Contacts of the helix formed by residues 517 - 526 (chain X) in PDB entry 2W6C
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 ARG 517 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375X TYR* 4.5 1.8 - - - -
393X ASP* 3.9 27.3 + - - +
397X ASP* 2.9 41.7 + - - -
401X ILE* 4.2 19.9 - - + +
422X PHE* 5.0 8.3 - - + -
515X ARG 3.2 3.0 + - - -
516X LEU* 1.3 84.6 - - + +
518X VAL* 1.4 59.5 + - - +
519X GLN* 3.4 2.7 - - - -
520X MET* 3.3 21.9 + - + +
521X CYS* 2.9 36.9 + - - -
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Residues in contact with VAL 518 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500X GLN* 4.9 4.7 - - - +
515X ARG* 3.1 47.6 - - + +
516X LEU 3.2 4.9 + - - -
517X ARG* 1.4 70.4 - - - +
519X GLN* 1.3 71.1 + - + +
521X CYS* 4.4 3.8 - - - +
522X VAL* 2.7 39.6 + - + +
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Residues in contact with GLN 519 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374X GLN* 4.8 5.6 + - - +
517X ARG 3.4 0.6 - - - -
518X VAL* 1.3 86.4 - - + +
520X MET* 1.3 84.8 + - + +
522X VAL* 3.5 6.2 + - - +
523X PHE* 3.4 13.3 + - - +
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Residues in contact with MET 520 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374X GLN* 3.2 40.2 - - + +
375X TYR* 3.3 46.9 - - - +
397X ASP* 3.6 10.8 - - - +
402X CYS* 4.9 0.4 - - - -
517X ARG* 3.3 29.5 + - + +
518X VAL 3.3 0.4 - - - -
519X GLN* 1.3 98.3 - - + +
521X CYS* 1.3 57.4 + - - +
523X PHE* 3.0 20.9 + - - +
524X TRP* 3.0 18.4 + - - -
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Residues in contact with CYS 521 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401X ILE* 4.1 14.1 - - - -
402X CYS* 2.0 59.7 - - + -
405X MET* 4.5 11.2 - - + -
516X LEU 5.1 0.4 - - - +
517X ARG* 2.9 26.1 + - - +
518X VAL* 4.1 3.8 - - - +
520X MET* 1.3 71.9 - - - +
522X VAL* 1.3 61.1 + - - +
525X ASN* 2.7 44.7 + - - +
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Residues in contact with VAL 522 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518X VAL* 2.7 35.7 + - + +
519X GLN* 3.9 5.6 - - - +
521X CYS* 1.3 72.4 - - - +
523X PHE* 1.3 59.6 + - - +
525X ASN* 5.1 0.7 - - - -
526X GLN* 3.0 34.7 + - + +
527X PHE* 3.0 23.6 + - + +
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Residues in contact with PHE 523 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370X ALA* 3.9 18.8 - - + -
371X VAL* 3.8 33.9 - - + -
374X GLN* 4.2 31.6 - - + +
375X TYR* 4.6 4.3 - + - -
519X GLN 3.4 9.1 + - - +
520X MET* 3.0 10.2 + - - +
522X VAL* 1.3 82.6 - - - +
524X TRP* 1.3 103.7 + + - +
527X PHE* 3.4 33.4 + + + -
528X LEU* 2.8 41.8 + - + +
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Residues in contact with TRP 524 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360X VAL* 3.7 17.0 - - + -
371X VAL* 3.5 21.5 - - + -
375X TYR* 2.9 31.5 + + - -
394X ILE* 4.0 17.0 - - + -
397X ASP* 3.6 6.4 - - + +
398X HIS* 3.4 48.9 - + + +
402X CYS* 3.7 32.3 - - + -
520X MET 3.0 24.8 + - - +
523X PHE* 1.3 91.7 - + - +
525X ASN* 1.3 61.3 + - - +
528X LEU* 3.4 33.5 - - + +
529X PRO* 3.2 19.4 - - - +
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Residues in contact with ASN 525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402X CYS* 3.1 34.5 + - - +
403X PRO* 4.4 2.8 - - - +
405X MET* 4.8 1.4 - - - +
406X HIS* 3.8 35.9 + - + +
521X CYS* 2.7 36.7 + - - +
522X VAL* 5.1 0.9 - - - -
524X TRP* 1.3 77.8 - - - +
526X GLN* 1.3 63.7 + - + +
529X PRO* 3.5 14.2 - - - +
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Residues in contact with GLN 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522X VAL* 3.0 36.6 + - + +
525X ASN* 1.3 83.7 - - + +
527X PHE* 1.3 67.0 + - - +
528X LEU 3.7 0.4 - - - -
529X PRO* 3.8 3.9 - - - +
530X LYS* 3.4 20.6 + - - +
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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