Contacts of the strand formed by residues 528 - 533 (chain A) in PDB entry 5HQG
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 LEU 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A PHE* 3.9 7.3 - - - -
522A ASN* 2.9 44.9 + - + +
525A ASP* 3.2 37.2 + - + +
527A LYS* 1.3 81.0 - - + +
529A LEU* 1.3 63.1 + - - +
540A LEU* 4.9 15.3 - - + -
541A TRP 3.3 14.6 - - - +
542A SER* 4.3 14.6 - - - +
549A VAL* 4.4 13.9 - - + -
563A PHE* 5.8 0.2 - - + -
568A ARG 4.9 2.9 - - - +
585A LEU* 6.4 2.0 - - + -
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Residues in contact with LEU 529 (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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487A ALA* 4.2 3.8 - - + -
495A VAL* 4.1 11.2 - - + -
497A LEU* 3.8 26.9 - - + -
509A TYR* 4.6 2.0 - - + -
519A VAL* 3.7 27.1 - - + -
520A ASP 3.2 14.1 - - - +
521A PHE* 3.7 23.8 - - + -
527A LYS 4.2 0.2 - - - +
528A LEU* 1.3 77.0 - - - +
530A ALA* 1.3 60.3 + - - +
540A LEU* 3.5 6.4 - - - +
541A TRP* 2.9 57.7 + - + +
543A THR* 4.2 16.6 - - + +
563A PHE* 3.8 7.2 - - - -
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Residues in contact with ALA 530 (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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519A VAL* 3.2 6.9 - - - +
520A ASP 2.8 31.3 + - - -
529A LEU* 1.3 76.6 - - - +
531A SER* 1.3 61.3 + - - +
538A VAL* 4.5 3.4 - - + -
539A LYS 3.3 10.1 - - - +
540A LEU* 4.1 7.0 - - + -
541A TRP* 4.5 2.9 - - - -
561A VAL* 3.7 8.9 - - + +
563A PHE* 3.5 20.0 - - + -
571A LEU* 3.5 22.9 - - + -
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Residues in contact with SER 531 (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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495A VAL* 3.7 23.5 - - - +
512A HIS* 3.0 14.4 + - - -
516A CYS* 3.7 4.5 - - - -
518A SER 3.0 15.5 - - - -
519A VAL* 4.4 2.7 - - - -
530A ALA* 1.3 77.0 - - - +
532A GLY* 1.3 59.8 + - - +
537A LYS 3.9 0.3 - - - +
538A VAL* 3.2 6.2 - - - +
539A LYS 2.9 29.0 + - - -
541A TRP* 2.8 26.6 + - - -
561A VAL* 3.9 7.6 - - - -
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Residues in contact with GLY 532 (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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512A HIS* 4.5 0.4 - - - -
516A CYS* 3.4 6.0 - - - -
517A TRP* 2.8 31.2 + - - +
518A SER* 3.1 12.0 + - - -
531A SER* 1.3 74.4 - - - +
533A SER* 1.3 55.5 + - - -
537A LYS 3.5 8.7 - - - -
538A VAL* 4.5 0.2 - - - -
558A VAL* 3.8 24.5 - - - -
561A VAL* 3.7 7.4 - - - +
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Residues in contact with SER 533 (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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512A HIS* 3.2 31.6 - - - -
514A LYS 2.9 13.5 + - - -
515A ARG 2.6 22.6 + - - -
516A CYS* 3.9 2.2 - - - +
517A TRP 4.2 0.7 - - - +
532A GLY* 1.3 74.8 - - - -
534A ASP* 1.3 64.0 + - - +
535A ASP* 3.0 22.0 + - - +
536A ALA 3.1 7.3 + - - -
537A LYS 3.3 5.3 + - - -
558A VAL* 3.1 27.9 + - - +
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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