Contacts of the strand formed by residues 523 - 528 (chain D) in PDB entry 2Y7Q
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 ILE 523 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478D TRP* 3.0 36.6 - - - -
479D LEU* 3.2 38.0 + - + +
522D PHE* 1.3 83.8 - - + +
524D CYS* 1.3 66.9 + - - +
525D ARG* 4.1 4.5 - - + +
538D GLN* 5.8 1.3 - - - -
539D ARG 3.3 18.6 - - - +
540D ALA* 3.4 19.3 - - + -
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Residues in contact with CYS 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D VAL* 3.8 7.1 - - + +
447D ALA* 5.0 4.9 - - - -
464D CYS* 2.0 54.5 - - - -
466D ILE* 6.1 0.2 - - - -
476D VAL* 4.7 13.7 - - - -
477D GLN 3.8 2.7 - - - -
478D TRP* 3.5 25.3 - - + -
522D PHE 4.3 0.2 + - - -
523D ILE* 1.3 72.5 - - - +
525D ARG* 1.3 61.4 + - - +
526D ALA* 6.4 0.2 - - - -
538D GLN* 3.3 4.7 - - - -
539D ARG 3.0 32.5 + - - +
540D ALA* 4.9 0.4 - - - +
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Residues in contact with ARG 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D PHE* 5.0 4.8 - - - -
350D ILE* 5.2 10.0 - - - +
475D SER 3.5 0.7 - - - +
476D VAL* 3.3 8.5 - - - +
477D GLN* 2.8 69.5 + - + +
479D LEU* 3.3 51.0 - - + +
484D GLN* 5.5 1.0 - - - +
523D ILE* 3.9 4.8 - - + +
524D CYS* 1.3 74.3 - - - +
526D ALA* 1.3 64.9 + - - +
527D VAL* 4.0 16.5 - - + +
536D THR* 4.2 16.8 - - - -
537D VAL 3.9 9.0 - - - +
538D GLN* 4.4 2.0 - - - +
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Residues in contact with ALA 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D PRO* 4.6 8.1 - - + -
445D VAL* 4.0 25.8 - - + -
466D ILE* 4.6 6.5 - - + -
474D ILE* 4.3 18.2 - - + -
475D SER 3.3 6.1 - - - +
476D VAL* 4.7 2.5 - - + -
524D CYS* 3.9 1.0 + - - -
525D ARG* 1.3 74.0 - - - +
527D VAL* 1.3 61.9 + - - +
528D HIS 3.4 3.5 + - - -
531D ALA* 4.6 0.7 - - - +
536D THR* 3.4 3.3 - - - -
537D VAL* 3.0 34.9 + - + +
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Residues in contact with VAL 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D PRO* 3.0 44.9 - - - +
346D PHE* 3.4 29.6 - - + -
349D PHE* 4.8 3.4 - - + -
350D ILE* 3.8 19.5 - - + +
475D SER* 2.7 34.6 + - - +
477D GLN* 4.1 7.0 - - + +
525D ARG* 4.0 18.4 - - + -
526D ALA* 1.3 71.0 - - - +
528D HIS* 1.3 58.7 + - - +
535D GLN 3.6 15.3 - - - +
536D THR* 4.6 0.9 - - - +
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Residues in contact with HIS 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D PRO* 4.3 2.9 - - - -
349D PHE* 4.7 1.8 - - - -
441D ALA 3.5 9.9 + - - -
443D PRO* 3.3 33.7 - - + -
469D PHE* 3.5 21.6 - - + +
471D PRO* 2.8 53.4 - - + +
473D ASP 3.4 13.7 + - - -
474D ILE* 3.8 8.9 - - + +
526D ALA 3.4 4.0 + - - +
527D VAL* 1.3 77.1 - - - +
529D GLU* 1.3 66.4 + - - +
530D ALA* 2.9 33.6 + - - -
531D ALA* 3.2 19.2 + - + +
535D GLN* 3.3 14.1 + - - +
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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