Contacts of the strand formed by residues 522 - 527 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A ILE* 4.0 3.4 - - + +
502A ILE* 3.6 20.2 - - + +
504A ALA* 3.6 30.3 - - + -
517A LYS* 3.0 20.5 + - + +
518A ILE* 3.3 23.2 + - + +
521A GLY* 1.3 78.0 - - - +
523A SER* 1.3 61.1 + - - +
524A VAL 3.6 5.2 - - - +
562A ILE* 3.6 10.7 - - - +
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 2.7 29.7 + - - +
211A ASN 4.1 10.6 + - - -
212A ILE* 4.1 21.8 - - - -
220A PRO* 4.8 1.2 - - - +
501A PRO* 4.4 7.4 - - - +
502A ILE 2.9 20.7 + - - -
518A ILE* 5.0 2.7 - - - -
521A GLY 3.8 0.9 + - - -
522A ALA* 1.3 72.7 - - - +
524A VAL* 1.4 56.4 + - - +
558A LEU* 4.0 9.0 - - - +
562A ILE* 3.8 26.5 - - - +
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A THR* 3.5 25.4 - - + -
212A ILE* 3.4 32.8 - - + -
217A PHE* 3.9 21.3 - - + -
220A PRO* 3.6 19.7 - - + +
244A PHE* 3.8 21.5 - - + -
502A ILE 3.6 0.5 + - - +
503A ILE* 3.6 16.8 - - + -
504A ALA* 2.8 33.3 + - - +
518A ILE* 5.7 0.4 - - - -
522A ALA* 3.6 2.6 - - - +
523A SER* 1.4 72.9 - - - +
525A CYS* 1.3 58.6 + - - +
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Residues in contact with CYS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PRO* 2.9 17.3 + - - +
221A PHE* 3.5 18.4 - - + -
222A GLY 3.0 22.5 + - - -
244A PHE* 3.8 5.1 - - - -
504A ALA* 3.6 4.7 - - - -
508A ILE* 3.7 23.6 - - + -
514A ALA* 4.1 33.2 - - - -
517A LYS* 4.3 8.1 - - - -
518A ILE* 4.4 12.8 - - - -
524A VAL* 1.3 77.0 - - - +
526A GLN* 1.3 63.3 + - - +
527A LEU* 4.8 0.2 - - + -
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Residues in contact with GLN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLY 3.4 4.5 - - - +
223A VAL 4.3 0.6 + - - -
224A ALA* 3.8 31.6 - - + +
244A PHE* 3.5 21.0 - - + -
246A GLU* 2.9 35.2 + - - +
338A TYR* 3.5 11.5 + - - -
429A LYS* 4.6 3.8 + - - -
455A ILE* 3.6 20.1 - - - +
503A ILE* 3.6 23.3 - - + +
504A ALA 2.8 13.5 + - - +
505A SER* 4.1 13.5 + - - -
508A ILE* 3.7 12.5 - - - +
525A CYS* 1.3 73.0 - - - +
527A LEU* 1.3 67.3 + - - +
800A FMN 4.5 5.2 + - - -
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A PHE* 4.1 16.4 - - + -
222A GLY 2.8 14.8 + - - +
223A VAL* 3.5 10.6 - - - +
224A ALA* 3.0 22.1 + - - -
242A PHE* 3.7 26.9 - - + -
508A ILE* 3.7 39.9 - - + +
525A CYS* 4.8 0.2 - - + -
526A GLN* 1.3 82.0 - - - +
528A TYR* 1.3 61.3 + - - +
530A CYS* 4.0 29.4 - - + -
531A LEU* 5.1 4.2 - - + +
538A SER* 4.7 2.9 - - - -
542A ILE* 4.1 22.2 - - + -
800A FMN 4.3 2.9 - - - -
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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