Contacts of the helix formed by residues 518 - 523 (chain B) in PDB entry 2XOY
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 CYS 518 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B ARG* 4.9 2.2 - - - -
485B CYS* 3.4 15.7 - - + +
488B CYS* 4.1 4.0 - - - -
490B GLN 5.3 0.9 - - - +
492B MET* 3.5 22.0 - - + -
517B PHE* 1.3 71.1 - - - +
519B HIS* 1.3 67.0 + - - +
520B LEU 3.3 2.9 - - - -
521B TYR* 3.1 13.4 + - - +
522B TRP* 3.1 42.1 + - + +
523B GLY 3.9 0.4 - - - -
524B CYS* 3.5 19.3 - - - -
992B ZN 2.6 30.3 - - - -
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Residues in contact with HIS 519 (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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517B PHE* 3.4 3.2 - - - +
518B CYS* 1.3 79.6 - - - +
520B LEU* 1.3 65.3 + - + +
523B GLY* 3.0 23.2 + - - -
524B CYS* 3.1 44.7 + - + +
529B CYS* 4.7 1.0 - - - -
530B TYR 5.2 1.1 - - - -
531B GLY* 3.8 23.1 - - - -
532B CYS* 3.6 19.9 - - - +
533B LEU 3.8 22.4 - - - +
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Residues in contact with LEU 520 (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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506B ALA* 3.7 11.0 - - + +
507B PRO* 3.8 31.4 - - + +
517B PHE 4.7 1.0 + - - -
518B CYS 3.3 0.4 - - - -
519B HIS* 1.3 83.1 - - + +
521B TYR* 1.3 64.5 + - - +
523B GLY 5.1 0.2 + - - -
533B LEU* 3.2 49.3 - - + +
534B ALA* 4.1 4.9 - - + +
535B PRO* 4.3 15.9 - - + -
599B VAL* 3.8 19.3 - - + -
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Residues in contact with TYR 521 (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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430B GLN* 2.7 35.8 + - - -
474B TYR* 3.7 1.6 - - - +
492B MET* 4.7 2.2 - - + -
493B PRO* 3.7 12.8 - - + +
495B ARG* 3.0 45.6 + - - -
505B VAL* 4.9 5.2 - - + -
506B ALA* 3.7 23.2 - - + +
507B PRO 4.2 1.8 + - - +
508B GLN* 3.5 37.9 - - + +
518B CYS* 3.1 13.4 + - - +
520B LEU* 1.3 82.3 - - - +
522B TRP* 1.3 85.0 + + + +
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Residues in contact with TRP 522 (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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428B CYS* 3.9 0.4 - - - -
429B ARG* 2.8 81.0 + - + +
430B GLN* 3.7 25.6 - - + +
490B GLN* 5.5 3.4 - - + -
491B PRO 3.2 29.2 - - - -
492B MET* 3.6 11.7 - - + -
493B PRO* 3.4 25.8 - - + -
518B CYS* 3.1 37.4 + - + +
521B TYR* 1.3 96.4 - + + +
523B GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 523 (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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429B ARG* 3.1 24.4 + - - -
518B CYS* 3.7 4.3 + - - -
519B HIS* 3.0 24.2 + - - -
520B LEU 4.8 0.2 - - - -
522B TRP* 1.3 77.4 - - - +
524B CYS* 1.3 65.5 + - - -
525B THR* 4.5 2.8 + - - -
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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