Contacts of the strand formed by residues 499 - 509 (chain B) in PDB entry 1XI1
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 THR 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B LEU* 2.9 34.6 + - + +
496B ARG* 2.9 23.7 + - + +
497B GLN 3.1 11.1 + - - -
498B LYS* 1.3 81.0 + - - +
500B TYR* 1.3 60.6 + - - +
529B LYS 3.2 3.1 - - - -
530B CYS* 4.1 21.6 - - - -
531B ALA* 4.6 3.5 + - - +
546B PHE* 3.6 20.6 - - + -
574B ILE* 4.2 14.8 - - + -
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Residues in contact with TYR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B TYR* 3.8 31.9 - + - -
456B ASP* 5.8 0.2 - - - -
461B HIS* 3.6 15.3 + + - -
493B LYS 3.1 14.1 - - - +
494B TYR* 3.4 30.1 - + + -
498B LYS* 4.8 2.5 - - - -
499B THR* 1.3 80.8 - - - +
501B ILE* 1.3 70.2 + - - +
502B GLN* 3.5 40.9 + - + -
527B SER* 5.7 1.1 - - - -
528B VAL* 4.0 0.3 - - - +
529B LYS* 3.0 65.1 + - + +
546B PHE* 3.9 3.3 - - - -
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ALA* 3.0 7.5 - - - +
493B LYS* 2.9 55.6 + - + +
500B TYR* 1.3 80.3 - - - +
502B GLN* 1.3 63.9 + - - +
526B PHE* 3.9 12.6 - - + -
527B SER 3.5 4.0 - - - -
528B VAL* 3.6 28.0 - - + -
541B VAL* 4.2 0.2 - - + -
543B PHE* 3.6 36.1 - - + -
546B PHE* 3.4 42.8 - - + -
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Residues in contact with GLN 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B VAL* 4.0 9.5 - - - +
461B HIS* 3.7 9.5 + - - -
487B SER* 5.0 1.6 + - - -
489B PHE* 3.6 27.4 - - + -
491B ARG 3.5 9.9 - - - +
492B ALA* 3.9 6.1 - - + -
494B TYR* 2.8 26.3 + - - -
500B TYR* 3.5 29.6 + - + -
501B ILE* 1.3 80.3 - - - +
503B ASP* 1.3 62.0 + - - +
504B ILE* 3.7 23.1 + - + +
525B LYS 3.6 1.0 - - - +
526B PHE* 3.5 6.5 - - - -
527B SER* 3.1 37.3 + - - +
543B PHE* 4.5 1.3 - - - -
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Residues in contact with ASP 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B PHE* 3.1 3.2 - - - -
490B LYS* 2.8 34.0 + - + +
491B ARG* 2.5 62.3 + - + +
502B GLN* 1.3 69.8 - - - +
504B ILE* 1.3 61.3 + - - +
505B TYR 3.9 0.2 + - - -
524B ILE* 3.6 25.9 - - + +
525B LYS 3.4 2.9 - - - -
526B PHE* 3.5 27.9 + - - +
543B PHE* 3.4 7.0 - - - -
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Residues in contact with ILE 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B SER* 4.1 24.5 - - - +
488B THR 3.7 12.8 - - - +
489B PHE* 4.3 2.7 - - + +
502B GLN* 4.0 26.0 - - + +
503B ASP* 1.3 72.8 - - - +
505B TYR* 1.3 74.2 + - - +
506B MET* 3.1 28.9 + - + +
515B GLU* 4.3 7.0 - - + +
524B ILE* 3.5 3.5 - - - -
525B LYS* 2.8 35.2 + - + +
527B SER* 3.7 23.1 - - - +
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Residues in contact with TYR 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLU* 2.9 21.5 + - - -
488B THR* 3.2 32.1 + - + +
489B PHE 3.6 22.0 - - - -
490B LYS* 3.5 28.5 + - + +
503B ASP 3.9 0.2 + - - -
504B ILE* 1.3 75.8 - - - +
506B MET* 1.3 61.4 + - - +
516B GLY 2.7 44.6 + - - +
517B SER 4.1 2.5 - - - -
518B PRO* 3.8 23.9 - - + +
521B TYR* 3.5 38.4 - + + -
523B ASP 3.7 3.6 - - - -
524B ILE* 3.5 23.6 - - + -
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Residues in contact with MET 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B ILE* 3.1 38.3 + - + +
505B TYR* 1.3 80.6 - - - +
507B LYS* 1.3 54.1 + - - +
513B LEU* 3.4 26.2 - - + +
514B VAL 3.0 27.8 - - - +
515B GLU* 4.1 7.9 - - - +
516B GLY 4.2 1.3 - - - -
521B TYR* 3.1 6.8 - - - +
522B THR 2.7 30.0 + - - -
523B ASP* 2.7 33.1 + - + +
525B LYS* 3.0 44.0 - - + +
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Residues in contact with LYS 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B MET* 1.3 77.7 - - - +
508B GLU* 1.3 63.8 + - - +
509B VAL* 3.1 32.8 + - + +
513B LEU* 3.4 5.8 - - - -
514B VAL* 2.9 32.1 + - + +
515B GLU 4.4 4.3 - - - +
516B GLY* 4.1 15.0 - - - -
520B ASP* 2.7 53.8 + - + +
521B TYR* 4.3 1.6 - - - -
522B THR* 4.0 8.1 - - - +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B LYS* 1.3 73.9 - - - +
509B VAL* 1.3 62.1 + - - +
510B ASP 4.2 1.2 + - - +
511B GLY* 3.3 27.8 + - - +
512B LYS 3.6 13.8 - - - +
513B LEU* 3.9 18.1 - - + +
522B THR* 3.9 22.1 + - + +
523B ASP* 5.0 1.2 - - - +
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LYS* 3.1 43.7 + - + +
508B GLU* 1.3 78.6 - - - +
510B ASP* 1.3 74.9 + - + +
512B LYS 3.2 11.3 + - - +
514B VAL* 3.9 22.6 - - + +
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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