Contacts of the strand formed by residues 494 - 501 (chain A) in PDB entry 5JG8
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 GLY 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LEU* 5.0 0.9 - - - -
483A PRO* 4.1 6.5 - - - +
484A SER 3.4 10.6 + - - +
485A ALA* 3.0 28.9 + - - +
492A ASN 3.7 0.2 + - - -
493A PRO* 1.3 77.2 - - - +
495A TYR* 1.3 65.6 + - - +
516A THR* 5.5 0.2 - - - -
517A TYR 2.8 15.3 - - - -
518A ILE* 4.0 4.9 - - - -
533A TRP* 4.4 1.3 - - - -
576A LYS* 4.4 6.7 - - - -
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Residues in contact with TYR 495 (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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202A LEU* 3.8 18.2 - - + -
203A PHE 3.9 3.6 - - - +
204A LEU* 3.8 23.6 - - + +
260A LEU* 3.3 38.5 + - + -
263A GLY 4.1 11.1 + - - -
264A LEU* 3.7 24.4 - - + +
267A ALA 5.8 0.9 - - - -
270A PHE* 5.5 0.7 - + - -
483A PRO* 5.1 6.1 - - - -
485A ALA* 5.6 0.2 - - + -
494A GLY* 1.3 75.9 - - - +
496A ARG* 1.3 62.4 + - - +
497A VAL* 4.6 2.7 - - + -
516A THR* 3.5 8.0 - - - +
517A TYR* 2.9 65.3 + + + +
533A TRP* 3.6 38.6 + + - +
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Residues in contact with ARG 496 (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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202A LEU* 3.3 4.3 - - - +
203A PHE* 2.9 37.8 + - + +
461A ASP* 2.5 43.6 + - - -
462A GLU 4.9 1.6 + - - -
480A PHE* 4.7 4.4 - - - +
481A LEU 4.0 4.6 + - - -
482A ALA* 4.0 21.6 - - + +
483A PRO* 3.7 12.7 - - + +
495A TYR* 1.3 77.0 - - - +
497A VAL* 1.3 85.8 + - - +
498A TYR* 3.0 48.3 + - + -
514A HIS* 3.5 22.9 + - - -
515A GLU 3.4 6.1 - - - +
516A THR* 2.9 22.4 + - - +
537A TYR* 2.9 6.1 + - - -
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Residues in contact with VAL 497 (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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200A ARG* 3.8 25.8 - - - +
201A ILE 3.4 12.3 - - - +
202A LEU* 4.0 7.4 - - + -
267A ALA 4.4 2.5 - - - +
270A PHE* 3.7 26.9 - - + -
495A TYR* 4.6 1.6 - - + -
496A ARG* 1.3 83.1 - - - +
498A TYR* 1.3 69.8 + - - +
499A GLN* 3.9 13.5 - - - +
514A HIS* 3.1 4.2 - - - +
515A GLU* 2.8 41.6 + - - +
517A TYR* 4.0 21.1 - - + -
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Residues in contact with TYR 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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199A SER 3.5 1.7 - - - +
200A ARG* 3.4 6.2 - - - -
201A ILE* 2.9 40.3 + - + +
203A PHE* 3.7 23.5 - + + -
454A PHE* 3.5 35.3 - + - -
480A PHE* 3.1 33.3 + + - +
482A ALA* 4.4 5.2 - - - +
496A ARG* 3.0 40.8 + - + -
497A VAL* 1.3 74.8 - - - +
499A GLN* 1.3 62.2 + - - +
500A ILE* 3.8 22.3 - - + +
511A VAL* 3.8 15.0 - - + -
513A ASP 3.5 0.9 - - - +
514A HIS* 3.4 24.2 - - + -
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Residues in contact with GLN 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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198A VAL* 4.2 17.3 - - + -
199A SER 3.9 3.4 - - - -
200A ARG* 2.8 39.2 - - + +
497A VAL* 3.9 8.9 - - - +
498A TYR* 1.3 70.1 - - - +
500A ILE* 1.3 53.0 + - - +
511A VAL* 3.5 1.4 - - - -
512A LEU* 2.5 37.7 + - + -
513A ASP* 2.9 40.1 + - + +
514A HIS* 3.8 3.6 + - - -
515A GLU* 3.5 31.0 + - - +
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Residues in contact with ILE 500 (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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198A VAL* 3.5 5.9 - - - +
199A SER* 2.8 35.1 + - - +
201A ILE* 3.1 38.6 - - + -
421A HIS* 4.0 17.3 - - + +
454A PHE* 4.2 12.3 - - + -
498A TYR* 3.8 20.4 - - + -
499A GLN* 1.3 79.1 - - - +
501A ASP* 1.3 73.6 - - - +
502A GLY 3.1 0.2 + - - -
509A HIS* 3.6 23.3 - - - +
510A VAL 3.5 14.1 - - - +
511A VAL* 4.2 8.1 - - + +
512A LEU* 3.9 4.3 - - - -
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Residues in contact with ASP 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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190A SER 5.5 0.9 - - - +
192A PRO* 3.7 27.1 - - - +
196A ALA* 4.8 0.2 - - - +
197A PRO 3.9 5.0 - - - +
199A SER* 4.5 1.9 - - - -
372A TYR* 5.7 0.3 - - - -
500A ILE* 1.3 78.3 - - - +
502A GLY* 1.3 68.2 + - - +
504A TYR* 2.7 28.5 + - - -
507A SER* 3.2 6.5 + - - -
508A SER* 3.0 32.3 + - - +
509A HIS* 3.5 29.5 + - - +
510A VAL 3.1 9.2 + - - +
512A LEU* 3.7 12.4 - - + +
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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