Contacts of the helix formed by residues 426 - 440 (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 ASN 426 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B ALA* 5.6 7.4 - - + +
422F GLN 3.0 4.1 + - - -
423F LYS* 3.4 8.4 + - - +
424F SER 3.3 4.9 - - - +
425F ALA* 1.3 80.2 - - - +
427F PHE* 1.3 66.0 + - - +
428F THR 3.1 1.6 + - - -
429F THR* 3.2 34.0 + - - +
430F ARG* 3.1 30.4 + - + +
433F GLU* 4.4 1.2 - - - +
644F ARG* 5.3 2.5 - - - +
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Residues in contact with PHE 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F ASP* 5.5 0.4 - - - -
369F ALA* 3.9 13.9 - - + -
422F GLN* 2.7 68.4 + - + +
425F ALA* 3.2 4.2 - - - -
426F ASN* 1.3 71.7 - - - +
428F THR* 1.3 54.3 + - - +
430F ARG* 3.4 4.5 + - - +
431F ARG* 2.8 74.2 + - - +
448F ILE* 4.1 28.7 - - + -
449F ALA* 4.8 2.0 - - - -
450F LEU* 4.4 14.8 - - + -
628F ILE* 4.0 27.4 - - + -
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Residues in contact with THR 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426F ASN 3.1 1.2 + - - -
427F PHE* 1.3 77.3 - - - +
429F THR* 1.3 64.8 + - - +
431F ARG* 3.3 26.7 + - - +
432F ALA* 2.9 27.2 + - + +
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Residues in contact with THR 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426F ASN* 3.2 29.4 + - - +
428F THR* 1.3 80.7 - - - +
430F ARG* 1.3 53.3 + - - +
432F ALA* 3.1 8.4 + - + +
433F GLU* 2.7 63.7 + - - +
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Residues in contact with ARG 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F ALA* 2.7 25.8 + - - +
426F ASN* 3.1 31.9 + - - +
427F PHE* 3.5 4.6 - - - +
429F THR* 1.3 73.6 - - - +
431F ARG* 1.3 64.3 + - - +
433F GLU* 3.2 13.0 + - - +
434F ILE* 2.9 33.0 + - + +
448F ILE* 4.0 16.8 - - + +
628F ILE* 3.7 21.6 + - - +
630F GLU* 3.5 26.1 + - - +
644F ARG* 3.3 39.7 + - - +
646F ASP* 2.9 23.4 + - - -
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Residues in contact with ARG 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F ASP* 3.0 44.8 + - - +
369F ALA* 4.6 1.0 - - - +
422F GLN* 5.4 0.2 - - - +
427F PHE* 2.8 52.8 + - - +
428F THR* 3.3 25.0 + - - +
430F ARG* 1.3 74.3 - - - +
432F ALA* 1.3 63.2 + - - +
434F ILE* 3.3 11.4 + - - +
435F ALA* 3.3 11.4 + - - +
448F ILE* 4.0 30.2 - - + +
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Residues in contact with ALA 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428F THR* 2.9 16.8 + - + +
429F THR* 3.3 11.9 - - + +
431F ARG* 1.3 71.8 - - - +
433F GLU* 1.3 65.6 - - - +
435F ALA* 3.2 17.9 + - - +
436F ALA* 3.4 10.9 + - - +
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Residues in contact with GLU 433 (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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426F ASN* 4.4 1.1 - - - +
429F THR* 2.7 48.1 + - - +
430F ARG* 3.2 18.8 - - - +
432F ALA* 1.3 71.5 - - + +
434F ILE* 1.3 58.1 + - + +
436F ALA* 3.3 8.9 + - - +
437F TRP* 2.9 29.2 + - - +
446F ARG* 5.4 7.9 - - - +
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Residues in contact with ILE 434 (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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430F ARG* 2.9 18.6 + - + +
431F ARG 3.5 7.4 - - - +
432F ALA 3.2 0.2 + - - -
433F GLU* 1.3 72.6 - - + +
435F ALA* 1.3 60.8 + - - +
437F TRP* 3.1 7.1 + - - +
438F ASN* 2.8 37.7 + - - +
446F ARG* 3.8 41.1 - - + +
447F GLY* 4.4 5.2 - - - +
448F ILE* 3.6 39.5 - - + -
630F GLU* 3.9 28.3 - - + +
745F ASP* 5.4 3.1 - - - +
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Residues in contact with ALA 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F ARG 3.3 6.9 + - - +
432F ALA* 3.2 12.2 + - - +
434F ILE* 1.3 81.5 - - - +
436F ALA* 1.3 61.2 + - - +
438F ASN* 3.2 6.4 + - - +
439F SER* 2.9 25.8 + - - -
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Residues in contact with ALA 436 (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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432F ALA 3.4 7.0 + - - +
433F GLU* 3.3 10.6 + - - +
435F ALA* 1.3 78.9 - - - +
437F TRP* 1.3 59.5 + - - +
439F SER* 2.7 21.0 + - - -
440F THR* 2.9 18.9 + - - -
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Residues in contact with TRP 437 (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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454E ALA* 6.2 1.1 - - + -
460E VAL* 4.8 11.7 - - + -
433F GLU 2.9 18.0 + - - +
434F ILE* 3.1 8.0 + - - +
436F ALA* 1.3 75.7 - - - +
438F ASN* 1.3 87.5 + - - +
440F THR* 3.3 15.8 + - - -
441F ASN* 3.0 43.8 + - - +
444F LEU* 3.6 31.4 - - + -
445F ALA* 4.0 8.1 - - - -
446F ARG* 3.4 55.5 - - + +
632F VAL* 4.2 4.7 - - + -
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Residues in contact with ASN 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F ILE* 2.8 26.3 + - - +
435F ALA* 3.2 6.8 + - - +
437F TRP* 1.3 84.9 - - - +
439F SER* 1.3 54.4 + - - +
440F THR 3.0 4.0 - - - -
441F ASN* 2.8 35.7 + - - +
444F LEU 5.0 1.5 - - - +
445F ALA* 3.4 8.4 - - + +
446F ARG* 2.9 44.9 + - - +
635F ARG* 5.5 0.7 + - - -
749F ALA* 3.6 24.9 - - + +
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Residues in contact with SER 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435F ALA 2.9 14.6 + - - -
436F ALA* 2.7 22.1 + - - -
438F ASN* 1.3 72.9 - - - +
440F THR* 1.3 56.8 + - - +
441F ASN 3.7 1.7 + - - +
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Residues in contact with THR 440 (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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436F ALA 2.9 15.3 + - - -
437F TRP* 3.4 14.5 + - - -
438F ASN 3.0 1.2 - - - -
439F SER* 1.3 75.5 - - - +
441F ASN* 1.3 67.9 + - - +
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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