Contacts of the strand formed by residues 496 - 504 (chain F) in PDB entry 6Q2N
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 ALA 496 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402F LEU* 3.5 26.2 - - + +
403F HIS* 5.5 0.7 - - - -
404F LEU* 5.0 6.3 - - + +
486F VAL* 3.3 8.8 - - - +
487F ALA* 2.9 35.5 + - + +
495F GLN* 1.3 79.3 - - - +
497F GLN* 1.3 69.7 + - - +
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Residues in contact with GLN 497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F LEU* 4.9 5.5 - - - +
406F SER* 4.4 7.8 + - - -
484F MET* 3.3 36.2 - - + +
485F VAL 3.1 12.6 - - - +
486F VAL* 3.9 16.7 - - + +
487F ALA 4.6 0.2 - - - +
495F GLN* 6.0 2.0 + - - +
496F ALA* 1.3 82.2 - - - +
498F ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F LEU* 3.7 21.8 - - + -
405F PRO 3.6 24.0 - - - +
406F SER* 3.6 11.7 - - - +
408F TYR* 4.1 8.1 - - + +
484F MET* 3.3 16.6 - - - +
485F VAL* 2.8 30.0 + - - +
497F GLN* 1.3 77.5 - - - +
499F GLN* 1.3 60.4 + - - +
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Residues in contact with GLN 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F SER* 2.8 32.4 + - - +
407F THR* 4.4 12.7 + - - +
408F TYR* 3.6 21.2 + - - +
483F TYR 5.2 0.2 - - - -
484F MET* 3.6 28.5 - - + +
498F ALA* 1.3 70.8 - - - +
500F LEU* 1.3 63.6 + - - +
501F LEU* 3.9 18.3 + - + +
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Residues in contact with LEU 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408F TYR* 3.5 35.1 + - + +
410F LEU* 4.1 25.1 - - + -
442F LEU* 5.9 0.9 - - + -
452F LEU* 4.7 10.5 - - + -
465F LEU* 6.1 4.0 - - + -
482F HIS* 3.7 5.9 + - - +
483F TYR* 3.0 54.9 + - + +
485F VAL* 4.4 12.1 - - + -
498F ALA 3.9 0.2 + - - -
499F GLN* 1.3 73.5 - - - +
501F LEU* 1.3 72.6 + - - +
502F VAL* 3.7 29.3 + - + +
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Residues in contact with LEU 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407F THR* 4.8 18.2 - - + -
408F TYR 3.4 8.3 + - - +
409F SER* 3.3 32.4 - - - -
410F LEU 3.8 0.2 + - - -
480F GLU* 4.7 10.5 - - - +
481F LEU 4.2 2.9 - - - +
482F HIS* 3.5 34.3 - - + +
499F GLN* 3.9 19.5 + - + +
500F LEU* 1.3 78.0 - - - +
502F VAL* 1.3 64.0 + - - +
503F THR* 3.6 8.5 + - + +
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Residues in contact with VAL 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410F LEU* 3.6 9.0 - - + +
412F VAL* 4.0 17.0 - - + -
452F LEU* 3.9 22.4 - - + -
480F GLU* 3.7 10.4 - - - +
481F LEU* 3.5 48.6 + - + +
483F TYR* 3.8 20.2 - - + -
500F LEU* 3.7 18.1 - - + +
501F LEU* 1.3 73.1 - - - +
503F THR* 1.3 65.2 + - - +
504F VAL* 4.1 10.6 + - + +
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Residues in contact with THR 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F SER* 5.1 5.6 - - - -
410F LEU 2.9 15.7 + - - +
411F SER* 3.0 16.7 - - - -
412F VAL* 2.9 24.4 + - - +
479F ALA 4.3 3.1 - - - -
480F GLU* 5.1 9.2 - - + +
501F LEU* 3.8 13.0 - - + +
502F VAL* 1.3 75.9 - - - +
504F VAL* 1.3 66.3 + - - +
505F GLU* 5.1 1.6 - - - -
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Residues in contact with VAL 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412F VAL* 3.6 13.5 - - + +
414F ARG* 3.8 27.8 - - + -
451F THR* 6.3 2.9 - - + -
478F CYS 4.7 3.8 - - - +
479F ALA* 3.1 45.8 + - + +
480F GLU* 4.6 0.9 - - - +
481F LEU* 5.6 5.2 - - + +
502F VAL* 4.5 17.3 - - + +
503F THR* 1.3 80.1 - - - +
505F GLU* 1.3 64.6 + - - +
506F GLY 3.6 6.2 + - - +
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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