Contacts of the strand formed by residues 452 - 461 (chain J) in PDB entry 2FRV
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 GLU 452 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450J PRO* 3.9 6.5 - - - +
451J THR* 1.3 77.4 - - + +
453J SER* 1.3 61.2 + - - +
472J GLN* 3.2 11.0 - - - +
473J ARG* 3.6 37.8 + - + +
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Residues in contact with SER 453 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J CYS* 2.6 35.2 + - - -
450J PRO* 3.1 12.4 - - - +
452J GLU* 1.3 72.6 - - - +
454J GLN* 1.3 60.1 + - - +
471J VAL* 3.5 3.8 - - - +
472J GLN* 2.7 58.0 + - - +
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Residues in contact with GLN 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J ASN* 4.4 3.1 + - - +
83J CYS* 3.2 15.2 - - - +
337J TYR* 3.6 41.9 + - + +
453J SER* 1.3 74.9 - - - +
455J GLY* 1.3 57.7 + - - +
470J ILE 3.0 14.4 - - - +
471J VAL* 4.0 18.4 - - + +
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Residues in contact with GLY 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J ALA* 3.7 9.2 - - - -
82J ASN* 3.3 13.0 - - - -
83J CYS* 3.3 16.3 - - - +
337J TYR* 3.1 13.4 + - - -
454J GLN* 1.3 74.8 - - - +
456J VAL* 1.3 59.8 + - - +
468J HIS 4.0 0.2 - - - +
469J TRP* 3.6 0.3 - - - -
470J ILE* 2.8 32.6 + - - +
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Residues in contact with VAL 456 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ARG 4.0 1.0 - - - +
79J ALA* 3.7 4.9 - - - -
82J ASN* 3.0 30.4 + - - +
316J PRO* 5.9 0.9 - - + -
337J TYR* 3.8 13.0 - - + +
455J GLY* 1.3 74.8 - - - +
457J GLY* 1.3 65.0 + - - +
458J PHE* 3.5 49.4 + - + -
467J SER* 4.2 0.9 - - - -
468J HIS 3.3 11.4 - - - +
469J TRP* 3.8 27.6 - - + -
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Residues in contact with GLY 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J ALA* 3.6 25.8 - - - +
78J ARG* 3.8 9.6 - - - -
79J ALA* 3.6 8.5 - - - +
456J VAL* 1.3 72.9 - - - +
458J PHE* 1.3 61.8 + - - -
459J VAL 4.0 0.4 - - - -
466J LEU 3.7 0.7 - - - +
467J SER* 3.0 8.5 - - - -
468J HIS 3.0 30.5 + - - -
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Residues in contact with PHE 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ARG* 3.0 15.7 + - - +
283J CYS* 3.7 17.5 - - + -
293J LEU* 4.3 19.5 - - + -
296J ARG* 2.9 27.9 + - - +
314J PHE* 4.0 11.0 - + - -
316J PRO* 3.6 33.9 - - + -
319J ILE* 5.2 0.2 - - + -
456J VAL* 3.5 35.2 + - + -
457J GLY* 1.3 70.8 - - - -
459J VAL* 1.3 61.2 - - - +
465J MET* 3.0 35.4 - - + -
466J LEU 3.4 0.7 - - - -
467J SER* 3.6 15.5 - - - -
469J TRP* 4.3 4.5 - + - -
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Residues in contact with VAL 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J VAL* 4.0 11.9 - - + +
74J LEU* 3.8 7.0 - - + -
75J ALA* 3.5 36.3 - - + +
78J ARG* 3.6 14.6 - - - +
100J MET* 3.3 33.7 - - + -
283J CYS* 3.5 6.7 - - - -
285J GLU* 3.4 6.3 - - - +
458J PHE* 1.3 78.1 - - - +
460J ASN* 1.3 59.7 + - - +
461J ALA 3.5 7.9 - - - +
466J LEU* 2.6 50.7 + - + +
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Residues in contact with ASN 460 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J MET* 4.5 0.7 - - - +
104J TYR* 2.6 37.1 + - - -
281J LEU 5.0 1.0 + - - -
282J THR* 3.1 24.9 + - - +
283J CYS* 4.0 2.8 - - - +
284J GLY 3.5 24.2 - - - +
285J GLU* 2.7 21.4 + - + +
298J THR* 5.7 0.9 + - - -
370J GLY 5.4 0.4 - - - +
374J SER* 3.1 21.8 + - - -
417J GLN* 4.2 3.8 - - - +
459J VAL* 1.3 75.3 - - - +
461J ALA* 1.3 63.9 + - - +
464J GLY* 3.4 5.8 - - - -
465J MET* 3.3 31.1 - - - +
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Residues in contact with ALA 461 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J VAL* 3.9 17.7 - - + -
100J MET* 4.8 0.2 - - - -
104J TYR* 4.1 2.7 + - - -
417J GLN* 4.5 1.9 + - - -
459J VAL* 3.5 3.8 - - - -
460J ASN* 1.3 82.0 - - - +
462J PRO* 1.3 79.1 - - + +
463J ARG 3.0 0.7 - - - +
464J GLY* 2.8 25.9 + - - +
466J LEU* 4.4 5.6 - - + -
485J PRO* 4.6 0.2 - - + -
537J FCO 3.5 33.9 - - - +
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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