Contacts of the strand formed by residues 499 - 505 (chain B) in PDB entry 1XR2
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 499 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B PRO* 4.8 3.8 - - + -
286B TRP* 3.9 31.2 - - + -
324B LEU* 5.7 2.0 - - + -
328B LEU* 4.5 11.9 - - + -
332B LEU* 4.1 25.1 - - + -
334B PHE* 4.5 11.7 - - + -
479B ILE* 3.3 1.2 - - - -
480B ALA* 2.7 48.6 + - + +
482B THR* 3.9 23.6 - - + -
497B PRO 4.1 6.5 - - - +
498B PRO* 1.3 81.5 - - - +
500B ILE* 1.3 62.2 + - - +
501B TYR* 3.3 6.9 + - - +
541B TYR* 3.7 20.0 - - + -
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Residues in contact with ILE 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B TRP* 3.8 1.4 - - - -
478B GLY 3.4 5.2 - - - +
479B ILE* 4.0 17.5 - - + +
499B ILE* 1.3 71.9 - - - +
501B TYR* 1.3 58.3 + - - +
502B GLY 3.9 7.2 - - - +
504B VAL* 3.6 27.8 - - + -
536B ILE 4.5 1.8 - - - +
537B MET* 3.8 31.6 - - + -
540B SER* 4.1 11.0 - - - -
541B TYR 2.9 19.3 + - - +
542B TYR* 3.4 11.9 - - + -
543B ARG* 3.2 25.4 + - + +
551B ILE* 4.2 14.8 - - + -
555B ILE* 3.9 16.4 - - + -
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Residues in contact with TYR 501 (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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286B TRP* 3.8 12.1 - - + -
325B PRO* 3.6 29.4 - - + +
326B GLY 6.1 0.2 - - - -
328B LEU* 3.6 31.4 - - + -
364B PHE* 3.8 21.6 - + + +
365B ALA* 3.7 25.0 - - + +
478B GLY* 2.8 49.5 + - - -
479B ILE 3.5 6.0 + - - -
480B ALA* 3.5 22.9 - - + -
499B ILE* 3.5 10.1 - - + +
500B ILE* 1.3 73.1 - - - +
502B GLY* 1.3 49.1 + - - -
543B ARG* 2.6 33.6 + - - -
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Residues in contact with GLY 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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365B ALA* 3.4 18.2 - - - -
366B VAL* 5.4 1.3 - - - -
478B GLY* 3.3 8.7 + - - +
500B ILE* 3.5 6.0 - - - +
501B TYR* 1.3 80.8 - - - +
503B THR* 1.3 69.7 + - - +
504B VAL* 3.4 13.7 + - - +
543B ARG* 4.1 8.5 - - - +
546B ILE* 6.2 3.6 - - - -
554B GLN* 4.2 1.7 - - - +
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Residues in contact with THR 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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365B ALA 3.2 7.1 + - - +
366B VAL* 3.5 6.7 - - - +
367B ASP* 2.8 39.4 + - - +
370B ALA* 3.6 29.8 - - + -
371B VAL* 3.6 12.3 - - + +
477B ASN* 3.3 4.7 - - - +
478B GLY* 3.2 14.2 - - - -
502B GLY* 1.3 73.0 - - - +
504B VAL* 1.3 66.8 + - - +
505B THR* 4.0 3.0 + - + +
554B GLN* 3.3 28.4 + - + +
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Residues in contact with VAL 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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370B ALA* 5.2 0.2 - - - +
476B LEU* 4.0 26.0 - - + -
477B ASN 3.1 12.1 - - - +
478B GLY* 4.7 0.2 - - - -
479B ILE* 4.1 12.3 - - + -
500B ILE* 3.6 22.2 - - + -
502B GLY 3.6 13.5 - - - +
503B THR* 1.3 72.8 - - - +
505B THR* 1.3 74.9 + - - +
551B ILE* 5.1 1.6 - - + -
554B GLN* 3.0 36.1 + - + +
555B ILE* 4.2 30.5 - - + -
558B ALA* 4.9 1.1 - - + -
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Residues in contact with THR 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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367B ASP* 4.4 7.4 + - + +
370B ALA* 3.8 27.4 - - + -
476B LEU* 3.5 8.8 - - - +
477B ASN* 2.8 52.0 + - - +
503B THR* 4.0 4.4 + - + +
504B VAL* 1.3 83.1 - - - +
506B ARG* 1.3 62.1 + - - +
507B PRO* 3.6 0.9 - - - +
558B ALA* 4.4 6.1 - - - -
561B GLU* 5.7 0.9 - - - -
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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