Contacts of the strand formed by residues 558 - 563 (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 VAL 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A TRP* 3.4 19.3 - - - +
532A GLY* 3.8 18.3 - - - -
533A SER 3.1 24.6 + - - +
537A LYS 3.9 19.5 - - - +
538A VAL* 3.8 19.5 - - + -
554A ALA* 3.8 27.6 - - + -
556A ALA 3.9 1.6 - - - +
557A ASN* 1.3 75.2 - - - +
559A CYS* 1.3 62.1 + - - +
560A CYS 4.0 3.6 - - - +
561A VAL* 3.9 11.0 - - + -
573A PHE* 3.9 11.2 - - + -
574A GLY 3.6 10.5 - - - +
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Residues in contact with CYS 559 (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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517A TRP* 3.4 36.0 - - + +
518A SER* 3.9 4.2 - - - -
557A ASN* 4.4 15.7 - - - -
558A VAL* 1.3 76.2 - - - +
560A CYS* 1.3 60.8 + - - +
574A GLY 2.9 6.4 + - - -
576A ALA* 4.4 11.0 - - - -
601A ALA* 4.5 14.6 - - - -
602A VAL 3.3 26.2 - - - +
603A SER* 3.9 13.6 - - - +
645A PHE* 5.0 15.0 - - + -
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Residues in contact with CYS 560 (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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518A SER* 3.5 10.7 - - - -
558A VAL* 3.6 2.4 - - - +
559A CYS* 1.3 82.0 - - - +
561A VAL* 1.3 74.9 + - - +
573A PHE* 2.9 10.2 - - - +
574A GLY* 2.9 29.6 + - - +
603A SER 3.6 15.5 - - - +
604A TYR* 4.0 11.0 - - + -
605A ALA* 3.5 35.9 - - - +
606A LYS* 4.6 13.7 - - - -
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Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A SER* 3.0 24.6 + - - +
519A VAL 5.0 0.2 - - - +
520A ASP* 3.8 12.0 - - + +
530A ALA* 3.7 27.4 - - + +
531A SER* 3.9 11.2 - - - +
532A GLY* 3.7 19.7 - - - +
538A VAL* 4.0 10.8 - - + -
558A VAL* 3.9 9.6 - - + -
560A CYS* 1.3 84.4 - - - +
562A LYS* 1.3 74.7 + - - +
571A LEU* 4.7 9.2 - - + -
572A ALA 3.5 6.1 - - - +
573A PHE* 3.8 12.6 - - + -
606A LYS* 5.5 0.2 + - - -
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Residues in contact with LYS 562 (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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428A GLU* 6.0 1.6 - - - -
520A ASP* 3.4 30.4 + - + +
523A LEU* 4.9 11.3 - - - +
560A CYS* 5.4 0.2 - - - -
561A VAL* 1.3 81.9 - - - +
563A PHE* 1.3 68.1 + - - +
571A LEU* 3.4 5.6 - - - +
572A ALA* 2.9 37.7 + - + +
605A ALA 3.6 21.3 - - - +
606A LYS* 3.8 37.7 - - + +
607A PHE* 3.2 21.0 - - + +
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Residues in contact with PHE 563 (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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520A ASP* 2.9 37.0 + - + +
521A PHE 3.5 7.4 - - - +
522A ASN* 3.4 59.9 - - + +
523A LEU* 3.9 12.5 - - + +
528A LEU* 4.8 0.4 - - + -
529A LEU* 3.8 3.6 - - - -
530A ALA* 3.5 28.7 - - + -
540A LEU* 3.7 20.4 - - + -
562A LYS* 1.3 78.1 + - - +
564A SER* 1.3 70.1 + - - +
565A PRO* 3.6 1.2 - - - +
567A SER 5.3 0.4 - - - -
568A ARG 4.5 3.1 - - - -
570A HIS 3.6 13.9 - - - -
571A LEU* 3.9 13.2 - - + +
585A LEU* 4.2 11.0 - - + -
607A PHE* 3.3 12.4 - - - -
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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