in contact with CYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 4.3 17.5 - - - -
446A VAL* 4.1 15.3 - - + -
473A TYR* 4.4 14.1 - - + -
475A ALA* 3.6 28.3 - - - -
478A THR* 3.7 11.0 - - - -
479A GLY 3.3 14.8 - - - -
480A LYS 3.1 7.7 + - - +
482A SER* 1.3 79.4 - - - +
484A PHE* 1.3 58.1 + - - +
486A ARG* 3.2 11.1 + - - +
487A ILE* 2.9 34.1 + - - +
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL* 3.5 30.7 - - + -
273A TRP 6.4 0.4 - - - -
446A VAL* 3.7 24.0 - - + -
480A LYS* 2.8 24.8 + - + -
481A GLU* 3.2 13.2 + - - +
483A CYS* 1.3 76.6 - - - +
485A GLU* 1.3 61.9 + - - +
487A ILE* 3.4 6.3 + - - +
488A MET* 3.2 27.0 + - - +
499A VAL* 3.9 24.9 - - + -
506A GLU* 3.6 37.7 - - + -
509A GLY* 3.9 11.0 - - - -
510A ALA 4.1 1.8 - - - -
513A HIS* 4.7 3.4 - - + -
515A MET* 3.5 31.3 - - + +
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLU 2.9 10.9 + - - +
482A SER* 3.8 5.8 - - - +
484A PHE* 1.3 74.1 - - - +
486A ARG* 1.3 65.9 + - - +
488A MET* 3.1 5.6 + - + +
489A GLN* 2.9 49.3 + - + +
513A HIS* 3.3 32.9 + - + +
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 3.1 31.5 - - - +
332A HIS* 3.2 19.5 + - - +
335A ASP* 2.8 34.1 + - - -
473A TYR* 3.7 22.2 + - + +
482A SER 3.0 13.1 + - - +
483A CYS* 3.2 11.4 + - - +
485A GLU* 1.3 78.4 - - - +
487A ILE* 1.3 57.9 + - - +
489A GLN* 3.4 11.9 + - + +
490A ARG* 3.2 24.1 + - - +
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Residues in contact with ILE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A VAL* 4.5 8.1 - - + -
272A VAL* 4.1 13.9 - - + -
444A VAL* 3.4 25.8 - - + -
446A VAL* 3.5 25.4 - - + -
473A TYR* 3.8 28.7 - - + +
483A CYS 2.9 19.0 + - - +
484A PHE* 3.6 7.9 - - - +
485A GLU 3.1 0.2 - - - -
486A ARG* 1.3 75.2 - - - +
488A MET* 1.3 58.8 + - - +
490A ARG* 3.3 5.2 + - - -
491A PHE* 3.0 47.7 + - + +
497A TYR* 4.2 12.6 - - + -
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Residues in contact with MET 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A PHE 3.2 13.2 + - - +
485A GLU* 3.1 8.6 + - - +
487A ILE* 1.3 74.3 - - + +
489A GLN* 1.3 67.4 + - - +
492A GLY* 2.7 38.6 + - - +
493A ARG* 5.8 4.7 - - - -
497A TYR* 3.5 43.1 - - + -
513A HIS* 4.3 27.4 - - + +
515A MET* 3.7 29.4 - - + +
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A GLU* 2.9 48.9 + - + +
486A ARG* 3.5 12.3 - - - +
488A MET* 1.3 84.2 - - - +
490A ARG* 1.3 61.1 + - - +
492A GLY* 4.1 3.8 + - - -
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A HIS* 4.4 1.4 + - - -
470A GLU* 2.8 34.2 + - - +
471A ASN* 3.1 21.6 + - - +
473A TYR* 3.0 22.0 + - - +
486A ARG* 3.2 11.1 + - + +
487A ILE* 3.6 9.6 - - - +
488A MET 3.1 0.8 - - - -
489A GLN* 1.3 81.7 - - - +
491A PHE* 1.3 94.5 + - + +
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Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A VAL* 3.8 19.3 - - + -
442A VAL* 4.2 23.1 - - + -
444A VAL* 3.9 22.4 - - + -
471A ASN* 4.6 1.8 - - - -
473A TYR* 5.0 1.1 - - - -
487A ILE* 3.0 44.5 + - + +
490A ARG* 1.3 122.9 - - + +
492A GLY* 1.3 59.5 + - - +
494A LYS* 6.1 0.2 - - - +
495A ALA* 4.2 9.3 + - + +
497A TYR* 3.0 20.8 + - + +
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Residues in contact with GLY 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A MET* 2.7 21.5 + - - +
489A GLN 4.1 4.1 + - - -
490A ARG 3.6 2.0 - - - -
491A PHE* 1.3 74.3 - - - +
493A ARG* 1.3 63.8 + - - -
494A LYS* 3.3 3.8 + - - -
495A ALA 3.7 1.9 + - - -
497A TYR* 2.6 29.7 + - - -
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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