Contacts of the helix formed by residues 496 - 505 (chain B) in PDB entry 2XPH
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 496 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468B ASP* 3.3 33.0 - - + -
472B ASN* 4.6 3.6 - - - -
494B ASN* 3.2 22.5 + - - +
495B THR* 1.3 79.9 - - - +
497B PHE* 1.3 57.6 + - - +
498B PHE 3.5 1.1 - - - -
499B THR* 3.9 11.0 + - - -
500B LYS* 3.1 34.9 + - + +
512B TRP* 4.1 13.5 - - + -
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Residues in contact with PHE 497 (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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493B PHE* 3.5 59.0 - + + -
494B ASN* 3.2 17.1 + - - +
495B THR 3.2 0.2 - - - -
496B PHE* 1.3 76.7 - - - +
498B PHE* 1.3 66.0 + - - +
500B LYS* 4.7 0.2 - - - -
501B LEU* 3.0 34.7 + - + +
509B VAL* 3.8 27.5 - - + +
512B TRP* 3.6 33.7 - + + -
513B THR* 6.1 0.2 - - + -
526B VAL* 4.2 19.3 - - + -
527B PRO* 6.0 0.4 - - + -
563B LEU* 4.5 7.4 - - + -
566B TYR* 3.9 28.0 - + - -
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Residues in contact with PHE 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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465A TRP* 5.6 3.6 - + - -
532A VAL* 4.4 22.7 - - + -
494B ASN 4.8 0.4 + - - -
495B THR 4.4 2.4 + - - -
496B PHE 3.5 0.2 - - - -
497B PHE* 1.3 79.5 - - - +
499B THR* 1.3 80.0 + - + +
500B LYS 2.9 1.2 + - - -
501B LEU* 2.9 13.0 + - + +
502B LYS* 2.8 28.9 + - + -
526B VAL* 4.2 12.3 - - + -
527B PRO 4.1 18.5 + - - +
528B ILE* 3.5 39.7 - - + -
530B LEU* 5.9 0.2 - - + -
556B ASN* 5.3 3.1 - - - -
559B ALA* 3.8 42.0 - - + -
562B ILE* 4.0 23.8 - - + -
563B LEU* 4.8 7.0 - - + -
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Residues in contact with THR 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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531A GLY* 4.8 13.6 - - - -
532A VAL* 3.5 23.9 - - + +
495B THR 4.3 10.1 - - - +
496B PHE* 3.9 10.1 + - - +
498B PHE* 1.3 77.8 - - + +
500B LYS* 1.3 57.9 + - - +
503B THR* 2.9 35.8 + - - +
529B HIS* 3.5 42.8 - - + +
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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 PHE* 3.1 23.7 + - + +
498B PHE 2.9 2.0 + - - -
499B THR* 1.3 72.3 + - - +
501B LEU* 1.3 69.1 + - - +
503B THR* 3.6 6.5 - - - +
504B ALA* 2.9 31.6 + - + -
505B GLY 3.5 3.3 + - - +
508B ALA* 4.5 20.6 - - + +
509B VAL* 4.1 17.0 - - + -
512B TRP* 4.5 17.9 - - + -
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Residues in contact with LEU 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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497B PHE* 3.0 30.7 + - + +
498B PHE* 2.9 11.4 + - + +
500B LYS* 1.3 74.7 - - - +
502B LYS* 1.3 58.2 + - - +
505B GLY* 2.9 28.8 + - - -
506B TYR* 3.7 22.0 - - + +
509B VAL* 3.5 31.6 - - + +
562B ILE* 3.9 26.7 - - + +
563B LEU* 4.8 7.2 - - + -
566B TYR* 3.9 33.9 - - + -
569B GLN* 5.3 2.2 - - - +
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Residues in contact with LYS 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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465A TRP* 3.7 53.9 + - + +
466A LEU 5.7 0.4 + - - -
529A HIS* 6.3 0.7 - - - -
532A VAL* 4.2 26.2 - - + +
498B PHE* 2.8 26.1 + - + +
499B THR 4.0 2.9 - - - +
501B LEU* 1.3 75.6 - - - +
503B THR* 1.3 74.8 + - - +
504B ALA 3.0 0.3 + - - -
505B GLY* 3.7 3.1 + - - -
562B ILE* 3.7 34.3 - - + +
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Residues in contact with THR 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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529A HIS* 4.9 11.9 - - + -
531A GLY 3.6 24.0 - - - +
532A VAL* 4.4 6.3 - - + -
499B THR* 2.9 27.0 + - - +
500B LYS* 3.3 12.5 + - - +
502B LYS* 1.3 84.8 - - - +
504B ALA* 1.3 68.0 + - - +
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Residues in contact with ALA 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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500B LYS* 2.9 22.1 + - + +
503B THR* 1.3 81.0 + - - +
505B GLY* 1.3 64.4 + - - +
507B GLN* 4.6 4.9 + - - +
508B ALA* 4.5 21.1 + - + +
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Residues in contact with GLY 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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500B LYS 3.5 1.6 + - - +
501B LEU* 2.9 27.8 + - - +
502B LYS 3.7 2.9 + - - -
503B THR 3.7 0.2 - - - -
504B ALA* 1.3 79.7 - - - +
506B TYR* 1.3 64.7 + - - -
507B GLN* 2.9 8.3 + - - -
508B ALA* 3.3 8.7 + - - +
509B VAL 4.0 3.6 + - - -
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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