Contacts of the strand formed by residues 495 - 505 (chain E) in PDB entry 6Q2J
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 GLN 495 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E LEU* 5.8 2.2 - - - -
486E VAL* 3.3 23.4 - - + +
487E ALA 3.0 13.5 - - - +
488E THR* 4.1 13.2 - - + +
493E SER 3.0 11.8 + - - +
494E ARG* 1.3 76.2 - - - +
496E ALA* 1.3 66.0 + - - +
497E GLN* 5.4 12.3 + - + +
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Residues in contact with ALA 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E LEU* 3.2 29.4 - - + +
403E HIS* 4.8 2.2 - - - -
404E LEU* 4.4 14.2 - - + +
485E VAL 3.8 0.7 - - - +
486E VAL* 4.8 0.4 - - - -
487E ALA* 2.8 37.3 + - + +
495E GLN* 1.3 79.3 - - - +
497E GLN* 1.3 63.2 + - - +
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Residues in contact with GLN 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E LEU* 4.5 7.3 - - - +
405E PRO 5.0 1.7 - - - +
406E SER* 5.8 1.0 - - - -
484E MET* 3.5 37.1 - - + +
485E VAL 3.1 11.0 - - - +
486E VAL* 4.6 10.9 - - + +
495E GLN* 5.4 11.9 + - + +
496E ALA* 1.3 78.1 - - - +
498E ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E LEU* 3.7 18.3 - - + +
405E PRO 3.4 24.2 - - - +
406E SER 4.2 4.7 - - - +
408E TYR* 3.9 18.6 - - + -
484E MET* 3.3 11.4 - - - +
485E VAL* 2.9 34.2 + - + +
497E GLN* 1.3 72.8 - - - +
499E GLN* 1.3 64.2 + - - +
500E LEU 4.1 0.2 - - - -
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Residues in contact with GLN 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406E SER 3.5 11.7 + - - +
407E THR* 3.6 14.3 + - - +
408E TYR* 3.3 22.8 + - - +
483E TYR 3.5 4.9 - - - +
484E MET* 3.7 30.5 - - + +
498E ALA* 1.3 74.6 - - - +
500E LEU* 1.3 61.7 + - - +
501E LEU* 3.6 19.7 + - + +
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Residues in contact with LEU 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E TYR* 3.9 19.5 - - + +
410E LEU* 3.7 33.4 - - + +
442E LEU* 4.9 5.8 - - + -
452E LEU* 4.3 9.2 - - + -
465E LEU* 4.2 22.4 - - + -
481E LEU 3.3 6.6 - - - +
482E HIS* 3.4 2.8 - - - -
483E TYR* 2.9 62.1 + - + +
485E VAL* 4.4 12.7 - - + +
498E ALA 4.1 1.2 - - - -
499E GLN* 1.3 70.4 - - - +
501E LEU* 1.3 61.8 + - - +
502E VAL* 3.7 25.6 - - + -
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Residues in contact with LEU 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E THR* 3.7 27.6 - - + +
408E TYR 3.4 16.2 + - - +
409E SER* 4.4 4.6 - - - -
410E LEU 4.1 8.1 + - - +
481E LEU 3.7 4.5 - - - -
482E HIS* 3.3 32.3 - - + +
499E GLN* 4.4 20.6 - - + +
500E LEU* 1.3 72.6 - - - +
502E VAL* 1.3 59.9 + - - +
503E THR* 3.9 9.8 + - + +
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Residues in contact with VAL 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E LEU* 3.7 24.5 - - + +
412E VAL* 3.7 29.8 - - + -
422E ILE* 5.8 0.2 - - + -
452E LEU* 3.9 14.8 - - + -
465E LEU* 6.1 0.7 - - + -
480E GLU* 3.7 2.8 - - - +
481E LEU* 2.9 60.1 + - + +
483E TYR* 3.9 17.5 - - + -
500E LEU* 3.7 15.3 - - + -
501E LEU* 1.3 74.8 - - - +
503E THR* 1.3 63.5 + - - +
504E VAL* 4.1 2.7 + - + +
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Residues in contact with THR 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E LEU 3.5 10.6 + - - +
411E SER* 3.7 7.8 - - - -
412E VAL 3.2 18.3 + - - -
479E ALA 3.8 6.7 - - - -
480E GLU* 4.5 18.4 - - + +
501E LEU* 4.2 9.9 - - + +
502E VAL* 1.3 81.7 - - - +
504E VAL* 1.3 66.4 + - - +
505E GLU* 3.1 12.8 + - - +
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Residues in contact with VAL 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E VAL* 3.6 14.6 - - + +
413E SER 5.1 0.2 - - - -
414E ARG* 4.0 35.8 + - + +
451E THR* 5.7 0.7 - - + -
473E LEU* 3.9 46.4 - - + +
478E CYS 4.2 15.5 - - - +
479E ALA* 3.2 23.6 + - - +
481E LEU* 4.6 15.3 - - + -
502E VAL* 4.1 3.1 + - + +
503E THR* 1.3 68.8 - - - +
505E GLU* 1.3 59.7 + - - +
506E GLY 4.2 1.1 + - - -
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Residues in contact with GLU 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411E SER* 3.5 22.6 + - - -
412E VAL 2.7 24.2 + - - +
413E SER* 3.3 6.6 + - - -
414E ARG 3.2 12.5 + - - -
503E THR* 3.1 13.8 + - - +
504E VAL* 1.3 73.5 - - - +
506E GLY* 1.3 62.8 + - - +
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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