Contacts of the helix formed by residues 460 - 468 (chain B) in PDB entry 1OFD
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 VAL 460 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B GLU 4.1 8.3 - - - +
456B ASP* 3.3 19.6 + - - +
458B GLU 3.7 0.2 - - - -
459B MET* 1.3 85.1 - - + +
461B VAL* 1.3 63.1 + - - +
462B VAL 3.5 0.9 - - - -
463B PRO* 3.5 2.5 - - - +
464B MET* 2.8 61.8 + - + +
471B PRO* 4.2 11.3 - - + +
648B TRP* 4.4 7.4 - - + +
649B SER* 4.2 20.6 - - - -
786B VAL* 6.2 0.4 - - + -
1070B LEU* 4.1 20.2 - - + -
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Residues in contact with VAL 461 (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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452B TYR* 4.7 9.4 - - + -
456B ASP 2.9 20.1 + - - +
457B VAL* 3.8 14.8 - - + +
460B VAL* 1.3 71.7 - - - +
462B VAL* 1.3 67.8 + - + +
464B MET* 3.3 13.3 + - + +
465B ALA* 3.1 20.7 + - + +
648B TRP* 3.9 35.2 - - + -
669B ALA* 4.5 3.1 - - + +
672B SER* 4.3 16.6 - - - -
673B VAL* 3.8 26.5 - - + +
676B TRP* 6.4 0.9 - - + -
703B TYR* 4.4 6.9 - - + -
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B VAL* 2.9 35.0 + - + +
458B GLU* 3.9 10.5 - - + +
461B VAL* 1.3 78.0 - - + +
463B PRO* 1.3 58.3 - - + +
465B ALA* 3.1 5.6 + - - +
466B SER* 2.7 40.2 + - - +
676B TRP* 3.4 54.9 - - + +
690B ARG* 3.9 18.2 - - - +
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Residues in contact with PRO 463 (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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458B GLU 3.4 14.6 - - - +
459B MET* 3.3 22.0 - - - +
460B VAL 3.5 12.8 - - - +
462B VAL* 1.3 95.6 - - + +
464B MET* 1.3 56.1 + - - +
466B SER* 3.7 7.9 - - - +
467B GLN* 2.8 51.5 + - - +
469B LYS 3.6 8.1 - - - +
471B PRO* 4.3 16.4 - - + -
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Residues in contact with MET 464 (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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460B VAL* 2.8 54.4 + - + +
461B VAL* 3.4 16.4 - - + +
462B VAL 3.3 0.2 - - - -
463B PRO* 1.3 77.5 - - - +
465B ALA* 1.3 57.6 + - - +
468B GLY* 3.0 22.7 + - - -
469B LYS 3.6 2.7 - - - -
470B GLU* 4.1 19.5 - - - -
471B PRO* 4.5 0.9 - - + -
648B TRP 3.7 17.9 - - - +
649B SER* 4.8 3.6 - - - -
650B THR* 5.1 5.6 - - - -
702B ASN 3.3 5.5 - - - +
703B TYR* 3.8 24.2 - - + -
706B SER* 3.1 35.7 + - - +
707B VAL* 5.0 5.6 - - - -
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Residues in contact with ALA 465 (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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461B VAL 3.1 15.0 + - - +
462B VAL* 3.9 3.1 - - - +
464B MET* 1.3 74.8 - - - +
466B SER* 1.3 60.9 + - - +
673B VAL* 3.8 28.3 - - + -
676B TRP* 4.2 14.1 - - + -
694B ILE* 4.5 0.9 - - - +
699B ALA* 3.5 30.7 - - - +
702B ASN* 3.0 24.0 + - - +
703B TYR* 4.0 4.0 - - + +
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Residues in contact with SER 466 (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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462B VAL* 2.7 26.8 + - - +
463B PRO* 3.7 8.8 - - - +
465B ALA* 1.3 73.4 - - - +
467B GLN* 1.3 75.4 + - - +
676B TRP* 3.7 26.9 - - - -
690B ARG* 5.6 7.9 - - - -
691B LEU* 5.5 5.3 - - - +
694B ILE* 3.1 28.1 - - - +
702B ASN* 3.6 2.4 + - - -
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Residues in contact with GLN 467 (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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463B PRO* 2.8 28.0 + - - +
466B SER* 1.3 93.8 + - - +
468B GLY* 1.3 60.9 + - - +
469B LYS* 3.2 20.8 + - + +
471B PRO* 6.0 1.6 - - - +
691B LEU* 6.2 5.2 - - + -
702B ASN* 4.3 4.6 - - - +
705B GLN* 5.2 0.9 + - - -
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Residues in contact with GLY 468 (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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463B PRO 3.7 0.2 + - - -
464B MET 3.0 17.6 + - - -
466B SER 3.8 0.8 - - - -
467B GLN* 1.3 78.1 - - - +
469B LYS* 1.3 62.7 + - - +
702B ASN* 3.7 21.5 - - - +
705B GLN* 3.3 25.3 + - - +
706B SER* 2.9 17.3 + - - -
709B ALA* 5.6 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