Contacts of the strand formed by residues 497 - 502 (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 ILE 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A THR* 4.0 20.0 - - + -
289A ARG 5.8 1.1 - - - +
290A GLU* 5.9 5.6 - - + +
414A LEU* 2.8 34.0 + - + +
415A PHE* 3.6 34.4 - - + +
439A TRP 5.1 0.2 - - - +
495A PRO* 3.4 17.8 - - - +
496A LYS* 1.3 81.3 - - + +
498A LEU* 1.3 62.1 + - - +
499A VAL* 3.8 10.6 + - + -
544A TYR* 3.3 40.6 - - + +
595A PHE* 4.8 1.3 - - + -
596A TYR 3.5 5.4 - - - +
597A GLU* 3.9 14.4 - - + +
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Residues in contact with LEU 498 (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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438A PHE* 3.9 18.2 - - + -
440A ASP* 5.6 0.7 - - - -
441A LEU* 4.1 14.4 - - + -
459A MET* 5.5 0.4 - - - -
491A ILE* 6.3 0.4 - - + -
494A PHE* 5.8 1.8 - - + -
495A PRO* 3.6 22.4 - - + -
497A ILE* 1.3 71.7 - - - +
499A VAL* 1.3 63.1 + - - +
500A LEU* 3.8 30.5 + - + -
526A LEU* 4.8 2.5 - - + -
528A LEU* 3.6 30.1 - - + -
541A TYR* 3.7 30.5 - - + +
594A LEU 3.4 4.2 - - - +
596A TYR* 2.9 39.9 + - + +
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Residues in contact with VAL 499 (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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362A LEU* 3.8 16.4 - - + -
363A ARG* 5.0 0.4 - - - +
415A PHE* 3.7 37.0 - - + -
439A TRP 4.1 5.1 + - - +
440A ASP* 3.3 23.5 - - + +
441A LEU 2.9 25.6 + - - -
497A ILE* 3.8 3.2 + - + -
498A LEU* 1.3 74.4 - - - +
500A LEU* 1.3 63.7 + - - +
593A LEU* 3.8 24.9 - - + -
594A LEU 3.4 6.3 - - - +
595A PHE* 3.8 23.1 - - + -
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A LEU* 3.6 38.6 - - + -
443A LEU* 3.9 17.7 - - + -
455A LEU* 4.0 29.6 - - + -
459A MET* 4.0 15.5 - - + -
498A LEU* 4.0 26.7 - - + +
499A VAL* 1.3 76.9 - - - +
501A HIS* 1.3 61.6 + - - +
502A LEU* 4.0 2.0 + - + +
526A LEU* 4.4 2.0 - - + -
592A TYR 3.7 1.2 - - - +
593A LEU* 3.3 7.5 - - - -
594A LEU* 2.9 50.8 + - + +
596A TYR* 4.1 11.7 - - + -
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Residues in contact with HIS 501 (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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359A GLN* 3.6 37.7 - - + +
440A ASP* 5.0 4.9 - - + +
441A LEU 2.8 13.1 + - - +
442A SER* 2.7 29.0 + - - +
443A LEU* 2.7 33.2 + - - +
500A LEU* 1.3 71.5 - - - +
502A LEU* 1.3 64.3 + - - +
503A LYS* 5.2 0.2 - - + -
505A PHE* 4.3 6.3 - + - -
592A TYR* 2.8 48.0 + + - -
593A LEU* 3.8 15.3 - - + -
42B ARG* 4.2 0.7 - - - -
70B VAL* 3.6 25.4 - - + -
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Residues in contact with LEU 502 (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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443A LEU* 3.9 13.5 - - + -
445A ILE* 4.4 6.1 - - + -
455A LEU* 4.3 24.2 - - + -
458A CYS* 5.6 2.5 - - + -
500A LEU 4.5 6.7 - - - +
501A HIS* 1.3 78.5 - - - +
503A LYS* 1.3 60.2 + - - +
504A ARG* 2.8 35.0 + - + +
519A VAL* 4.3 23.8 - - + +
521A PHE* 5.6 0.7 - - + -
591A ALA* 3.3 31.9 - - + +
592A TYR* 3.0 37.8 + - - +
594A LEU* 4.6 11.9 - - + -
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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