Contacts of the helix formed by residues 479 - 492 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475D ALA* 3.1 23.9 + - - -
476D THR 4.9 0.2 - - - -
477D LYS 4.0 0.2 - - - -
478D THR* 1.3 78.2 + - - +
480D LYS* 1.3 65.3 + - - -
481D GLU 3.3 2.7 - - - -
482D SER 3.2 2.1 + - - -
483D CYS* 3.1 24.6 + - - -
505D GLU* 3.5 9.4 - - - -
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Residues in contact with LYS 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASP* 2.8 31.7 + - - +
446D VAL* 3.6 26.4 + - + -
447D THR* 4.4 1.1 - - - +
448D THR* 3.6 32.9 + - + +
475D ALA* 3.7 14.8 - - + -
479D GLY* 1.3 69.9 - - - -
481D GLU* 1.3 58.9 + - - +
483D CYS* 3.4 0.7 + - - +
484D PHE* 2.9 51.4 + - + -
505D GLU* 2.6 34.9 + - + +
506D GLU* 3.5 35.2 + - + +
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Residues in contact with GLU 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D GLY* 3.3 1.0 - - - -
480D LYS* 1.3 75.4 - - - +
482D SER* 1.3 68.3 + - - +
484D PHE* 3.3 10.9 + - - +
485D GLU* 3.2 22.7 + - - +
505D GLU* 4.4 5.5 + - + +
509D GLY* 4.0 23.3 - - - +
512D LYS* 4.0 27.5 + - + +
513D HIS* 3.0 34.6 + - + +
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Residues in contact with SER 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D THR* 2.9 52.0 + - - +
479D GLY 3.2 2.5 + - - -
481D GLU* 1.3 82.4 - - - +
483D CYS* 1.3 62.2 + - - +
485D GLU* 3.2 14.3 + - - +
486D ARG* 3.1 20.0 + - - +
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Residues in contact with CYS 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ILE* 4.4 13.0 - - - -
446D VAL* 4.1 19.5 - - + -
473D TYR* 4.4 9.2 - - + -
474D SER 3.5 27.1 - - - -
475D ALA* 3.7 10.8 - - - -
478D THR* 4.2 9.6 - - - -
479D GLY 3.1 15.9 + - - +
480D LYS 3.7 4.3 - - - +
482D SER* 1.3 77.7 - - - +
484D PHE* 1.3 65.8 + - - +
486D ARG* 3.1 9.7 + - - +
487D ILE* 3.0 29.5 + - - +
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Residues in contact with PHE 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D VAL* 3.8 31.2 - - + -
446D VAL* 4.1 18.4 - - + -
480D LYS* 2.9 38.7 + - + +
481D GLU* 3.5 7.6 - - - +
482D SER 3.3 0.2 - - - -
483D CYS* 1.3 76.1 - - - +
485D GLU* 1.3 57.9 + - - +
487D ILE* 3.4 7.5 + - - +
488D MET* 3.0 33.4 + - - +
499D VAL* 3.8 22.4 - - + -
505D GLU 4.4 0.2 - - - -
506D GLU* 3.7 34.8 - - + -
509D GLY* 3.8 11.9 - - - -
510D ALA 4.0 4.0 - - - -
513D HIS* 4.5 1.3 - - - +
515D MET* 3.7 34.4 - - + +
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Residues in contact with GLU 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481D GLU* 3.2 12.3 + - - +
482D SER* 3.3 13.4 + - - +
483D CYS 3.1 0.6 - - - -
484D PHE* 1.3 77.9 - - - +
486D ARG* 1.3 66.9 + - - +
488D MET* 3.2 9.1 + - + +
489D GLN* 3.1 36.8 + - + +
513D HIS* 3.9 18.4 - - + -
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Residues in contact with ARG 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ILE* 3.6 25.4 - - - +
332D HIS* 3.2 24.7 + - - +
335D ASP* 2.7 43.4 + - - -
473D TYR* 3.5 25.0 + - + +
482D SER 3.1 11.8 + - - +
483D CYS* 3.1 11.9 + - - +
485D GLU* 1.3 76.9 - - - +
487D ILE* 1.3 62.3 + - - +
489D GLN* 3.2 10.7 + - - +
490D ARG* 3.1 20.6 + - + +
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Residues in contact with ILE 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D VAL* 4.3 6.1 - - + -
272D VAL* 4.0 12.3 - - + -
444D VAL* 3.4 26.7 - - + -
446D VAL* 3.5 24.2 - - + -
473D TYR* 3.8 26.7 - - + -
483D CYS 3.0 20.1 + - - +
484D PHE* 3.5 7.2 - - - +
486D ARG* 1.3 75.4 - - - +
488D MET* 1.3 63.5 + - - +
490D ARG* 3.1 12.3 + - - -
491D PHE* 3.0 48.9 + - + -
497D TYR* 4.1 15.0 - - + -
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Residues in contact with MET 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484D PHE 3.0 17.4 + - - +
485D GLU* 3.2 10.9 + - + +
487D ILE* 1.3 75.1 - - - +
489D GLN* 1.3 60.5 + - + +
492D GLY* 2.9 30.3 + - - -
493D ARG* 5.9 0.3 - - - +
497D TYR* 3.3 42.0 + - + -
513D HIS* 3.5 39.5 - - + +
515D MET* 3.8 28.9 - - + +
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Residues in contact with GLN 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D GLU* 3.1 26.9 + - + +
486D ARG* 3.5 9.6 - - - +
487D ILE 3.2 0.2 - - - -
488D MET* 1.3 78.2 - - + +
490D ARG* 1.3 61.9 + - - +
491D PHE 3.7 0.2 + - - -
492D GLY* 4.1 4.9 + - - -
493D ARG* 4.8 20.3 + - - +
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Residues in contact with ARG 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D HIS* 4.4 2.4 + - - -
444D VAL* 5.1 0.2 - - - +
470D GLU* 2.5 31.7 + - - +
471D ASN* 2.6 29.7 + - - +
473D TYR* 2.7 40.3 + - - +
486D ARG* 3.1 14.8 + - + +
487D ILE* 3.1 9.1 + - - +
489D GLN* 1.3 78.9 - - - +
491D PHE* 1.3 90.7 + - + +
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Residues in contact with PHE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D GLU* 5.1 10.1 - - - +
270D VAL* 3.8 20.2 - - + -
442D VAL* 3.9 20.6 - - + -
444D VAL* 3.8 21.1 - - + -
471D ASN* 4.8 0.7 - - - -
473D TYR* 4.9 0.2 - - - -
487D ILE* 3.0 45.1 + - + -
490D ARG* 1.3 122.9 - - + +
492D GLY* 1.3 60.2 + - - +
494D LYS* 5.7 1.4 - - - +
495D ALA* 4.5 10.5 + - + +
497D TYR* 3.1 17.9 - + + +
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Residues in contact with GLY 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D MET* 2.9 16.0 + - - -
489D GLN* 4.1 4.7 + - - -
490D ARG 3.7 1.2 - - - -
491D PHE* 1.3 79.9 - - - +
493D ARG* 1.3 65.4 + - - -
494D LYS* 3.1 7.4 + - - -
495D ALA 3.7 2.9 + - - -
497D TYR* 2.6 28.9 + - - -
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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