Contacts of the helix formed by residues 671 - 680 (chain A) in PDB entry 1XJP
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 GLN 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLY 3.7 8.7 + - - -
226A ILE* 3.3 47.9 - - - +
423A TRP 4.1 0.5 - - - +
424A ASN 3.2 5.6 - - - +
425A THR* 3.5 28.9 - - + +
426A ARG* 3.6 22.7 - - - +
427A ASN* 4.0 12.4 + - + +
615A LEU* 4.8 12.5 - - + +
667A ARG 3.9 1.6 + - - -
670A SER* 1.4 89.8 + - - +
672A LYS* 1.3 66.8 + - - +
673A SER 3.7 1.3 - - - -
674A ILE* 3.6 24.5 + - - +
675A VAL* 4.0 6.2 + - - +
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Residues in contact with LYS 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A TRP* 2.9 39.8 - - + +
424A ASN* 3.1 24.2 - - - +
425A THR* 2.9 13.7 - - - +
664A SER 4.6 1.8 + - - -
667A ARG* 2.3 72.1 + - - +
668A SER* 3.0 28.7 + - - +
671A GLN* 1.3 75.5 - - - +
673A SER* 1.4 57.9 + - - +
674A ILE 3.1 0.4 - - - -
675A VAL* 3.0 15.8 + - - +
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Residues in contact with SER 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A TRP* 4.1 12.7 - - - +
668A SER 2.7 21.8 + - - -
669A THR* 4.3 13.7 + - - +
671A GLN 3.7 0.2 - - - -
672A LYS* 1.4 75.5 - - - +
674A ILE* 1.4 56.3 + - - +
675A VAL 3.4 0.4 - - - -
676A ALA* 3.7 7.4 + - - +
677A TYR* 3.0 26.0 + - - +
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Residues in contact with ILE 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ILE* 4.4 17.5 - - + -
234A ILE* 4.7 15.5 - - + -
615A LEU* 5.6 8.3 - - + -
669A THR 5.2 3.6 - - - +
670A SER 3.7 24.5 - - - +
671A GLN* 3.6 20.4 + - - +
672A LYS 3.1 1.2 + - - -
673A SER* 1.4 73.9 - - - +
675A VAL* 1.3 60.3 + - - +
677A TYR* 3.4 10.0 - - + +
678A THR* 2.8 50.3 + - + +
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Residues in contact with VAL 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 4.7 8.7 - - + -
422A ALA 4.6 2.7 - - - +
423A TRP* 3.1 34.3 - - - +
424A ASN* 4.1 8.5 - - - +
614A GLN* 2.7 39.5 - - - +
615A LEU* 4.0 22.9 - - + -
671A GLN 4.4 2.9 - - - +
672A LYS 3.0 2.9 + - - +
674A ILE* 1.3 75.4 - - + +
676A ALA* 1.4 60.4 + - - +
678A THR* 3.4 5.6 - - - +
679A MET* 2.8 44.2 + - + +
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Residues in contact with ALA 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 5.0 3.6 - - + -
423A TRP* 2.6 43.4 - - + +
672A LYS 3.7 1.0 + - - -
673A SER* 3.7 7.4 + - - +
675A VAL* 1.4 79.5 - - - +
677A TYR* 1.4 57.0 + - - +
679A MET* 4.1 4.6 - - - +
680A SER* 3.0 30.1 + - - -
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Residues in contact with TYR 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 3.2 35.9 - - + +
337A VAL* 6.0 3.8 - - + -
339A ALA* 3.8 23.5 - - + +
340A TRP* 4.1 13.2 + - - +
341A GLU* 5.0 8.3 - - - +
673A SER 3.0 20.0 + - - +
674A ILE* 3.4 11.9 - - + +
676A ALA* 1.4 73.1 - - - +
678A THR* 1.3 76.7 + - + +
680A SER* 2.8 24.7 + - - -
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Residues in contact with THR 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 5.2 9.4 - - + -
501A PHE* 5.5 8.0 - - - -
584A ILE* 5.1 1.0 - - - +
614A GLN* 4.6 4.3 + - - -
674A ILE* 2.8 42.9 + - + +
675A VAL* 3.1 15.1 + - - +
677A TYR* 1.3 80.6 - - + +
679A MET* 1.3 69.7 + - - +
680A SER 4.7 2.1 - - - -
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Residues in contact with MET 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 5.4 12.1 - - + -
497A VAL* 5.1 15.3 - - - -
527A PHE* 5.6 1.0 - - - -
584A ILE* 2.6 61.3 - - + +
590A ALA* 5.5 8.7 - - + -
594A VAL* 5.8 4.7 - - + -
612A ALA* 5.6 10.8 - - + -
614A GLN* 4.7 10.5 - - - +
675A VAL* 2.8 40.1 + - + +
676A ALA* 4.1 5.8 - - - +
678A THR* 1.3 80.0 + - - +
680A SER* 1.4 59.2 + - - +
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Residues in contact with SER 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 3.6 29.0 - - - +
501A PHE* 6.5 0.9 - - - -
527A PHE* 4.6 41.6 - - - -
584A ILE* 5.5 0.2 - - - -
676A ALA 3.0 18.0 + - - -
677A TYR* 2.8 24.1 + - - -
678A THR 4.7 1.8 - - - -
679A MET* 1.4 79.8 - - - +
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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