Contacts of the strand formed by residues 522 - 527 (chain B) in PDB entry 4CQ8
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 ALA 522 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ILE* 4.0 3.6 - - + +
502B ILE* 3.6 20.6 - - + +
504B ALA* 3.6 30.1 - - + -
517B LYS* 3.0 19.5 + - + +
518B ILE* 3.3 22.8 + - + +
521B GLY* 1.3 78.0 - - - +
523B SER* 1.3 61.5 + - - +
524B VAL 3.9 4.7 - - - +
525B CYS* 5.4 0.2 - - - -
562B ILE* 3.6 10.7 - - - +
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Residues in contact with SER 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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210B THR* 2.7 27.9 + - - +
211B ASN 4.1 19.9 + - - -
212B ILE* 4.1 12.1 - - - -
220B PRO* 4.8 0.9 - - - +
501B PRO* 4.4 8.3 - - - +
502B ILE 2.9 19.5 + - - -
518B ILE* 5.1 2.2 - - - -
521B GLY 3.9 0.7 + - - -
522B ALA* 1.3 73.1 - - - +
524B VAL* 1.4 56.9 + - - +
558B LEU* 3.9 9.4 - - - +
562B ILE* 3.8 27.9 - - - +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR* 3.5 26.7 - - + -
212B ILE* 3.5 31.9 - - + -
217B PHE* 3.9 22.7 - - + -
220B PRO* 3.6 19.5 - - + +
244B PHE* 3.8 22.2 - - + -
502B ILE 3.6 0.4 + - - +
503B ILE* 3.6 16.0 - - + -
504B ALA* 2.8 33.4 + - - +
518B ILE* 5.6 0.4 - - - -
522B ALA* 3.6 2.9 - - - +
523B SER* 1.4 71.8 - - - +
525B CYS* 1.3 59.2 + - - +
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Residues in contact with CYS 525 (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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220B PRO* 2.9 15.6 + - - +
221B PHE* 3.5 16.8 - - + -
222B GLY 3.0 22.9 + - - -
244B PHE* 3.8 6.1 - - - -
504B ALA* 3.6 4.7 - - - -
508B ILE* 3.7 24.5 - - + -
514B ALA* 4.1 33.4 - - - -
517B LYS* 4.3 8.3 - - - -
518B ILE* 4.3 12.6 - - - -
522B ALA* 5.4 0.4 - - - -
524B VAL* 1.3 78.1 - - - +
526B GLN* 1.3 63.5 + - - +
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Residues in contact with GLN 526 (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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222B GLY 3.4 4.3 - - - +
223B VAL 4.3 0.4 + - - -
224B ALA* 3.8 32.3 - - + +
244B PHE* 3.5 20.5 - - + -
246B GLU* 2.9 35.1 + - - +
338B TYR* 3.5 10.5 + - - -
429B LYS* 4.6 2.8 + - - -
455B ILE* 3.6 21.4 - - - +
503B ILE* 3.6 22.2 - - + +
504B ALA 2.8 12.8 + - - +
505B SER* 4.1 11.8 + - - -
508B ILE* 3.7 12.5 - - - +
525B CYS* 1.3 73.3 - - - +
527B LEU* 1.3 66.8 + - - +
800B FMN 4.5 5.2 + - - +
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Residues in contact with LEU 527 (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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221B PHE* 4.1 12.8 - - + -
222B GLY 2.8 16.5 + - - +
223B VAL* 3.5 10.7 - - - +
224B ALA* 3.0 22.6 + - - -
242B PHE* 3.7 28.7 - - + -
508B ILE* 3.7 39.3 - - + +
525B CYS* 4.8 0.4 - - + -
526B GLN* 1.3 81.4 - - - +
528B TYR* 1.3 60.4 + - - +
530B CYS* 4.0 29.6 - - + -
531B LEU* 5.1 4.0 - - + +
538B SER* 4.8 2.9 - - - -
542B ILE* 4.1 25.1 - - + -
800B FMN 4.3 2.2 - - - -
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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