Contacts of the helix formed by residues 426 - 441 (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 ASN 426 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422D GLN 3.0 4.1 + - - -
423D LYS* 3.1 12.3 + - - +
424D SER 3.1 2.8 - - - +
425D ALA* 1.3 80.1 - - - +
427D PHE* 1.3 61.6 + - - +
428D THR* 3.6 1.1 - - - -
429D THR* 3.4 33.6 + - - +
430D ARG* 2.9 29.1 + - + +
433D GLU* 5.4 0.2 - - - +
644D ARG* 5.6 1.8 - - - +
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Residues in contact with PHE 427 (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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369D ALA* 3.9 9.6 - - + -
422D GLN* 2.8 66.9 + - + +
425D ALA* 4.2 3.1 - - - -
426D ASN* 1.3 69.5 - - - +
428D THR* 1.3 61.5 + - - +
430D ARG* 3.3 6.9 + - - +
431D ARG* 2.9 76.0 + - - +
448D ILE* 3.8 33.0 - - + -
449D ALA* 4.8 1.3 - - - -
450D LEU* 4.3 18.6 - - + -
628D ILE* 3.8 22.7 - - + -
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Residues in contact with THR 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D GLN* 4.8 1.2 + - - +
426D ASN* 3.6 0.4 - - - -
427D PHE* 1.3 77.5 - - - +
429D THR* 1.3 67.1 + - - +
431D ARG* 3.0 39.8 + - - +
432D ALA* 3.2 7.8 + - + +
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Residues in contact with THR 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D ASN* 3.4 31.2 + - - +
427D PHE 3.5 0.2 - - - -
428D THR* 1.3 79.1 - - - +
430D ARG* 1.3 64.8 + - + +
432D ALA* 3.1 9.7 + - + +
433D GLU* 3.0 45.2 + - + +
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Residues in contact with ARG 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ALA* 2.8 28.3 + - - +
426D ASN* 2.9 30.2 + - - +
427D PHE* 3.5 5.0 - - - +
429D THR* 1.3 77.5 - - + +
431D ARG* 1.3 62.0 + - - +
433D GLU* 3.4 15.4 + - - +
434D ILE* 3.1 29.4 + - + +
448D ILE* 4.0 20.8 - - + +
628D ILE* 4.2 14.8 + - - +
630D GLU* 2.9 32.7 + - - +
644D ARG* 3.4 34.2 + - - +
646D ASP* 2.7 27.7 + - - -
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Residues in contact with ARG 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D ASP* 2.8 43.2 + - - +
369D ALA* 4.4 1.4 - - - +
422D GLN* 5.7 0.2 - - - +
427D PHE* 2.9 56.2 + - - +
428D THR* 3.0 24.8 + - - +
430D ARG* 1.3 76.8 - - - +
432D ALA* 1.3 60.4 + - - +
434D ILE* 3.2 16.6 + - + +
435D ALA* 3.2 13.3 + - - +
448D ILE* 3.7 23.9 - - + +
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Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D THR* 3.2 7.2 + - + +
429D THR* 3.1 12.4 + - + +
431D ARG* 1.3 76.7 - - - +
433D GLU* 1.3 63.4 + - + +
434D ILE 3.2 0.3 + - - -
435D ALA* 3.2 9.1 + - - +
436D ALA* 3.0 22.8 + - - +
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Residues in contact with GLU 433 (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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429D THR* 3.0 37.3 + - + +
430D ARG* 3.7 14.6 - - - +
431D ARG 3.4 0.2 - - - -
432D ALA* 1.3 77.0 - - + +
434D ILE* 1.3 57.6 + - + +
436D ALA* 3.4 8.2 - - - +
437D TRP* 2.9 29.1 + - - +
446D ARG* 5.8 1.8 - - - +
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Residues in contact with ILE 434 (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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430D ARG* 3.1 19.7 + - + +
431D ARG* 3.4 8.3 - - - +
432D ALA 3.1 0.4 - - - -
433D GLU* 1.3 75.4 - - + +
435D ALA* 1.3 57.7 + - - +
437D TRP* 3.1 7.3 + - - +
438D ASN* 2.8 51.8 + - - +
446D ARG* 3.7 37.0 - - + +
447D GLY* 4.4 3.8 - - - +
448D ILE* 3.6 43.5 - - + +
630D GLU* 4.1 17.5 - - - +
745D ASP* 5.4 2.5 - - - +
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Residues in contact with ALA 435 (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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431D ARG 3.2 7.4 + - - +
432D ALA* 3.2 10.7 + - - +
434D ILE* 1.3 82.2 - - - +
436D ALA* 1.3 68.6 + - - +
438D ASN* 3.1 8.2 + - - +
439D SER* 3.1 19.2 + - - -
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Residues in contact with ALA 436 (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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432D ALA 3.0 10.7 + - - +
433D GLU* 3.4 13.9 - - - +
435D ALA* 1.3 78.1 - - - +
437D TRP* 1.3 63.2 + - - +
439D SER* 2.6 28.3 + - - -
440D THR* 3.6 5.3 + - - -
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Residues in contact with TRP 437 (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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454C ALA* 5.9 0.4 - - + -
460C VAL* 4.6 9.6 - - + -
433D GLU 2.9 21.7 + - - +
434D ILE* 3.1 6.9 + - - +
436D ALA* 1.3 73.5 - - - +
438D ASN* 1.3 79.9 + - - +
440D THR* 3.0 20.2 + - - -
441D ASN* 3.1 46.3 + - - +
444D LEU* 3.6 45.5 - - + -
445D ALA 4.0 0.4 - - - -
446D ARG* 3.2 62.0 - - + +
632D VAL* 4.2 6.7 - - + -
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Residues in contact with ASN 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D ILE* 2.8 30.8 + - - +
435D ALA* 3.1 7.0 + - - +
437D TRP* 1.3 81.2 - - - +
439D SER* 1.3 58.2 + - - +
441D ASN* 2.9 29.1 - - - +
444D LEU 5.0 1.0 - - - +
445D ALA* 3.3 11.5 - - + -
446D ARG* 2.8 44.2 + - - -
635D ARG* 5.4 2.1 + - - -
749D ALA* 3.6 24.7 - - + +
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Residues in contact with SER 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D ALA 3.1 9.8 + - - -
436D ALA* 2.6 23.2 + - - -
438D ASN* 1.3 77.7 - - - +
440D THR* 1.3 60.9 + - - +
441D ASN 3.8 1.9 + - - +
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Residues in contact with THR 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ALA 3.7 9.7 + - - -
437D TRP* 3.0 13.6 + - - -
439D SER* 1.3 81.8 + - - +
441D ASN* 1.3 64.5 + - - +
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Residues in contact with ASN 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C GLU* 6.3 0.2 - - - +
454C ALA* 3.7 30.1 + - - +
437D TRP* 3.1 56.4 + - + +
438D ASN 2.9 17.0 + - - +
439D SER 4.3 2.6 - - - +
440D THR* 1.3 88.5 + - - +
442D ARG* 1.3 64.2 + - - +
444D LEU* 3.2 28.7 - - - +
635D ARG* 4.4 6.4 + - - -
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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