Contacts of the strand formed by residues 468 - 475 (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 SER 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A GLU* 3.3 9.7 - - - +
464A LEU 3.7 3.6 + - - -
465A PHE* 3.5 16.2 + - - -
466A ARG 3.7 2.6 + - - -
467A ASN* 1.3 82.6 + - - +
469A ARG* 1.3 64.6 + - - +
470A MET* 5.2 1.6 - - - +
525A LEU* 3.5 29.9 - - - +
526A ILE 3.2 13.9 - - - -
527A PRO* 3.4 20.4 - - - +
528A TYR* 3.8 8.6 + - - -
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Residues in contact with ARG 469 (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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433A VAL* 6.3 0.2 - - + -
436A GLY 4.0 5.1 + - - -
437A GLU* 2.6 62.5 + - + +
438A ASN 4.0 18.2 + - - +
439A LEU* 5.0 15.9 - - + -
468A SER* 1.3 77.5 - - - +
470A MET* 1.4 63.9 + - - +
471A VAL* 5.6 0.4 - - + -
509A ARG* 4.4 18.3 - - - +
525A LEU* 3.3 2.6 - - - -
526A ILE* 2.9 52.9 + - + +
528A TYR* 3.4 37.2 + - + -
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Residues in contact with MET 470 (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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433A VAL* 3.1 13.2 - - - +
434A ASN* 2.7 72.6 + - + +
435A HIS 5.9 0.2 - - - +
437A GLU* 3.6 2.6 - - - +
468A SER 5.2 2.0 - - - +
469A ARG* 1.4 76.0 - - - +
471A VAL* 1.3 65.2 + - - +
472A GLN* 5.6 4.9 - - - +
523A MET* 5.3 11.2 - - + -
524A GLY 3.6 5.4 - - - +
525A LEU* 3.7 36.3 - - + -
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Residues in contact with VAL 471 (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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431A VAL* 4.1 10.8 - - + -
432A TYR 3.1 12.8 - - - +
433A VAL* 3.9 11.9 - - + +
439A LEU* 6.0 0.7 - - + -
444A TRP* 5.0 6.5 - - + -
469A ARG* 5.6 0.2 - - + -
470A MET* 1.3 82.9 - - - +
472A GLN* 1.3 71.1 + - - +
473A PHE* 3.5 28.7 - - + -
511A LEU* 3.5 18.8 - - + -
523A MET* 3.5 1.0 - - - +
524A GLY* 2.7 41.9 + - - +
526A ILE* 4.0 23.3 - - + -
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Residues in contact with GLN 472 (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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397A ASN 5.7 0.4 + - - -
398A LYS* 3.1 37.1 - - + +
431A VAL* 3.4 4.7 - - - +
432A TYR* 2.7 49.9 + - + +
434A ASN* 5.0 15.6 - - + +
470A MET* 5.6 5.1 - - + +
471A VAL* 1.3 82.1 - - - +
473A PHE* 1.3 64.1 + - - +
519A LYS* 6.1 1.2 - - - +
521A ILE* 4.2 21.1 - - + +
522A PHE 3.2 12.6 - - - +
523A MET* 4.2 6.4 - - + +
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Residues in contact with PHE 473 (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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402A TRP* 5.1 0.4 - + - -
406A LEU* 3.6 38.6 - - + -
429A CYS* 4.1 6.7 - - + -
430A GLN 3.7 1.3 - - - -
431A VAL* 3.4 30.7 - - + -
432A TYR* 5.2 0.2 - - - -
444A TRP* 5.9 0.2 - + - -
448A LEU* 5.4 1.6 - - + -
471A VAL* 3.5 26.5 - - + -
472A GLN* 1.3 78.0 - - - +
474A HIS* 1.3 61.2 + - - +
475A PHE* 4.1 9.4 - + + -
498A VAL* 4.8 3.6 - - + -
511A LEU* 3.5 27.1 - - + -
512A MET 4.8 1.1 - - - -
513A LEU* 3.7 29.8 - - + -
521A ILE* 4.1 4.4 - - - +
522A PHE* 2.7 52.0 + - + +
523A MET 4.8 2.7 - - - -
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Residues in contact with HIS 474 (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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429A CYS* 3.6 1.0 - - - -
430A GLN* 2.7 60.6 + - - +
432A TYR* 3.6 29.4 + + + +
472A GLN 4.0 0.4 + - - -
473A PHE* 1.3 74.0 - - - +
475A PHE* 1.3 75.2 + - - +
477A ASN* 5.5 4.3 + - - -
521A ILE* 4.4 20.0 - - + -
522A PHE* 5.4 0.7 - - - -
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Residues in contact with PHE 475 (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* 3.8 23.6 - - + -
427A LEU* 3.6 28.5 - - + -
428A PRO 3.5 15.9 - - - +
429A CYS* 3.5 15.7 - - + -
430A GLN* 5.2 0.2 - - - -
450A MET* 5.4 1.1 - - - -
473A PHE* 4.3 7.4 - - + -
474A HIS* 1.3 93.6 + - - +
476A THR* 1.3 60.8 + - - +
477A ASN* 3.1 15.3 + - - +
483A LEU* 3.7 26.7 - - + -
486A LEU* 4.8 9.2 - - + -
513A LEU* 4.2 12.8 - - + -
522A PHE* 3.6 51.8 - + - -
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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