Contacts of the strand formed by residues 477 - 483 (chain D) 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 ILE 477 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.8 37.7 - - + +
50D LYS* 4.3 4.2 + - - +
51D GLY* 2.7 30.8 + - - -
52D ARG* 2.8 25.9 + - + +
53D ASP 4.5 1.1 - - - +
54D PRO* 3.8 26.7 - - + -
57D ALA* 4.4 6.5 - - + -
470D ILE* 3.9 8.5 - - + -
471D VAL 3.9 4.5 - - - -
472D GLN* 4.6 1.6 - - - +
476D LYS* 1.3 70.0 - - - +
478D GLU* 1.3 64.4 + - - +
479D ASN* 3.7 26.7 - - - +
480D PHE* 3.9 26.2 - - + +
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Residues in contact with GLU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS* 2.8 40.5 + - - +
471D VAL* 2.9 28.3 + - + +
472D GLN 4.4 1.6 - - - -
473D ARG* 4.0 32.7 - - + +
476D LYS* 3.5 9.9 + - - +
477D ILE* 1.3 80.8 - - - +
479D ASN* 1.3 62.3 + - + +
307L ASP* 5.7 0.9 - - - +
309L SER* 6.6 0.4 - - - -
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Residues in contact with ASN 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS* 5.7 1.8 - - - -
336D PRO 5.0 0.2 - - - -
337D TYR 3.3 23.4 + - - +
338D LYS 4.2 1.0 - - - -
339D GLY 3.2 27.9 + - - +
469D TRP 4.3 1.8 - - - -
470D ILE* 3.4 6.9 - - - +
471D VAL* 2.9 45.1 + - + +
477D ILE* 3.6 4.3 - - - +
478D GLU* 1.3 81.5 - - + +
480D PHE* 1.3 66.8 + - - +
481D GLN* 3.4 22.4 - - - +
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Residues in contact with PHE 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 3.2 29.5 + - - +
49D LEU* 3.5 28.0 - - + -
57D ALA* 3.6 19.5 - - + -
61D THR* 4.0 3.1 - - + -
76D SER* 3.1 28.7 - - - -
79D ALA* 5.0 1.6 - - + -
80D VAL* 4.7 6.1 - - + -
468D HIS* 3.7 28.0 - - + -
469D TRP 3.2 4.7 - - - -
470D ILE* 3.8 33.9 - - + -
477D ILE* 3.9 24.1 - - + +
479D ASN* 1.3 74.9 + - - +
481D GLN* 1.3 64.8 + - - +
482D LEU* 3.6 19.1 - - + -
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Residues in contact with GLN 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 3.7 13.7 + - - +
321D GLU* 3.9 9.2 + - - +
336D PRO* 3.0 39.7 - - + +
339D GLY* 3.8 22.0 - - - +
340D VAL* 4.5 1.0 - - - -
341D THR* 3.5 14.0 + - - -
358D LYS* 3.4 26.3 - - - +
468D HIS* 3.5 2.3 - - - -
469D TRP* 2.7 41.3 + - + +
479D ASN* 3.4 20.2 - - - +
480D PHE* 1.3 80.3 - - - +
482D LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 5.2 4.0 - - + -
46D GLU* 3.4 14.8 + - + +
49D LEU* 4.6 2.7 - - + -
61D THR* 4.0 13.9 - - + -
64D ALA* 4.4 8.1 - - + -
72D HIS* 3.9 16.8 - - + +
321D GLU* 4.0 0.7 - - - +
467D SER 3.7 3.8 - - - -
468D HIS* 3.7 26.0 - - + +
480D PHE* 3.6 33.0 - - + -
481D GLN* 1.3 70.3 - - - +
483D VAL* 1.3 68.3 + - - +
484D VAL* 4.0 5.6 - - + -
536D HIS* 3.1 38.0 + - + +
540D MG 2.2 31.0 - - - -
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Residues in contact with VAL 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ILE* 4.9 4.9 - - + -
321D GLU* 3.3 39.9 - - + +
336D PRO* 3.9 29.4 - - + -
360D PRO* 3.8 23.3 - - + -
465D MET 3.8 3.2 - - - +
466D LEU* 3.7 3.3 - - - +
467D SER* 2.9 41.1 + - - +
469D TRP* 4.1 4.9 - - + +
481D GLN* 5.1 0.2 - - + -
482D LEU* 1.3 76.6 - - - +
484D VAL* 1.3 58.5 + - - +
487D THR* 4.9 1.1 - - - -
488D TRP* 3.8 18.8 + - + +
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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