Contacts of the helix formed by residues 497 - 505 (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 VAL 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ARG* 3.2 31.5 - - + +
496A VAL* 1.4 74.9 - - - +
498A VAL* 1.3 71.8 + - + +
499A LEU* 3.2 4.6 + - - +
500A SER* 3.1 26.0 + - - -
501A PHE* 4.4 1.3 + - + +
584A ILE* 5.3 4.7 - - + +
588A THR* 3.7 2.8 + - - +
590A ALA* 3.9 10.8 - - + +
591A SER* 3.4 25.6 - - - +
614A GLN* 3.6 19.3 - - + +
679A MET* 5.1 15.0 - - - -
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Residues in contact with VAL 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 4.6 18.8 - - + +
232A ARG* 4.6 26.6 - - + +
400A GLY* 5.1 4.7 - - - +
402A THR* 3.9 18.8 - - + -
497A VAL* 1.3 85.8 - - + +
499A LEU* 1.3 69.0 + - + +
500A SER 3.4 0.7 + - - -
501A PHE* 3.5 16.2 + - + +
502A GLU* 3.6 12.6 + - + +
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Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 5.2 9.0 - - + -
402A THR* 3.9 30.9 + - + +
404A VAL* 3.4 34.3 - - + +
494A TYR 3.8 11.2 - - - +
495A ARG* 3.5 36.8 - - + -
496A VAL 4.4 7.2 - - - +
497A VAL 3.2 2.0 + - - +
498A VAL* 1.3 89.6 - - + +
500A SER* 1.3 62.2 + - - +
503A LEU* 3.3 20.4 + - - +
587A GLY 4.5 2.4 - - - +
588A THR* 3.6 1.8 - - + -
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Residues in contact with SER 500 (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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497A VAL 3.1 9.7 + - - -
499A LEU* 1.3 74.4 - - - +
501A PHE* 1.4 61.3 + - - +
503A LEU* 2.9 5.8 + - - +
504A LEU* 2.5 48.0 + - - +
584A ILE* 2.9 35.7 + - - +
585A THR 4.1 2.7 - - - -
587A GLY 4.3 5.4 - - - -
588A THR* 2.1 37.9 - - - +
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Residues in contact with PHE 501 (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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344A LYS* 4.9 19.1 - - - -
497A VAL* 5.2 0.7 - - + +
498A VAL* 3.5 13.2 + - + +
500A SER* 1.4 81.2 + - - +
502A GLU* 1.3 56.1 + - - +
504A LEU* 3.3 13.1 + - + +
505A ASN* 2.4 70.9 + - - -
584A ILE* 4.9 21.5 - - + -
678A THR 5.5 7.9 - - - -
680A SER 6.5 1.1 - - - -
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Residues in contact with GLU 502 (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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400A GLY 4.4 7.2 - - - +
401A GLN* 5.6 4.3 + - - +
402A THR* 3.1 47.5 + - + +
498A VAL* 3.6 7.5 + - + +
499A LEU 4.2 0.2 - - - +
501A PHE* 1.3 78.5 - - - +
503A LEU* 1.4 61.5 + - - +
505A ASN* 3.1 33.4 - - + +
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Residues in contact with LEU 503 (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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402A THR* 4.6 3.3 + - - +
404A VAL* 4.6 21.1 - - + +
405A ILE* 5.0 13.0 - - + -
499A LEU 3.3 15.0 + - - +
500A SER* 2.9 15.7 + - - +
502A GLU* 1.4 76.4 + - - +
504A LEU* 1.4 68.9 + - + +
505A ASN 3.6 2.9 + - - +
534A GLY* 6.0 5.2 - - - -
587A GLY* 5.5 9.2 - - - +
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Residues in contact with LEU 504 (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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500A SER* 2.5 43.5 + - - +
501A PHE* 3.6 13.2 - - + +
503A LEU* 1.4 83.6 - - + +
505A ASN* 1.3 57.3 + - - +
506A ALA* 3.4 6.5 + - - +
532A LEU 5.3 0.4 - - - +
533A THR 5.5 0.7 - - - +
534A GLY* 4.8 17.7 - - - +
583A VAL* 3.1 51.6 - - + +
584A ILE* 4.0 9.4 - - + +
586A PRO* 4.9 7.4 - - + -
587A GLY* 5.4 2.0 - - - +
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Residues in contact with ASN 505 (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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344A LYS* 5.4 4.2 - - - -
345A ILE* 5.6 10.6 - - + +
501A PHE* 2.4 75.2 + - - +
502A GLU* 3.1 32.9 + - + +
503A LEU 4.5 2.4 - - - +
504A LEU* 1.3 73.3 - - - +
506A ALA* 1.4 66.7 + - - +
507A PRO* 3.8 1.4 - - - +
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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