Contacts of the helix formed by residues 582 - 592 (chain D) in PDB entry 2W3S
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 PHE 582 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D ILE* 4.2 17.0 - - + -
477D GLY* 4.1 22.2 - - - -
479D VAL* 4.8 1.3 - - + -
504D LEU* 3.8 28.7 - - + -
505D GLY 5.5 0.4 - - - -
506D ILE* 3.7 33.2 - - + -
510D GLN* 5.2 3.6 - - - +
551D LEU* 4.0 18.4 - - + -
568D PHE* 4.0 25.8 - + + -
571D GLY* 3.0 22.2 + - - +
572D GLN 5.7 0.7 - - - -
573D VAL* 3.9 13.3 - - + +
580D TRP 3.7 1.4 + - - -
581D ARG* 1.3 70.0 - - - +
583D ALA* 1.3 58.2 + - - +
585D ILE* 3.1 5.8 + - + +
586D VAL* 2.9 51.4 + - + +
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Residues in contact with ALA 583 (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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475D THR 4.6 3.3 - - - +
476D ASP* 3.4 26.7 - - - +
477D GLY* 4.3 11.2 - - - -
510D GLN* 5.9 2.2 - - - +
581D ARG* 3.1 20.2 - - + +
582D PHE* 1.3 78.7 - - - +
584D GLU* 1.3 57.5 + - - +
586D VAL* 3.9 1.8 - - - +
587D ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 584 (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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558D ARG* 5.2 0.6 + - - -
580D TRP* 4.4 22.0 - - + -
581D ARG* 2.7 67.0 + - - +
583D ALA* 1.3 72.1 - - - +
585D ILE* 1.3 61.0 + - - +
587D ALA* 3.5 6.5 + - - +
588D ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D LEU* 3.7 22.7 - - + +
554D PHE* 4.1 7.2 - - + -
555D VAL* 3.7 29.8 - - + -
558D ARG* 4.3 13.2 - - - +
568D PHE* 5.1 1.6 - - + -
573D VAL* 3.8 33.2 - - + -
580D TRP* 3.6 40.8 - - + -
581D ARG 3.1 6.2 + - - +
582D PHE* 3.1 7.6 + - + +
584D GLU* 1.3 76.5 - - - +
586D VAL* 1.3 52.1 + - - +
588D ALA* 3.0 4.6 + - - +
589D ALA* 2.6 34.0 + - - +
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Residues in contact with VAL 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D ILE* 3.7 15.5 - - + -
474D TYR 3.5 25.4 - - - +
475D THR* 4.3 4.5 - - - -
477D GLY* 4.6 2.2 - - - -
551D LEU* 4.2 19.5 - - + -
582D PHE* 2.9 51.5 + - + +
583D ALA* 3.9 6.7 - - - +
585D ILE* 1.3 73.4 - - - +
587D ALA* 1.3 59.5 + - - +
589D ALA* 3.3 2.1 + - - +
590D TYR* 2.8 27.9 + - - +
596D LEU* 3.8 17.8 - - + +
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Residues in contact with ALA 587 (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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475D THR* 4.3 16.8 + - - +
583D ALA 2.9 17.3 + - - +
584D GLU* 3.7 7.2 - - - +
586D VAL* 1.3 76.6 - - - +
588D ALA* 1.3 64.7 + - - +
590D TYR* 3.2 10.0 + - - +
591D MET* 3.2 32.2 + - + +
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Residues in contact with ALA 588 (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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554D PHE* 3.5 19.1 - - + -
558D ARG* 3.6 20.2 - - - +
584D GLU 2.9 18.6 + - - +
585D ILE* 3.4 5.2 - - - +
587D ALA* 1.3 76.8 - - - +
589D ALA* 1.3 56.5 + - - +
591D MET* 3.4 15.5 + - + +
592D ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 589 (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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551D LEU* 3.8 22.7 - - + -
554D PHE* 3.6 17.9 - - + -
585D ILE 2.6 20.1 + - - +
586D VAL* 3.7 4.9 - - - +
588D ALA* 1.3 70.0 - - - +
590D TYR* 1.3 65.8 + - - +
592D ALA* 3.3 5.9 + - - +
593D ARG 3.1 5.0 + - - -
594D ILE* 3.1 38.7 + - + +
596D LEU* 4.6 8.1 - - + -
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Residues in contact with TYR 590 (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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463B HIS* 3.9 18.6 - + - -
464B LEU* 3.8 20.8 - - + +
466B GLN* 3.0 52.0 + - - +
523B ASN* 3.6 28.0 + - + -
524B THR 5.1 4.0 + - - -
525B SER* 4.9 4.0 + - - -
475D THR* 3.6 31.6 - - + -
586D VAL 2.8 13.8 + - - +
587D ALA* 3.3 9.6 - - - +
589D ALA* 1.3 76.3 - - - +
591D MET* 1.3 67.2 + - + +
593D ARG* 2.8 17.3 + - - -
594D ILE 4.9 2.5 - - - -
596D LEU* 4.4 9.4 - - + +
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Residues in contact with MET 591 (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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463B HIS* 3.2 47.3 - - + +
587D ALA* 3.2 21.7 + - + +
588D ALA* 3.9 15.0 - - + +
590D TYR* 1.3 82.2 - - + +
592D ALA* 1.3 57.5 + - - +
593D ARG* 3.0 12.1 + - - +
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Residues in contact with ALA 592 (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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554D PHE* 3.4 29.4 - - + -
588D ALA 2.9 18.8 + - - +
589D ALA 3.5 5.4 - - - +
590D TYR 3.2 0.2 - - - -
591D MET* 1.3 74.8 - - - +
593D ARG* 1.3 69.6 + - - +
594D ILE* 3.6 8.9 + - + +
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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