Contacts of the helix formed by residues 582 - 592 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473F ILE* 4.4 16.8 - - + -
477F GLY* 3.9 21.5 - - - -
479F VAL* 4.9 0.4 - - + -
504F LEU* 4.1 16.6 - - + -
506F ILE* 3.6 37.7 - - + -
510F GLN* 5.4 3.1 - - - -
551F LEU* 3.9 23.6 - - + -
568F PHE* 4.0 14.1 - + + -
571F GLY* 3.2 23.3 + - - +
572F GLN 5.8 0.2 - - - -
573F VAL* 3.8 23.3 - - + +
580F TRP 3.8 1.6 + - - -
581F ARG* 1.3 70.8 - - - +
583F ALA* 1.3 63.7 + - - +
585F ILE* 3.0 6.3 + - + +
586F VAL* 3.0 42.3 + - + +
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Residues in contact with ALA 583 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F THR 4.8 2.2 - - - +
476F ASP* 3.3 27.6 - - - +
477F GLY* 4.5 3.6 - - - -
510F GLN* 6.1 1.3 - - - +
581F ARG* 3.0 12.7 + - + +
582F PHE* 1.3 79.4 - - - +
584F GLU* 1.3 64.0 + - + +
586F VAL* 3.0 8.7 + - - +
587F ALA* 2.8 25.6 + - - +
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Residues in contact with GLU 584 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A THR* 4.5 3.8 + - - -
558F ARG* 5.2 1.1 + - - -
580F TRP* 3.9 20.8 - - + -
581F ARG* 2.7 72.9 + - - +
583F ALA* 1.3 74.0 - - + +
585F ILE* 1.3 58.7 + - - +
587F ALA* 3.6 6.7 - - - +
588F ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F LEU* 4.5 15.3 - - + +
554F PHE* 3.9 11.1 - - + -
555F VAL* 3.6 28.5 - - + -
558F ARG* 5.2 6.5 - - - +
568F PHE* 5.2 0.4 - - + -
573F VAL* 3.4 33.4 - - + -
580F TRP* 3.4 46.0 - - + -
581F ARG 3.6 10.1 - - - +
582F PHE* 3.4 4.9 - - + +
583F ALA 3.0 0.8 - - - -
584F GLU* 1.3 76.9 - - - +
586F VAL* 1.3 56.6 + - + +
588F ALA* 3.3 4.7 + - - +
589F ALA* 2.7 36.6 + - - +
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Residues in contact with VAL 586 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473F ILE* 3.8 7.4 - - + -
474F TYR 3.3 21.1 - - - +
475F THR* 4.2 6.5 - - - -
477F GLY* 4.3 4.0 - - - +
551F LEU* 4.3 13.2 - - + -
582F PHE* 3.0 46.5 + - + +
583F ALA* 3.0 8.9 + - - +
585F ILE* 1.3 75.8 - - - +
587F ALA* 1.3 52.8 + - - +
589F ALA* 3.3 7.1 + - - +
590F TYR* 2.7 32.6 + - - +
596F LEU* 3.3 27.1 - - + +
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Residues in contact with ALA 587 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F THR* 4.4 16.6 + - - +
583F ALA 2.8 15.9 + - - +
584F GLU* 3.6 9.2 - - - +
586F VAL* 1.3 73.7 - - - +
588F ALA* 1.3 66.0 + - - +
590F TYR* 3.1 10.7 + - - +
591F MET* 3.0 27.4 + - + +
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Residues in contact with ALA 588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F PHE* 3.5 21.3 - - + -
558F ARG* 3.6 18.2 - - - +
584F GLU 2.9 20.0 + - - +
585F ILE 3.6 3.1 - - - +
587F ALA* 1.3 75.5 - - - +
589F ALA* 1.3 56.0 + - - +
591F MET* 3.1 13.6 - - - +
592F ALA* 2.8 28.2 + - - +
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Residues in contact with ALA 589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551F LEU* 3.5 25.4 - - + -
554F PHE* 3.6 18.0 - - + -
585F ILE 2.7 22.0 + - - +
586F VAL 3.5 4.9 - - - +
588F ALA* 1.3 68.6 - - - +
590F TYR* 1.3 68.3 + - - +
592F ALA* 3.0 10.9 + - - +
593F ARG 3.1 7.8 + - - -
594F ILE* 3.2 25.4 + - + +
596F LEU* 4.4 8.5 - - + -
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Residues in contact with TYR 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F THR* 3.7 33.0 - - + -
586F VAL 2.7 17.3 + - - +
587F ALA* 3.3 11.9 - - - +
589F ALA* 1.3 70.3 - - - +
591F MET* 1.3 66.1 + - + +
593F ARG* 2.8 19.1 + - - -
594F ILE 4.9 6.3 - - - +
596F LEU* 4.9 8.2 - - + +
463H HIS* 3.9 18.5 + + - -
464H LEU* 3.9 22.2 - - - +
466H GLN* 3.1 50.3 + - + -
523H ASN* 3.9 24.3 + - + -
524H THR 5.2 3.6 + - - -
525H SER* 4.8 5.2 + - - -
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Residues in contact with MET 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587F ALA* 3.0 18.7 + - + +
588F ALA* 3.1 11.9 - - - +
590F TYR* 1.3 81.5 - - + +
592F ALA* 1.3 57.9 + - - +
593F ARG* 3.2 6.8 + - - +
463H HIS* 3.4 53.9 - - + +
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Residues in contact with ALA 592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554F PHE* 3.4 37.7 - - + -
588F ALA 2.8 10.6 + - - +
589F ALA 3.0 5.9 + - - +
591F MET* 1.3 72.8 - - - +
593F ARG* 1.3 69.6 + - - +
594F ILE* 4.1 6.8 - - + +
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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