Contacts of the strand formed by residues 591 - 598 (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 ALA 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A LEU* 3.3 7.9 - - + +
504A ARG* 2.8 31.2 + - - +
519A VAL 5.5 0.7 - - - +
521A PHE* 3.5 37.7 - - + -
546A VAL* 3.8 10.1 - - + -
548A ASN* 3.5 15.2 - - - +
588A THR* 3.5 10.8 + - - +
589A SER 3.3 0.4 - - - -
590A ASP* 1.3 72.6 - - - +
592A TYR* 1.3 59.7 + - - +
594A LEU* 4.2 4.9 - - + -
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Residues in contact with TYR 592 (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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357A ASP* 2.5 36.1 + - - -
359A GLN* 4.4 6.5 - - + -
500A LEU 3.7 0.5 - - - +
501A HIS* 2.8 30.0 + + - -
502A LEU* 3.0 58.6 + - - +
504A ARG* 4.1 8.3 - - + +
505A PHE* 3.5 15.6 - + - -
547A SER 2.9 12.2 + - - +
549A HIS* 4.3 8.3 - - + +
558A TYR* 3.6 28.7 - + - -
590A ASP 3.3 7.6 + - - +
591A ALA* 1.3 75.5 - - - +
593A LEU* 1.3 69.7 + - + +
42B ARG* 4.4 0.3 + - - -
73B LEU* 3.5 30.7 - - + -
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Residues in contact with LEU 593 (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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281A ILE* 3.9 27.8 - - + -
358A ALA* 4.2 2.0 - - + -
359A GLN* 4.0 30.5 - - + +
362A LEU* 4.6 5.8 - - + -
499A VAL* 3.8 24.9 - - + -
500A LEU 3.3 4.7 - - - +
501A HIS* 3.8 35.0 - - + -
546A VAL* 3.2 8.8 - - - +
547A SER* 2.8 40.7 + - - +
592A TYR* 1.3 83.6 - - + +
594A LEU* 1.3 61.8 + - - +
595A PHE* 4.1 12.3 - - + -
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Residues in contact with LEU 594 (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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455A LEU* 3.7 29.4 - - + -
498A LEU 3.4 3.8 - - - +
499A VAL* 3.4 2.9 - - - +
500A LEU* 2.9 43.5 + - + +
502A LEU* 4.6 13.9 - - + -
519A VAL* 6.1 0.2 - - + -
521A PHE* 3.5 57.0 - - + -
543A LEU* 3.9 1.8 - - + -
545A ALA 3.7 2.7 - - - -
546A VAL* 4.0 11.9 - - + -
591A ALA* 4.2 5.4 - - + -
593A LEU* 1.3 79.8 - - - +
595A PHE* 1.3 63.6 + - - +
596A TYR* 3.6 22.6 - - + -
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Residues in contact with PHE 595 (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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281A ILE* 4.4 15.7 - - + -
284A CYS* 3.4 36.1 - - + -
285A LEU* 4.7 7.4 - - + -
288A THR* 4.8 1.8 - - - -
362A LEU* 4.4 21.1 - - + -
415A PHE* 4.9 0.9 - + - -
497A ILE* 4.8 1.1 - - + -
498A LEU 3.8 2.2 - - - -
499A VAL* 3.8 28.9 - - + -
543A LEU* 3.4 5.0 - - - +
544A TYR* 2.9 59.8 + + + -
545A ALA* 2.7 30.7 + - + +
547A SER* 4.4 2.5 - - - -
593A LEU* 4.1 24.2 - - + -
594A LEU* 1.3 73.3 - - - +
596A TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 596 (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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455A LEU* 3.4 23.0 - - + +
497A ILE* 3.5 5.0 - - - +
498A LEU* 2.9 42.4 + - + +
500A LEU* 4.1 11.9 - - + -
521A PHE* 3.5 10.7 - - - +
522A PRO* 3.0 42.3 + - + +
523A LEU 4.7 0.7 - - - -
526A LEU* 4.0 19.1 - - + -
541A TYR* 3.6 29.6 - - + -
542A ASN 3.3 6.7 - - - -
543A LEU* 3.4 40.4 - - + -
544A TYR* 3.6 6.2 - - - -
594A LEU* 3.6 18.6 - - + -
595A PHE* 1.3 74.8 - - - +
597A GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 597 (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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287A ASN 5.6 0.3 - - - +
289A ARG* 4.3 28.2 + - - +
496A LYS 3.7 5.4 - - - +
497A ILE* 3.9 13.5 - - + +
541A TYR* 3.2 7.4 - - - -
542A ASN* 2.7 49.9 + - + +
544A TYR* 3.7 24.0 - - + +
563A ARG* 2.8 28.2 + - - +
596A TYR* 1.3 73.4 - - - +
598A LEU* 1.3 68.8 + - - +
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Residues in contact with LEU 598 (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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494A PHE* 5.4 4.9 - - + +
495A PRO 4.1 2.5 - - - +
496A LYS* 3.3 41.3 + - + +
538A HIS 5.3 2.9 - - - +
539A ALA* 5.0 6.5 - - + -
540A VAL 3.6 16.4 - - - +
541A TYR* 3.3 29.4 - - + +
597A GLU* 1.3 82.4 - - - +
599A ALA* 1.3 64.9 + - - +
600A SER 4.0 1.0 + - - -
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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