Contacts of the strand formed by residues 452 - 461 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450B PRO* 3.9 6.1 - - - +
451B THR* 1.3 77.2 + - + +
453B SER* 1.3 61.0 + - - +
472B GLN* 3.2 10.8 - - - +
473B ARG* 3.6 37.2 + - + +
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Residues in contact with SER 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B CYS* 2.6 35.6 + - - -
450B PRO* 3.1 12.4 - - - +
452B GLU* 1.3 73.8 - - - +
454B GLN* 1.3 59.2 + - - +
471B VAL* 3.5 3.8 - - - +
472B GLN* 2.7 58.2 + - - +
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Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASN* 4.4 2.9 + - - +
83B CYS* 3.2 14.8 - - - +
337B TYR* 3.6 42.5 + - + +
453B SER* 1.3 75.5 - - - +
455B GLY* 1.3 58.2 + - - +
470B ILE 3.0 14.8 - - - +
471B VAL* 4.0 18.4 - - + +
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Residues in contact with GLY 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA* 3.7 8.7 - - - -
82B ASN* 3.3 13.0 - - - -
83B CYS* 3.3 16.5 - - - +
337B TYR* 3.1 14.8 + - - -
454B GLN* 1.3 75.2 - - - +
456B VAL* 1.3 58.9 + - - +
468B HIS 4.0 0.2 - - - +
469B TRP* 3.6 0.3 - - - -
470B ILE* 2.8 31.3 + - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG 4.0 1.0 - - - +
79B ALA* 3.7 4.9 - - - -
82B ASN* 3.0 30.2 + - - +
316B PRO* 5.9 0.9 - - + -
337B TYR* 3.8 12.3 - - + +
455B GLY* 1.3 73.8 - - - +
457B GLY* 1.3 65.6 + - - +
458B PHE* 3.5 47.5 + - + -
467B SER* 4.2 1.1 - - - -
468B HIS 3.3 11.2 - - - +
469B TRP* 3.8 29.6 - - + -
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Residues in contact with GLY 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA* 3.6 26.0 - - - +
78B ARG* 3.8 10.1 - - - -
79B ALA* 3.6 8.1 - - - +
456B VAL* 1.3 71.2 - - - +
458B PHE* 1.3 61.1 + - - -
459B VAL 4.0 0.2 - - - -
466B LEU 3.7 0.3 - - - +
467B SER* 3.0 8.7 - - - -
468B HIS 3.0 31.2 + - - -
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Residues in contact with PHE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG* 3.0 15.3 + - - +
283B CYS* 3.7 18.4 - - + -
293B LEU* 4.3 20.2 - - + -
296B ARG* 2.9 27.1 + - - +
314B PHE* 4.0 11.0 - + - -
316B PRO* 3.6 34.5 - - + -
319B ILE* 5.2 0.2 - - + -
456B VAL* 3.5 35.9 - - + -
457B GLY* 1.3 70.6 - - - -
459B VAL* 1.3 63.0 - - - +
465B MET* 3.0 35.0 - - + -
466B LEU 3.4 0.7 - - - -
467B SER* 3.6 14.8 - - - -
469B TRP* 4.3 4.9 - + - -
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.9 12.6 - - + +
74B LEU* 3.8 6.3 - - + -
75B ALA* 3.5 36.3 - - + +
78B ARG* 3.6 15.7 - - - +
100B MET* 3.3 33.7 - - + -
283B CYS* 3.5 7.1 - - - -
285B GLU* 3.4 6.1 - - - +
457B GLY 4.0 0.2 - - - -
458B PHE* 1.3 78.1 - - - +
460B ASN* 1.3 61.0 + - - +
461B ALA* 3.5 7.9 - - - +
466B LEU* 2.6 50.8 + - + +
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Residues in contact with ASN 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET* 4.5 0.7 - - - +
104B TYR* 2.6 37.6 + - - -
281B LEU 5.0 0.8 + - - -
282B THR* 3.1 25.1 + - - +
283B CYS* 4.0 2.9 - - - +
284B GLY* 3.5 24.2 - - - +
285B GLU* 2.7 21.4 + - + +
298B THR* 5.7 0.7 + - - -
370B GLY 5.4 0.6 - - - +
374B SER* 3.1 22.1 + - - -
417B GLN* 4.2 3.6 - - - +
459B VAL* 1.3 73.9 - - - +
461B ALA* 1.3 64.5 + - - +
464B GLY* 3.4 6.7 - - - -
465B MET* 3.3 30.7 - - - +
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.9 17.3 - - + -
100B MET* 4.8 0.2 - - - -
104B TYR* 4.1 2.8 + - - -
417B GLN* 4.5 1.9 + - - -
459B VAL* 3.5 3.4 - - - -
460B ASN* 1.3 82.2 - - - +
462B PRO* 1.3 79.7 - - + +
463B ARG 3.0 0.7 - - - +
464B GLY* 2.8 25.7 + - - +
466B LEU* 4.4 5.6 - - + -
485B PRO* 4.6 0.4 - - + -
537B 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