Contacts of the helix formed by residues 501 - 505 (chain B) in PDB entry 3IW4
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 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A ALA 4.3 18.2 - - - +
647A ASN* 5.2 3.4 - - - +
648A ILE 4.6 14.8 - - - +
649A ASP* 5.1 10.7 - - - +
650A GLN 5.6 0.2 - - - +
463B ASP* 3.9 4.7 + - - +
465B LYS* 3.0 40.3 + - + +
500B GLY* 1.3 70.4 - - - -
502B PRO* 1.3 65.2 - - + +
503B ASP 4.8 0.4 - - - +
504B TYR* 2.6 49.1 + - + +
505B ILE* 3.5 3.1 + - - +
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Residues in contact with PRO 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A GLN* 5.2 21.1 - - + +
498B PHE* 6.3 0.2 - - + -
500B GLY 3.5 8.7 - - - +
501B THR* 1.3 88.4 - - + -
503B ASP* 1.3 61.8 + - - +
504B TYR 2.9 6.6 + - - -
505B ILE* 3.0 24.1 + - + +
543B GLU* 3.6 24.7 - - + +
546B LEU* 3.7 19.5 - - + -
547B PHE* 4.0 15.8 - - + -
550B ILE* 3.8 9.7 - - - +
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Residues in contact with ASP 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ILE* 4.7 2.4 - - - +
646A ALA* 3.3 50.3 + - + +
501B THR* 3.0 2.7 + - - +
502B PRO* 1.3 78.2 - - - +
504B TYR* 1.3 65.7 + - + +
505B ILE 3.8 0.3 + - - -
522B TRP* 4.9 1.0 + - - -
526B VAL* 3.8 19.8 - - + +
530B GLU* 6.0 0.2 - - - +
536B PRO* 4.3 3.2 - - + +
537B PRO* 5.4 2.8 - - + +
538B PHE* 3.9 19.8 - - - +
539B ASP* 5.3 0.2 - - - -
546B LEU* 3.5 31.9 - - - +
550B ILE* 4.4 10.4 - - - +
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Residues in contact with TYR 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A ALA 4.0 14.6 - - - -
647A ASN* 2.4 34.9 + - - -
464B LEU 3.1 23.3 - - - +
465B LYS* 3.5 22.0 - - + -
466B LEU 3.6 3.1 + - - -
501B THR* 2.6 36.0 + - + +
503B ASP* 1.3 80.7 - - + +
505B ILE* 1.3 60.4 + - - +
506B ALA 3.7 0.5 + - - -
519B VAL 4.7 1.2 - - - +
522B TRP* 3.4 15.3 - - - -
523B ALA* 3.8 23.9 - - + +
526B VAL* 3.9 21.5 - - + -
527B LEU* 4.2 8.3 - - + -
530B GLU* 3.0 30.8 + - - -
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Residues in contact with ILE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B PHE* 4.1 24.7 - - + -
499B CYS 3.9 24.0 - - - +
500B GLY* 4.0 15.9 - - - +
501B THR 3.8 9.2 - - - +
502B PRO* 3.0 24.2 + - + +
503B ASP 3.5 0.4 - - - -
504B TYR* 1.3 78.5 - - - +
506B ALA* 1.3 79.0 + - - +
509B ILE* 3.1 30.3 - - + -
510B ILE* 4.4 10.7 - - + +
522B TRP* 3.2 12.9 + - - -
547B PHE* 4.3 5.6 - - + -
550B ILE* 3.8 16.8 - - - +
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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