Contacts of the helix formed by residues 482 - 496 (chain D) in PDB entry 6V3O
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 482 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480D GLU 3.7 2.4 + - - -
481D TRP* 1.3 77.3 - - - +
483D GLU* 1.3 64.1 + - - +
484D ASP* 3.6 7.6 + - - +
485D LYS* 3.2 23.2 + - - +
486D ARG* 2.9 21.6 + - - +
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Residues in contact with GLU 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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482D SER* 1.3 75.3 - - - +
484D ASP* 1.3 66.0 + - - +
486D ARG* 3.2 12.3 + - - +
487D GLN* 2.8 51.4 + - - +
539D ALA* 3.2 30.5 - - + +
540D PRO* 5.0 0.7 - - + -
541D SER* 3.0 37.5 + - - -
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Residues in contact with ASP 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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482D SER* 3.2 7.2 + - - +
483D GLU* 1.3 80.7 - - - +
485D LYS* 1.3 63.3 + - - +
487D GLN* 3.1 15.4 + - - +
488D GLU* 2.6 40.8 + - - +
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Residues in contact with LYS 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 TRP* 3.7 49.2 - - + +
482D SER* 3.2 20.8 + - - +
484D ASP* 1.3 76.8 - - - +
486D ARG* 1.3 62.6 + - - +
488D GLU* 3.6 5.4 + - - +
489D TRP* 3.1 23.3 + - + +
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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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460D GLU* 4.7 7.3 + - - -
463D THR* 4.0 18.0 + - - +
478D TYR* 3.2 59.5 + - + +
479D ARG* 3.0 33.3 + - - +
481D TRP* 3.2 24.8 + - + +
482D SER 2.9 16.7 + - - +
483D GLU* 3.4 15.3 + - - +
485D LYS* 1.3 76.2 - - - +
487D GLN* 1.3 57.7 + - - +
489D TRP* 3.2 2.6 + - - +
490D LEU* 2.8 35.8 + - - +
541D SER* 3.8 19.6 + - - -
542D ASP* 5.0 4.2 + - - -
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Residues in contact with GLN 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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483D GLU* 2.8 48.9 + - - +
484D ASP* 3.6 17.6 + - - +
486D ARG* 1.3 75.1 - - - +
488D GLU* 1.3 68.0 + - - +
490D LEU* 3.2 7.8 + - - +
491D LEU* 2.9 39.0 + - + +
540D PRO* 3.6 26.3 - - + +
541D SER* 4.5 8.3 - - - +
544D LEU* 4.9 7.0 - - + -
580D ARG* 2.8 39.4 + - - +
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Residues in contact with GLU 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D ASP* 2.6 45.7 + - - +
485D LYS* 4.1 5.2 - - - +
487D GLN* 1.3 78.9 - - - +
489D TRP* 1.3 57.5 + - - +
491D LEU* 4.0 5.2 - - - +
492D SER* 3.0 26.2 + - - -
580D ARG* 3.5 24.0 + - - -
1003D SO4 3.9 7.4 + - - -
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Residues in contact with TRP 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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466D ILE* 3.9 18.4 - - + -
469D ILE* 5.3 0.4 - - + -
470D THR* 4.0 15.9 - - + -
475D ILE* 3.9 33.4 - - + +
478D TYR* 4.3 4.0 - + - -
481D TRP* 3.6 31.4 - + + -
485D LYS* 3.1 19.0 + - + +
486D ARG 3.7 2.5 - - - +
488D GLU* 1.3 75.2 - - - +
490D LEU* 1.3 91.3 + - + +
492D SER* 2.4 30.6 + - - -
493D GLU* 3.0 30.6 + - + +
500D LEU* 3.9 26.7 - - + -
548D LEU* 4.0 7.9 - - + -
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Residues in contact with LEU 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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466D ILE* 5.1 2.5 - - + -
478D TYR* 3.4 31.4 - - + +
486D ARG 2.8 24.7 + - - +
487D GLN* 3.8 5.2 - - - +
489D TRP* 1.3 96.6 - - + +
491D LEU* 1.3 57.6 + - - +
493D GLU* 3.2 5.3 + - - +
494D LEU* 2.9 34.2 + - + +
541D SER* 3.7 28.0 - - - +
544D LEU* 4.0 19.7 - - + +
545D ALA* 3.9 17.5 - - + +
548D LEU* 3.8 17.0 - - + +
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Residues in contact with LEU 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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487D GLN* 2.9 26.2 + - + +
488D GLU* 4.3 4.9 - - - +
490D LEU* 1.3 73.3 - - - +
492D SER* 1.3 67.5 + - - +
494D LEU* 4.3 7.6 - - + +
495D ARG* 3.0 53.5 + - + +
544D LEU* 4.2 26.5 - - + -
580D ARG* 4.0 23.1 - - - +
584D VAL* 3.4 35.2 - - + -
586D TRP* 4.6 11.0 - - + -
1003D SO4 4.2 8.7 - - - +
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Residues in contact with SER 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 GLU 3.0 17.1 + - - -
489D TRP* 2.4 32.0 + - - -
491D LEU* 1.3 74.5 - - - +
493D GLU* 1.3 67.8 + - - +
495D ARG* 4.0 3.5 - - - +
496D GLY* 3.1 23.4 + - - -
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Residues in contact with GLU 493 (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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498B ARG* 2.7 43.7 + - - -
475D ILE* 4.9 1.0 - - - +
489D TRP* 3.0 47.9 + - + +
490D LEU 3.7 6.5 - - - +
492D SER* 1.3 88.3 + - - +
494D LEU* 1.3 63.4 + - - +
496D GLY* 3.2 12.9 + - - +
498D ARG 4.4 4.2 - - - +
500D LEU* 4.4 6.7 - - + +
548D LEU* 3.9 19.3 - - + -
551D ARG* 2.9 18.3 + - - -
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Residues in contact with LEU 494 (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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490D LEU* 2.9 22.2 + - + +
491D LEU* 4.2 8.3 - - + +
493D GLU* 1.3 76.2 - - - +
495D ARG* 1.3 61.1 + - - +
496D GLY 3.5 1.9 + - - +
544D LEU* 4.0 33.9 - - + +
547D GLU* 4.4 2.5 - - + +
548D LEU* 3.6 39.9 - - + +
551D ARG* 2.9 34.4 + - - +
586D TRP* 3.3 55.4 + - + -
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Residues in contact with ARG 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D LEU* 3.0 45.5 + - - +
492D SER* 4.3 2.5 - - - +
494D LEU* 1.3 73.9 - - + +
496D GLY* 1.3 65.8 + - - +
497D LYS* 3.9 12.3 + - - +
584D VAL* 4.2 12.5 - - - +
585D ASP* 2.8 37.8 + - - +
586D TRP* 4.5 17.0 - - + +
1003D SO4 3.2 29.8 + - - -
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Residues in contact with GLY 496 (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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492D SER 3.1 17.2 + - - -
493D GLU* 3.2 16.8 + - - +
494D LEU 3.6 5.5 - - - +
495D ARG* 1.3 80.8 - - - +
497D LYS* 1.3 64.6 + - - +
498D ARG* 3.5 3.4 - - - -
551D ARG* 4.1 8.3 + - - -
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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