Contacts of the strand formed by residues 479 - 484 (chain B) in PDB entry 2G5T
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 LEU 479 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B ASN* 5.1 10.3 - - + +
453B ARG* 3.6 28.9 - - - +
454B CYS* 4.3 19.3 - - - -
457B TYR* 5.6 0.5 - - - -
470B LEU 3.7 2.4 - - - +
472B CYS* 2.9 33.6 + - + +
477B LEU 3.4 1.0 + - - -
478B PRO* 1.3 74.6 - - - +
480B TYR* 1.3 65.0 + - - +
481B THR* 4.2 16.3 + - + -
493B VAL* 3.6 27.6 - - + -
495B GLU 3.4 16.2 - - - +
496B ASP* 3.7 13.5 - - + -
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Residues in contact with TYR 480 (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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56B LYS 3.6 18.3 + - - -
57B LEU* 3.0 36.4 - - + +
58B TYR* 3.9 22.9 - - + -
469B GLN* 3.9 19.7 - - - +
470B LEU 3.3 4.7 - - - +
471B ARG* 3.4 41.5 - - + -
472B CYS 5.3 2.0 - - - -
473B SER* 6.1 0.7 - - - -
478B PRO* 4.0 24.0 - - + +
479B LEU* 1.3 76.3 - - - +
481B THR* 1.3 61.5 + - - +
493B VAL* 3.7 2.1 - - - +
494B LEU* 2.7 33.2 + - + -
495B GLU* 2.9 29.6 + - + +
497B ASN* 4.3 1.3 - - - -
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Residues in contact with THR 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 5.0 3.1 - - + +
457B TYR* 5.7 0.5 - - - -
469B GLN* 3.2 7.1 - - - +
470B LEU* 2.8 39.3 + - - +
479B LEU* 4.2 19.0 + - + -
480B TYR* 1.3 79.4 - - - +
482B LEU* 1.3 60.8 + - - +
483B HIS* 2.7 29.8 + - - +
492B ARG 3.4 14.4 - - - +
493B VAL* 4.0 17.5 - - + -
494B LEU* 4.0 6.5 - - - +
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 5.2 0.2 - - + -
62B TRP* 3.9 21.3 - - + -
68B TYR* 3.8 26.5 - - + +
81B ALA* 3.9 30.1 - - + +
467B TYR* 4.8 0.9 - - + -
468B TYR 3.3 24.0 - - - +
469B GLN* 4.1 6.7 - - + +
481B THR* 1.3 71.0 - - - +
483B HIS* 1.3 75.5 + - - +
490B GLY* 3.7 0.9 - - - -
491B LEU* 2.8 35.2 + - + +
492B ARG* 3.0 22.1 + - + +
494B LEU* 3.9 23.5 - - + +
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Residues in contact with HIS 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LEU 5.7 1.3 - - - -
449B LEU* 3.9 16.6 - - + +
467B TYR* 3.3 10.4 - - - +
468B TYR* 2.8 65.7 + + + +
470B LEU* 3.5 29.3 - - + +
481B THR* 2.7 39.8 + - - -
482B LEU* 1.3 75.6 + - - +
484B SER* 1.3 61.6 + - - +
488B ASP 4.2 7.6 - - - +
489B LYS 3.4 8.3 - - - +
490B GLY* 3.5 26.4 - - - -
491B LEU* 3.8 6.4 - - - +
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Residues in contact with SER 484 (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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82B GLU* 5.2 2.0 - - - -
466B LYS 3.7 5.6 - - - -
467B TYR* 3.7 22.0 - - - -
468B TYR* 4.2 1.8 - - - -
483B HIS* 1.3 74.9 - - - +
485B SER* 1.3 60.1 + - - +
486B VAL* 3.3 13.3 + - - +
487B ASN* 3.7 2.1 + - - -
488B ASP* 2.8 29.8 + - - -
489B LYS* 3.1 26.0 + - - +
491B LEU* 4.0 11.8 - - - +
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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