Contacts of the strand formed by residues 570 - 574 (chain A) in PDB entry 2IBI
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 TRP 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A LEU* 4.3 17.1 - - + +
543A LEU* 3.8 31.2 - - + -
544A TYR* 3.7 19.5 - - - -
545A ALA* 4.3 1.3 - - - -
546A VAL* 4.7 0.9 - - + -
561A TYR* 3.6 25.6 - - + -
562A CYS 3.3 22.2 - - - -
563A ARG* 3.4 32.3 - - + +
568A GLY 3.7 13.6 + - - -
569A GLU* 1.3 74.6 - - - +
571A HIS* 1.3 68.2 + - - +
580A PRO* 3.8 2.1 - - - +
581A MET* 3.0 46.4 + - + +
582A SER 4.8 0.9 - - - -
583A SER* 4.0 23.9 - - - -
586A VAL* 3.7 28.5 - - + -
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Residues in contact with HIS 571 (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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266A LEU* 3.5 42.8 - - + +
561A TYR* 3.3 5.4 - - - -
562A CYS 3.0 30.5 + - - -
564A SER* 5.3 2.8 - - - -
569A GLU* 3.9 29.3 + - + -
570A TRP* 1.3 78.4 - - - +
572A THR* 1.3 60.5 + - - +
573A PHE* 3.4 25.2 - - + -
578A VAL* 4.1 11.7 - - + -
579A THR 3.2 7.9 - - - +
580A PRO* 3.5 35.4 - - + +
581A MET* 3.7 6.4 - - - +
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Residues in contact with THR 572 (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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559A THR* 4.7 7.0 - - + -
560A ALA 3.5 3.8 - - - +
561A TYR* 3.4 22.5 - - + -
571A HIS* 1.3 71.2 - - - +
573A PHE* 1.3 66.0 + - - +
574A ASN* 4.6 10.8 - - + +
577A SER 3.5 1.6 - - - +
578A VAL* 3.4 4.3 - - - -
579A THR* 2.7 54.8 + - + +
581A MET* 3.0 28.1 - - - +
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Residues in contact with PHE 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLY 3.7 20.9 - - - -
266A LEU* 4.3 8.3 - - + -
267A ALA 4.3 0.9 - - - -
280A SER* 5.6 1.4 - - - -
283A GLN* 3.4 51.1 - - + +
287A ASN* 4.1 11.7 - - - -
559A THR* 3.5 5.0 - - - -
560A ALA* 2.7 37.1 + - + +
562A CYS* 3.6 31.0 - - + -
571A HIS* 3.4 38.1 - - + -
572A THR* 1.3 71.7 - - - +
574A ASN* 1.3 59.9 + - - +
575A ASP 3.8 3.9 + - - +
577A SER 3.6 3.6 - - - -
578A VAL* 3.7 26.5 - - + -
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Residues in contact with ASN 574 (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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557A HIS* 2.9 29.9 + - - -
558A TYR 4.4 0.4 - - - +
559A THR* 3.8 24.3 - - + +
572A THR* 4.6 9.8 - - + +
573A PHE* 1.3 75.1 - - - +
575A ASP* 1.3 67.6 + - - +
576A SER 3.2 1.6 + - - -
577A SER* 2.7 33.4 + - - +
579A THR* 6.0 0.7 - - + -
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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