Contacts of the helix formed by residues 503 - 513 (chain B) 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 503 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502B ASP* 1.3 91.4 - - - +
504B VAL* 1.3 65.0 + - - -
505B GLU* 3.6 6.7 - - - -
506B GLU* 2.9 27.1 + - - +
507B GLU* 3.4 16.1 - - - +
517B PHE* 4.3 0.5 - - - -
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Residues in contact with VAL 504 (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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503B GLY* 1.3 70.1 - - - -
505B GLU* 1.3 75.6 + - + +
506B GLU 3.2 2.0 - - - -
507B GLU* 3.1 14.3 + - + +
508B GLN* 3.0 32.2 + - + +
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Residues in contact with GLU 505 (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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448B THR* 4.9 8.8 + - - +
480B LYS* 4.3 26.7 - - + +
481B GLU 5.9 0.2 + - - -
484B PHE* 4.9 0.3 - - - -
503B GLY* 3.8 4.0 - - - -
504B VAL* 1.3 88.0 + - + +
506B GLU* 1.3 75.0 + - - +
508B GLN* 3.8 5.8 - - - +
509B GLY* 3.2 21.1 + - - -
512B LYS* 5.2 0.7 + - - -
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Residues in contact with GLU 506 (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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274B ASP* 3.6 22.2 - - + +
480B LYS* 3.3 30.4 - - - +
484B PHE* 3.8 11.5 - - - -
499B VAL* 3.7 13.8 - - + +
501B GLY* 3.2 6.2 - - - -
502B ASP 3.0 14.6 + - - -
503B GLY* 2.9 39.0 + - - +
504B VAL 3.2 0.6 - - - -
505B GLU* 1.3 86.7 - - - +
507B GLU* 1.3 57.0 + - - +
510B ALA* 3.1 27.2 + - - +
517B PHE* 3.8 18.2 - - + -
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Residues in contact with GLU 507 (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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502B ASP 3.9 6.9 - - - +
503B GLY 3.4 20.3 - - - +
504B VAL* 3.5 13.3 - - + +
506B GLU* 1.3 73.0 - - - +
508B GLN* 1.3 64.7 + - - +
509B GLY 3.3 0.2 - - - -
510B ALA* 4.0 6.5 - - - -
511B LYS* 3.0 47.1 + - - +
517B PHE* 3.2 36.3 - - + -
519B ARG* 2.8 41.0 + - - -
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Residues in contact with GLN 508 (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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504B VAL* 3.0 26.8 + - + +
505B GLU* 3.4 7.6 + - - +
507B GLU* 1.3 79.3 - - - +
509B GLY* 1.3 60.2 + - - +
511B LYS* 4.0 6.1 - - - +
512B LYS* 2.9 50.0 + - - +
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Residues in contact with GLY 509 (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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481B GLU* 4.6 7.6 - - - -
484B PHE* 4.2 12.0 - - - -
505B GLU 3.2 12.2 + - - -
506B GLU 4.1 0.4 - - - -
508B GLN* 1.3 79.7 - - - +
510B ALA* 1.3 61.4 + - - +
512B LYS* 3.3 21.5 + - - +
513B HIS* 3.3 18.7 + - - -
515B MET* 3.3 14.0 - - - +
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Residues in contact with ALA 510 (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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484B PHE* 4.4 0.2 - - - -
499B VAL* 3.8 22.9 - - + -
506B GLU 3.1 20.3 + - - +
507B GLU* 3.3 9.1 + - - +
509B GLY* 1.3 77.1 - - - +
511B LYS* 1.3 58.6 + - - +
513B HIS 3.4 2.8 + - - -
514B ASN 3.2 2.9 + - - -
515B MET* 2.7 56.4 + - - +
517B PHE* 4.0 9.0 - - + -
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Residues in contact with LYS 511 (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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507B GLU* 3.0 39.1 + - - +
508B GLN* 4.0 6.3 - - - +
510B ALA* 1.3 73.2 - - + +
512B LYS* 1.3 68.0 + - - +
513B HIS 3.1 1.6 - - - -
514B ASN* 2.9 24.5 + - - +
515B MET 4.6 2.9 - - - +
517B PHE* 4.6 4.1 - - + +
519B ARG* 5.3 1.6 - - - +
537C TYR* 3.2 44.5 - - - +
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Residues in contact with LYS 512 (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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481B GLU* 2.9 38.9 + - - +
505B GLU 5.2 0.8 + - - -
508B GLN* 2.9 50.7 - - - +
509B GLY* 3.3 19.7 - - - +
510B ALA 3.3 0.2 - - - -
511B LYS* 1.3 78.8 - - - +
513B HIS* 1.3 71.9 + - + +
514B ASN* 3.6 5.5 + - - +
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Residues in contact with HIS 513 (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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481B GLU* 2.8 38.3 + - + +
484B PHE* 5.8 2.0 - - + -
485B GLU* 3.2 27.7 + - - -
488B MET* 3.5 39.0 - - + +
509B GLY 3.3 6.9 + - - -
510B ALA 3.4 1.8 + - - -
511B LYS 3.1 0.4 - - - -
512B LYS* 1.3 84.3 - - + +
514B ASN* 1.3 72.2 + - - +
515B MET* 3.2 19.6 + - + +
265C SER* 4.6 7.0 - - - +
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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