Contacts of the helix formed by residues 479 - 492 (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 479 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475B ALA* 3.0 26.4 + - - +
477B LYS 3.3 4.8 + - - -
478B THR* 1.3 84.6 + - - +
480B LYS* 1.3 66.1 + - - -
481B GLU* 3.3 3.1 - - - -
483B CYS 3.6 10.7 + - - -
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Residues in contact with LYS 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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273B TRP 4.3 1.6 + - - -
274B ASP* 3.9 17.0 + - - +
446B VAL* 2.9 46.0 + - + +
447B THR* 4.9 1.7 - - - +
448B THR* 4.8 14.3 + - - +
475B ALA* 3.6 11.2 - - + +
479B GLY* 1.3 70.6 - - - -
481B GLU* 1.3 61.3 + - - +
483B CYS* 3.1 2.6 + - - +
484B PHE* 2.8 54.5 + - + -
505B GLU* 4.3 25.3 - - + +
506B GLU* 3.3 38.4 - - - +
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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
----------------------------------------------------------
479B GLY* 3.3 0.8 - - - -
480B LYS* 1.3 76.9 - - - +
482B SER* 1.3 55.6 + - - +
484B PHE* 2.9 12.6 + - - +
485B GLU* 2.7 46.2 + - - +
505B GLU 5.9 0.2 + - - -
509B GLY* 4.6 6.4 - - - -
512B LYS* 2.9 42.3 + - + +
513B HIS* 2.8 36.0 + - + -
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 6.2 0.2 - - - -
478B THR* 2.8 46.0 + - - +
479B GLY 3.7 1.2 + - - -
480B LYS 3.3 0.6 - - - -
481B GLU* 1.3 79.6 - - - +
483B CYS* 1.3 59.1 + - - +
485B GLU* 3.0 29.7 - - - +
486B ARG* 3.1 14.5 + - - +
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Residues in contact with CYS 483 (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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331B ILE* 3.7 25.1 - - - -
446B VAL* 3.6 17.3 - - + -
473B TYR* 3.9 16.7 - - + -
475B ALA* 3.4 37.7 - - - -
478B THR* 4.3 2.7 - - - -
479B GLY 3.6 2.4 + - - -
480B LYS 3.1 10.0 + - - +
482B SER* 1.3 77.3 - - - +
484B PHE* 1.3 63.9 + - - +
486B ARG* 3.5 8.8 + - - +
487B ILE* 2.9 30.7 + - - +
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Residues in contact with PHE 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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272B VAL* 3.7 15.0 - - + -
446B VAL* 3.6 32.5 - - + -
480B LYS* 2.8 49.9 + - + -
481B GLU* 2.9 18.8 + - + +
483B CYS* 1.3 77.2 - - - +
485B GLU* 1.3 65.5 + - - +
487B ILE* 3.3 6.1 + - + +
488B MET* 2.9 32.8 + - + +
499B VAL* 4.2 23.1 - - + -
506B GLU* 3.8 22.2 - - - -
509B GLY* 4.2 8.1 - - - -
510B ALA 4.4 2.0 - - - -
513B HIS* 5.7 2.7 - - + +
515B MET* 3.8 31.4 - - + -
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Residues in contact with GLU 485 (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* 2.7 36.3 + - - +
482B SER* 3.0 18.8 - - - +
484B PHE* 1.3 74.7 - - - +
486B ARG* 1.3 66.5 + - + +
488B MET* 2.8 20.1 + - - +
489B GLN* 3.0 31.3 + - - +
513B HIS* 3.2 28.3 + - - -
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Residues in contact with ARG 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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331B ILE* 3.7 32.8 - - - +
332B HIS* 3.5 24.4 + - - +
335B ASP* 3.1 40.1 + - - -
473B TYR* 3.6 25.1 + - + +
482B SER 3.1 11.6 + - - +
483B CYS* 3.7 7.9 - - - +
485B GLU* 1.3 81.3 - - + +
487B ILE* 1.3 57.5 + - - +
489B GLN* 3.5 15.5 - - - +
490B ARG* 3.0 28.2 + - - +
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Residues in contact with ILE 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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270B VAL* 4.4 0.4 - - + -
272B VAL* 4.1 16.4 - - + -
444B VAL* 3.4 29.8 - - + -
446B VAL* 3.5 25.1 - - + -
473B TYR* 4.0 23.8 - - + +
483B CYS 2.9 22.6 + - - +
484B PHE* 3.7 8.1 - - + +
485B GLU 2.9 1.0 + - - -
486B ARG* 1.3 75.5 - - - +
488B MET* 1.3 66.6 + - + +
490B ARG* 3.1 12.9 + - - -
491B PHE* 3.1 39.2 - - + -
497B TYR* 3.6 18.2 - - + -
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Residues in contact with MET 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 PHE 2.9 19.8 + - - +
485B GLU* 2.8 10.1 + - - +
487B ILE* 1.3 71.4 - - - +
489B GLN* 1.3 58.8 + - - +
492B GLY* 2.9 31.3 + - - +
497B TYR* 3.0 45.1 + - + -
513B HIS* 3.5 44.9 - - + +
515B MET* 3.9 26.9 - - + +
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Residues in contact with GLN 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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485B GLU* 3.0 38.4 + - - +
486B ARG* 3.5 18.3 - - - +
488B MET* 1.3 76.0 - - - +
490B ARG* 1.3 61.1 + - - +
491B PHE 3.3 0.8 + - - -
492B GLY* 4.1 6.4 + - - +
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Residues in contact with ARG 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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332B HIS* 5.4 0.6 - - - -
444B VAL* 5.4 0.4 - - - +
470B GLU* 3.1 36.9 + - - +
471B ASN* 3.3 28.5 + - - +
473B TYR* 3.4 20.9 + - - +
486B ARG 3.0 20.3 + - - +
487B ILE* 3.1 8.0 + - - +
489B GLN* 1.3 79.3 - - - +
491B PHE* 1.3 93.4 + - + +
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Residues in contact with PHE 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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268B GLU* 5.2 6.1 - - - +
270B VAL* 4.0 9.6 - - + -
442B VAL* 4.3 22.4 - - + -
444B VAL* 4.1 12.1 - - + -
471B ASN* 4.6 2.0 - - - -
487B ILE* 3.1 36.8 + - + -
489B GLN 4.8 0.2 - - - -
490B ARG* 1.3 130.3 - - + +
492B GLY* 1.3 56.3 + - - +
493B ARG 4.3 0.2 + - - -
494B LYS* 4.9 5.9 + - - +
495B ALA* 4.2 13.9 + - + +
497B TYR* 2.8 25.4 - + + +
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Residues in contact with GLY 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 MET* 2.9 15.6 + - - +
489B GLN* 4.1 6.1 + - - -
490B ARG 3.8 0.8 - - - -
491B PHE* 1.3 79.2 - - - +
493B ARG* 1.3 60.4 + - - -
494B LYS 3.5 1.6 - - - -
495B ALA 4.5 0.4 - - - -
497B TYR* 2.9 23.3 + - - -
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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