Contacts of the helix formed by residues 503 - 512 (chain A) in PDB entry 1SIW
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 THR 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ALA* 3.8 2.0 - - - -
311A HIS* 4.2 10.8 - - + +
482A GLY 5.4 0.2 - - - +
493A ALA* 3.4 26.9 - - + -
495A SER 4.4 2.0 - - - +
496A TYR 3.9 5.8 - - - -
498A ASP 2.9 28.9 + - - +
500A LYS* 3.3 15.1 + - + +
502A TYR* 1.3 83.0 - - - +
504A PRO* 1.3 62.6 - - - +
505A ALA 3.7 0.9 + - - -
506A TRP* 2.9 23.3 + - - +
507A ALA* 2.7 35.7 + - - +
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Residues in contact with PRO 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ALA* 3.8 17.3 - - + +
311A HIS* 4.0 16.4 - - + -
312A VAL* 3.7 26.9 - - + -
496A TYR* 3.9 17.5 - - + +
502A TYR 4.2 1.1 - - - +
503A THR* 1.3 89.6 - - - +
505A ALA* 1.3 55.9 + - - +
507A ALA* 3.8 1.4 - - + +
508A GLU* 3.0 28.1 + - - +
515A ARG* 3.7 17.7 - - + +
518A ILE* 4.1 7.8 - - + +
519A ILE* 4.0 24.5 - - + -
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Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A TYR 3.2 18.9 + - - +
497A ASP 3.2 14.8 - - - +
499A VAL* 4.2 11.2 - - + -
503A THR* 3.1 2.8 - - - +
504A PRO* 1.3 74.4 - - - +
506A TRP* 1.3 67.2 + - - +
508A GLU* 3.3 12.6 + - - +
509A GLN* 3.5 17.3 + - - +
515A ARG* 3.1 40.0 + - - +
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Residues in contact with TRP 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ALA* 3.5 43.5 - - + -
307A LEU* 4.8 0.7 - - + -
433A TYR* 2.9 26.7 + + - -
445A VAL* 3.5 26.0 - - + +
447A LEU* 4.6 2.2 - - + -
499A VAL* 4.4 11.1 - - + +
500A LYS 3.1 31.9 - - - +
502A TYR* 3.3 47.1 - + + -
503A THR* 2.9 20.9 + - - +
505A ALA* 1.3 76.9 - - - +
507A ALA* 1.3 82.1 + - + +
509A GLN* 3.3 16.1 + - - +
510A ILE* 3.4 30.4 + - + +
1061A TYR* 3.7 18.2 - + + -
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Residues in contact with ALA 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ALA 3.8 17.9 - - - +
305A MET* 4.4 1.3 - - - +
308A ALA* 3.6 22.0 - - + -
503A THR 2.7 18.0 + - - +
504A PRO 3.8 0.7 - - - +
506A TRP* 1.3 81.5 - - + +
508A GLU* 1.3 61.2 + - - +
510A ILE* 3.2 3.0 + - - +
511A THR* 2.8 37.3 + - - +
518A ILE* 3.7 15.5 - - + -
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A PRO 3.0 17.6 + - - +
505A ALA 3.5 7.2 - - - +
506A TRP 3.3 0.2 - - - -
507A ALA* 1.3 77.4 - - - +
509A GLN* 1.3 59.0 + - + +
511A THR* 4.2 0.2 - - - -
512A GLY* 2.9 27.0 + - - -
513A VAL 3.4 24.2 + - - +
514A SER* 3.7 5.5 + - - -
515A ARG* 2.7 62.2 + - + +
518A ILE* 4.4 0.2 - - - +
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Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ASN* 3.2 27.5 + - - +
444A LYS 4.6 4.9 - - - +
445A VAL* 3.8 21.1 - - + +
499A VAL* 3.5 42.2 - - - +
505A ALA 3.5 9.3 + - - +
506A TRP* 3.3 7.7 + - - +
507A ALA 3.2 0.4 - - - -
508A GLU* 1.3 83.0 - - + +
510A ILE* 1.3 61.3 + - - +
512A GLY* 4.4 0.7 + - - -
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Residues in contact with ILE 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LYS* 4.5 1.7 - - - +
301A THR* 3.7 16.4 - - + +
304A ALA* 3.9 15.9 - - + -
435A GLY 3.8 19.1 - - - +
443A ASN* 3.8 32.9 + - - +
445A VAL* 3.5 27.4 - - + +
506A TRP* 3.7 30.5 - - + +
507A ALA 3.2 5.7 + - - +
509A GLN* 1.3 78.7 - - - +
511A THR* 1.3 60.6 + - - +
1061A TYR* 3.7 36.1 - - + +
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Residues in contact with THR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA 4.7 0.5 - - - +
297A PRO* 3.6 14.2 - - + +
298A LYS* 2.9 30.5 + - - +
301A THR* 3.3 36.1 - - - +
304A ALA* 3.5 16.8 - - + -
305A MET* 3.8 15.9 - - + +
443A ASN* 5.3 1.6 - - - -
507A ALA 2.8 30.1 + - - +
509A GLN 4.9 0.2 - - - -
510A ILE* 1.3 74.1 - - - +
512A GLY* 1.3 57.7 + - - +
513A VAL* 3.1 19.5 + - - +
518A ILE* 4.7 2.6 - - - +
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Residues in contact with GLY 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA 5.2 4.3 - - - +
443A ASN* 5.5 4.0 - - - -
508A GLU* 2.9 18.7 + - - +
509A GLN 4.4 1.5 + - - -
510A ILE 3.7 0.6 - - - -
511A THR* 1.3 79.2 + - - +
513A VAL* 1.3 62.5 + - - +
514A SER 3.7 2.3 + - - -
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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