Contacts of the helix formed by residues 587 - 596 (chain B) in PDB entry 5IWM
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 587 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585B GLU 4.2 0.2 + - - -
586B MET* 1.3 75.3 - - - +
588B ALA* 1.3 67.0 + - - +
589B ASP* 3.3 17.7 + - - +
590B GLN* 3.0 34.1 + - - +
591B LEU* 3.1 11.9 + - - +
64C TYR* 5.7 2.2 + - - -
106C GLY 4.3 4.9 + - - +
107C GLN* 3.5 18.4 + - - +
108C GLY* 2.7 37.7 + - - +
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Residues in contact with ALA 588 (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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442B SER* 3.9 15.2 + - - +
445B SER* 3.6 31.9 - - - -
446B GLY* 3.6 10.4 - - - +
586B MET 3.9 1.2 + - - -
587B ASN* 1.3 71.9 - - - +
589B ASP* 1.3 61.6 + - - +
591B LEU* 3.4 4.2 + - - +
592B TRP* 3.1 22.5 + - - +
108C GLY 5.4 0.8 + - - -
298C LEU* 3.7 20.4 - - + -
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Residues in contact with ASP 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ASN* 3.3 21.3 + - - +
588B ALA* 1.3 74.2 - - - +
590B GLN* 1.3 77.3 + - - +
592B TRP* 3.2 8.0 + - + +
593B GLU* 2.9 37.7 + - + +
298C LEU* 3.7 17.3 - - + +
299C ARG* 5.9 0.4 - - - +
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Residues in contact with GLN 590 (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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580B TYR* 3.2 26.2 + - - +
586B MET* 3.7 12.6 - - + +
587B ASN* 3.0 34.9 + - + +
589B ASP* 1.3 90.2 + - - +
591B LEU* 1.3 60.9 + - - +
593B GLU* 4.1 3.1 - - - -
594B THR* 2.4 43.1 + - + +
107C GLN* 5.3 9.7 + - - -
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Residues in contact with LEU 591 (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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442B SER* 3.6 14.8 - - - +
443B THR* 3.6 44.9 - - - +
446B GLY* 6.0 0.4 - - - -
506B MET* 4.4 7.2 - - - -
542B PRO* 5.0 0.9 - - + -
583B LEU* 4.1 34.3 - - + +
586B MET* 3.7 17.7 - - + +
587B ASN 3.1 10.8 + - - +
588B ALA* 3.7 8.3 - - - +
589B ASP 3.2 0.2 - - - -
590B GLN* 1.3 80.4 - - - +
592B TRP* 1.3 61.7 + - - +
594B THR* 4.2 0.2 - - - -
595B THR* 3.1 37.2 + - + +
596B MET* 3.3 17.9 + - + +
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Residues in contact with TRP 592 (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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446B GLY 3.0 33.7 - - - +
447B ARG* 4.2 0.4 - - - -
448B ASP* 3.9 22.4 - - + -
452B GLN* 3.6 27.6 - - - -
588B ALA 3.1 14.9 + - - +
589B ASP* 3.2 6.0 + - + +
591B LEU* 1.3 77.6 - - - +
593B GLU* 1.3 83.8 + - + +
596B MET* 3.1 27.1 + - + -
597B ASN* 2.7 64.4 + - + +
598B PRO* 4.4 6.1 - - + -
299C ARG* 3.3 41.7 - - - +
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Residues in contact with GLU 593 (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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589B ASP* 2.9 23.3 + - + +
590B GLN* 4.7 2.9 - - - +
592B TRP* 1.3 96.1 + - + +
594B THR* 1.3 62.8 + - + +
597B ASN* 3.9 10.3 - - - +
600B HIS* 3.0 63.2 + - - +
299C ARG* 5.3 2.1 - - - -
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Residues in contact with THR 594 (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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541B GLN 4.7 5.7 - - - +
543B PRO* 3.7 23.6 - - + +
586B MET* 4.2 1.4 - - + +
590B GLN* 2.4 29.6 + - + +
593B GLU* 1.3 82.2 - - + +
595B THR* 1.3 69.8 + - - +
600B HIS* 4.9 1.5 - - - +
601B ARG* 4.0 13.6 - - - -
602B ALA 4.7 2.4 + - - -
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Residues in contact with THR 595 (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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432B PHE* 4.8 2.6 - - - -
506B MET* 3.8 13.2 - - - -
540B ALA* 3.7 27.8 - - + -
541B GLN 3.9 12.5 + - - +
542B PRO* 3.4 25.7 - - + +
543B PRO* 3.8 2.1 - - - +
591B LEU* 3.1 19.6 + - - +
594B THR* 1.3 91.7 + - - +
596B MET* 1.3 60.2 + - - +
601B ARG* 3.4 21.7 - - - +
602B ALA 5.6 0.4 - - - +
603B LEU* 4.1 8.6 - - + +
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Residues in contact with MET 596 (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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432B PHE* 3.9 25.1 - - + -
443B THR* 3.7 39.5 - - + +
446B GLY 4.8 2.9 - - - -
447B ARG* 3.7 17.0 - - + -
452B GLN* 3.1 32.8 + - + +
454B ILE* 5.3 0.4 - - + -
506B MET* 4.1 15.9 - - + -
591B LEU* 3.3 26.6 + - + +
592B TRP* 3.1 20.1 + - + +
595B THR* 1.3 79.9 - - - +
597B ASN* 1.3 61.7 + - - +
598B PRO 3.3 0.5 - - - -
601B ARG* 2.9 27.8 + - - +
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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