Contacts of the helix formed by residues 495 - 505 (chain B) in PDB entry 6IWQ
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 ILE 495 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B ASP* 4.2 3.6 - - - +
467B ARG* 3.4 28.9 - - + +
470B GLU* 5.3 5.8 - - + -
471B VAL* 4.1 22.9 - - + +
492B TYR* 4.3 25.8 - - + +
493B GLY 3.4 2.5 + - - +
494B ASP* 1.3 71.9 - - - +
496B SER* 1.3 64.2 + - - +
497B GLU 3.3 2.7 - - - -
498B LEU* 2.3 52.5 + - + -
499B LYS* 3.0 42.6 + - + +
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Residues in contact with SER 496 (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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494B ASP* 3.3 20.1 - - - +
495B ILE* 1.3 77.7 + - - +
497B GLU* 1.3 57.0 + - - +
499B LYS* 3.5 6.2 + - - +
500B LYS* 3.1 27.0 + - - +
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Residues in contact with GLU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ASP 5.1 1.3 + - - +
495B ILE 3.3 0.4 - - - -
496B SER* 1.3 81.5 + - - +
498B LEU* 1.3 62.9 + - + +
500B LYS* 3.3 23.7 + - - +
501B PHE* 3.0 26.8 + - + +
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Residues in contact with LEU 498 (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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406B ASP* 3.3 43.1 - - + +
407B PRO* 4.8 5.6 - - + -
418B GLU* 4.6 7.0 - - - +
422B LYS* 4.8 7.4 - - - +
467B ARG* 3.4 5.4 - - - +
471B VAL* 4.0 18.7 - - + +
472B TRP* 5.2 1.9 - - + +
494B ASP 4.7 1.6 - - - +
495B ILE* 2.3 54.0 + - + -
497B GLU* 1.3 79.6 - - + +
499B LYS* 1.3 63.7 + - - +
501B PHE* 3.3 11.8 + - + +
502B ARG* 3.3 16.5 + - - +
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Residues in contact with LYS 499 (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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470B GLU* 4.4 16.0 + - + +
471B VAL* 4.3 25.9 - - + +
477B LYS* 5.7 2.4 - - - +
495B ILE* 3.0 36.2 + - + +
496B SER* 3.8 6.7 - - - +
498B LEU* 1.3 76.1 - - - +
500B LYS* 1.3 63.8 + - - +
502B ARG* 3.3 8.4 + - + +
503B GLU* 3.1 38.6 + - - +
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Residues in contact with LYS 500 (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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496B SER 3.1 15.2 + - - +
497B GLU* 3.3 26.7 + - - +
498B LEU 3.2 0.4 - - - -
499B LYS* 1.3 78.6 - - - +
501B PHE* 1.3 52.5 + - - +
503B GLU* 3.1 11.4 + - + +
504B ASP* 2.7 61.4 + - - +
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Residues in contact with PHE 501 (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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115B PHE* 4.9 1.1 - + - -
401B GLU 3.3 26.0 - - - -
402B LEU* 3.7 32.3 - - + -
403B GLY* 5.2 2.0 - - - -
422B LYS* 4.1 16.8 - - + -
426B CYS* 3.9 23.6 - - - -
472B TRP* 4.3 7.9 - + - -
497B GLU* 3.0 13.6 + - + +
498B LEU* 3.6 14.8 - - + +
499B LYS 3.2 0.2 - - - -
500B LYS* 1.3 75.6 - - - +
502B ARG* 1.3 67.1 + - - +
504B ASP* 4.5 2.9 - - - +
505B HIS* 3.0 61.0 + + - +
507B CYS* 4.4 0.2 - - - -
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Residues in contact with ARG 502 (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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425B GLN* 3.6 6.8 + - - -
471B VAL* 3.4 18.4 + - + -
472B TRP* 3.1 50.3 + - + +
474B ASP* 2.9 40.1 + - - -
498B LEU 3.3 7.7 + - - +
499B LYS* 3.3 12.3 + - - +
500B LYS 3.2 0.2 - - - -
501B PHE* 1.3 82.8 - - - +
503B GLU* 1.3 62.4 + - + +
505B HIS 3.7 0.3 + - - -
506B ASN 3.3 2.3 + - - -
507B CYS* 3.1 49.3 + - + +
508B LYS 3.5 11.7 + - - -
509B SER* 3.4 19.8 - - - +
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Residues in contact with GLU 503 (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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112B TYR 5.1 0.3 + - - -
499B LYS* 3.1 26.8 + - - +
500B LYS* 3.1 13.2 + - - +
502B ARG* 1.3 80.6 - - + +
504B ASP* 1.3 68.7 + - - +
506B ASN* 3.1 18.8 + - - +
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Residues in contact with ASP 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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112B TYR 2.7 30.7 + - - +
113B LEU* 3.3 29.6 + - + +
500B LYS* 2.7 55.5 + - - +
501B PHE* 4.1 4.0 - - - +
503B GLU* 1.3 76.3 - - - +
505B HIS* 1.3 60.7 + - + +
506B ASN 3.3 1.6 + - - -
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Residues in contact with HIS 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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113B LEU* 3.5 55.7 + - + +
114B THR 4.7 0.9 + - - -
115B PHE* 3.9 29.4 - + + -
401B GLU* 4.1 15.9 + - - -
426B CYS* 5.0 5.6 - - + +
501B PHE* 3.0 62.4 + + - +
504B ASP* 1.3 75.1 - - + +
506B ASN* 1.3 70.9 + - - +
507B CYS* 3.0 17.4 + - - -
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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