Contacts of the helix formed by residues 479 - 493 (chain B) in PDB entry 1G6N
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 SER 479 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B LYS* 4.0 18.2 - - - +
478B CYS* 1.3 78.8 - - - +
480B ARG* 1.3 64.3 + - - +
481B GLU* 3.7 20.0 + - - +
482B THR* 3.0 27.4 + - - -
483B VAL* 3.2 21.5 + - - +
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Residues in contact with ARG 480 (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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469B ARG* 3.8 28.4 + - - +
470B GLN* 3.1 56.7 + - + +
473B GLY* 5.2 1.0 - - - -
479B SER* 1.3 71.0 - - - +
481B GLU* 1.3 80.2 + - - +
483B VAL* 3.2 12.4 + - - +
484B GLY* 2.9 24.8 + - - -
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Residues in contact with GLU 481 (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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469B ARG* 4.9 6.3 - - - +
479B SER* 3.2 17.9 + - - +
480B ARG* 1.3 102.7 - - + +
482B THR* 1.3 62.4 + - - +
484B GLY* 3.1 3.4 + - - +
485B ARG* 3.0 29.8 + - + +
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Residues in contact with THR 482 (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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439B VAL* 4.0 13.5 - - + -
443B ILE* 5.0 0.2 - - + -
478B CYS* 3.9 20.0 - - + +
479B SER* 3.0 24.3 + - - -
480B ARG 3.2 0.4 - - - -
481B GLU* 1.3 76.6 - - - +
483B VAL* 1.3 65.5 + - - +
485B ARG* 3.3 8.4 + - - +
486B ILE* 3.0 48.9 + - + +
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ILE* 4.1 9.9 - - + -
469B ARG* 3.6 32.5 - - + +
472B ILE* 3.8 21.5 - - + -
473B GLY* 3.6 11.9 - - - +
478B CYS* 3.6 18.4 - - - -
479B SER 3.2 15.4 + - - +
480B ARG 3.2 7.6 + - - +
482B THR* 1.3 76.2 - - - +
484B GLY* 1.3 57.8 + - - +
486B ILE 3.4 0.3 + - - -
487B LEU* 2.9 58.6 + - + +
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Residues in contact with GLY 484 (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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469B ARG* 3.7 30.5 - - - -
480B ARG 2.9 10.7 + - - -
481B GLU 3.1 5.1 + - - -
483B VAL* 1.3 77.8 - - - +
485B ARG* 1.3 61.6 + - - +
487B LEU* 3.8 4.5 - - - +
488B LYS* 3.0 24.4 + - - +
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Residues in contact with ARG 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B GLU* 3.0 19.9 + - + +
482B THR* 3.3 9.2 + - - +
484B GLY* 1.3 76.0 - - - +
486B ILE* 1.3 62.7 + - + +
488B LYS* 3.2 9.0 + - - +
489B MET* 3.0 27.3 + - - +
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Residues in contact with ILE 486 (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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439B VAL* 4.6 9.0 - - + -
440B THR* 3.9 29.6 - - + +
443B ILE* 3.7 35.0 - - + -
482B THR* 3.0 46.7 + - + +
485B ARG* 1.3 78.4 - - + +
487B LEU* 1.3 61.6 + - - +
489B MET* 3.3 11.5 + - + +
490B LEU* 2.9 51.3 + - + +
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Residues in contact with LEU 487 (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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443B ILE* 3.7 28.9 - - + -
447B LEU* 4.7 9.4 - - + -
469B ARG* 3.8 20.9 - - + -
472B ILE* 4.4 5.4 - - + -
483B VAL* 2.9 40.2 + - + +
484B GLY* 3.8 4.5 - - - +
486B ILE* 1.3 75.2 - - + +
488B LYS* 1.3 63.0 + - - +
490B LEU* 3.2 4.2 + - + +
491B GLU* 3.0 25.8 + - - +
496B ILE* 3.7 21.7 - - + +
498B ALA* 5.1 9.9 - - + -
503B ILE* 4.0 22.9 - - + -
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Residues in contact with LYS 488 (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 GLY 3.0 13.5 + - - +
485B ARG* 3.2 12.1 + - - +
487B LEU* 1.3 77.0 - - - +
489B MET* 1.3 62.2 + - - +
491B GLU* 3.1 24.6 + - - +
492B ASP* 3.2 45.8 + - - +
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Residues in contact with MET 489 (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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440B THR* 3.4 40.6 - - + +
485B ARG 3.0 12.5 + - - +
486B ILE* 3.6 14.6 - - + +
488B LYS* 1.3 78.4 - - - +
490B LEU* 1.3 72.2 + - + +
492B ASP* 3.1 12.4 + - + +
493B GLN* 3.1 44.3 + - + +
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Residues in contact with LEU 490 (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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440B THR* 4.4 8.7 - - + -
443B ILE* 4.5 4.7 - - + -
444B ALA* 4.6 16.6 - - + -
447B LEU* 3.9 27.6 - - + -
486B ILE* 2.9 36.1 + - + +
487B LEU* 3.2 5.8 + - - +
489B MET* 1.3 92.6 - - + +
491B GLU* 1.3 58.7 + - - +
493B GLN* 3.4 24.3 + - - +
495B LEU* 3.0 43.5 + - + +
496B ILE* 3.6 14.9 + - + -
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Residues in contact with GLU 491 (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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487B LEU 3.0 12.0 + - - +
488B LYS* 3.1 18.2 + - - +
490B LEU* 1.3 74.7 - - - +
492B ASP* 1.3 65.2 + - - +
494B ASN* 3.0 23.6 + - - -
496B ILE* 3.6 23.2 - - + +
497B SER* 4.1 6.6 + - - -
498B ALA* 3.5 43.2 + - - +
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Residues in contact with ASP 492 (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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488B LYS* 3.2 45.2 + - - +
489B MET* 3.1 11.5 + - - +
491B GLU* 1.3 80.4 - - - +
493B GLN* 1.3 59.7 + - + +
494B ASN* 3.1 12.6 + - - +
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Residues in contact with GLN 493 (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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489B MET* 3.1 39.0 + - + +
490B LEU* 3.8 17.6 - - - +
491B GLU 3.2 0.8 - - - -
492B ASP* 1.3 77.7 - - + +
494B ASN* 1.3 71.1 + - - +
495B LEU* 3.2 34.3 + - + +
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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