Contacts of the helix formed by residues 509 - 515 (chain B) in PDB entry 1W1J
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 PHE 509 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B VAL* 4.4 10.1 - - + -
64B MET* 5.6 0.2 - - - -
423B LEU* 4.3 15.9 - - + -
485B GLN* 4.5 21.5 - - + -
488B MET* 3.7 44.0 - - + -
489B ARG* 3.4 44.0 - - + +
492B ILE* 4.0 13.7 - - + -
505B SER* 3.1 14.8 + - - +
506B HIS* 3.1 23.1 + - + +
508B ALA* 1.3 94.3 - - + +
510B MET* 1.3 60.0 + - - +
511B ASP 3.2 2.5 - - - +
512B GLN* 3.3 5.6 + - - +
513B ILE* 2.8 31.6 + - + +
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Residues in contact with MET 510 (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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246A PHE* 4.1 5.6 - - + -
98B TRP* 4.9 0.9 - - + -
108B TYR 5.0 1.3 - - - +
114B ARG* 4.8 5.2 - - - +
505B SER* 3.4 29.2 - - - +
506B HIS 3.0 15.6 + - - +
507B LEU* 3.5 43.3 - - + +
508B ALA 3.6 0.2 - - - -
509B PHE* 1.3 76.5 - - - +
511B ASP* 1.3 62.8 + - - +
513B ILE* 4.0 0.2 - - - -
514B MET* 3.0 27.0 + - - +
544B GLY 4.2 5.4 - - - +
545B LYS* 3.9 35.7 - - + +
546B SER* 3.3 26.9 - - - +
547B GLY 4.2 12.1 + - - +
1561B FAD 5.6 0.9 - - - +
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Residues in contact with ASP 511 (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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114B ARG* 2.3 42.1 + - - -
508B ALA 5.1 1.2 - - - +
509B PHE* 3.2 1.2 - - - +
510B MET* 1.3 79.9 - - - +
512B GLN* 1.3 56.5 + - - +
514B MET* 3.3 2.6 + - - +
515B GLU* 2.8 29.6 + - - +
544B GLY 5.4 0.2 - - - -
547B GLY* 3.9 11.6 - - - +
549B TRP* 2.8 26.6 + - - -
559B LYS* 3.6 23.2 - - + +
560B LEU* 3.2 27.4 + - - +
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Residues in contact with GLN 512 (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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489B ARG* 2.7 76.1 + - - +
492B ILE* 3.8 19.5 - - + +
493B ASP* 2.8 31.4 + - - +
509B PHE* 3.3 6.0 + - - +
511B ASP* 1.3 77.8 - - - +
513B ILE* 1.3 64.0 + - - +
515B GLU* 3.1 19.4 + - + +
516B THR* 3.3 12.5 + - - -
560B LEU 4.5 5.2 + - - +
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Residues in contact with ILE 513 (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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246A PHE* 3.7 37.5 - - + -
488B MET* 4.7 7.9 - - + -
492B ILE* 3.8 25.6 - - + -
502B GLU* 3.4 47.3 - - + +
504B ARG 4.5 0.7 - - - +
505B SER* 3.6 22.2 - - - +
509B PHE* 2.8 21.1 + - + +
510B MET 4.1 0.2 - - - +
512B GLN* 1.3 74.2 - - - +
514B MET* 1.3 59.3 + - - +
516B THR* 2.7 30.8 - - - +
517B TYR* 3.5 10.5 - - + -
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Residues in contact with MET 514 (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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246A PHE* 3.8 18.6 - - + -
248A PRO* 4.8 5.2 - - + -
510B MET 3.0 18.8 + - - +
511B ASP 3.6 4.0 - - - +
513B ILE* 1.3 71.8 - - - +
515B GLU* 1.3 55.7 + - - +
516B THR 2.7 14.4 + - - -
517B TYR* 2.9 22.8 + - - +
518B ASN* 5.4 0.2 - - - +
524B PHE* 4.4 29.2 - - + -
525B LEU* 3.6 50.0 - - + +
528B ASN* 5.0 1.1 - - - +
546B SER* 2.9 31.9 - - - +
547B GLY* 4.3 4.5 - - - -
548B VAL* 3.9 10.3 - - + -
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Residues in contact with GLU 515 (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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511B ASP 2.8 17.6 + - - +
512B GLN* 3.1 14.3 + - + +
514B MET* 1.3 76.1 - - - +
516B THR* 1.3 58.2 + - - +
517B TYR 3.5 0.2 - - - -
518B ASN* 3.5 33.4 + - - +
522B SER* 4.3 8.9 + - - -
525B LEU* 5.9 5.0 - - - +
559B LYS* 4.6 16.6 + - + -
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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