Contacts of the strand formed by residues 510 - 516 (chain A) in PDB entry 2XNF
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 VAL 510 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A CYS* 5.3 0.9 - - - -
498A VAL 3.7 9.6 - - - +
499A HIS* 3.8 20.9 - - + +
500A PHE* 3.9 2.7 - - - +
507A GLU* 4.6 4.5 - - - +
509A ARG* 1.3 85.2 - - - +
511A LEU* 1.3 62.0 + - - +
526A ILE* 3.0 9.3 - - - +
527A PRO* 2.9 30.0 + - + +
530A GLN* 3.9 16.6 - - + +
533A PHE* 3.4 44.0 - - + -
534A VAL* 3.7 23.3 - - + -
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Residues in contact with LEU 511 (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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444A TRP* 4.6 12.6 - - + -
448A LEU* 4.9 1.1 - - + -
471A VAL* 3.5 22.4 - - + -
473A PHE* 3.5 30.3 - - + -
497A CYS* 3.7 7.1 - - - -
498A VAL* 2.7 55.2 + - + +
500A PHE* 3.9 22.2 - - + -
510A VAL* 1.3 76.5 - - - +
512A MET* 1.3 76.2 + - - +
525A LEU 3.4 13.7 - - - +
526A ILE* 3.5 18.6 - - + +
533A PHE* 4.8 3.6 - - - -
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Residues in contact with MET 512 (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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453A ILE* 4.2 4.0 - - + -
458A LEU* 3.6 26.0 - - + -
465A PHE* 3.7 18.6 - - + -
471A VAL* 4.6 0.5 - - - +
495A ALA* 3.5 26.9 - - - -
496A GLY 3.6 7.0 - - - +
497A CYS* 3.9 17.5 - - + -
498A VAL* 4.8 0.2 - - - -
511A LEU* 1.3 83.7 - - - +
513A LEU* 1.3 67.1 + - - +
514A LEU* 3.9 18.4 - - + -
524A GLY* 3.0 24.8 - - - -
525A LEU 3.0 17.3 + - - +
527A PRO* 4.7 0.2 - - - +
533A PHE* 3.5 29.4 - - + -
537A ILE* 4.1 3.6 - - + -
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Residues in contact with LEU 513 (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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406A LEU* 4.1 14.8 - - + -
450A MET* 3.7 33.4 - - + -
473A PHE* 3.7 20.0 - - + -
475A PHE* 4.2 11.9 - - + -
490A MET* 3.3 11.6 - - + +
495A ALA* 3.5 4.7 - - - -
496A GLY 2.7 45.9 + - - +
498A VAL* 4.2 7.0 - - + -
512A MET* 1.3 73.4 - - - +
514A LEU* 1.3 68.7 + - - +
522A PHE* 3.5 40.8 - - + -
523A MET 3.6 4.9 - - - +
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Residues in contact with LEU 514 (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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455A GLN* 3.6 32.3 - - + +
458A LEU* 4.0 10.3 - - + -
465A PHE* 5.3 5.4 - - + -
490A MET* 4.2 1.1 - - - -
494A PHE 5.0 0.4 - - - +
495A ALA* 3.5 29.8 - - + +
512A MET* 3.9 15.5 - - + -
513A LEU* 1.3 80.5 - - - +
515A TYR* 1.3 62.9 + - - +
522A PHE* 3.4 2.4 - - - -
523A MET* 2.7 69.1 + - + +
524A GLY* 5.4 4.0 - - - -
525A LEU* 6.0 3.6 - - + +
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Residues in contact with TYR 515 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A GLN* 5.4 4.1 + - - +
487A TYR* 3.7 34.6 - + + -
490A MET* 3.8 25.6 + - + +
491A GLY* 4.0 22.2 - - - -
494A PHE 5.2 0.6 + - - -
514A LEU* 1.3 75.4 - - - +
516A SER* 1.3 75.1 + - - +
517A SER* 3.4 33.8 + - - -
520A LYS* 3.5 42.9 + - - +
521A ILE 3.6 5.8 - - - -
522A PHE* 3.6 41.1 - + + -
523A MET* 4.9 2.8 - - - +
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Residues in contact with SER 516 (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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514A LEU 3.7 1.2 + - - -
515A TYR* 1.3 75.2 - - - +
517A SER* 1.3 58.5 + - - +
518A LYS* 4.5 3.8 - - - -
519A LYS* 3.7 15.6 - - - +
520A LYS* 2.9 22.0 + - - -
521A ILE* 2.7 49.9 + - - +
523A MET* 3.9 31.2 - - - +
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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