Contacts of the helix formed by residues 518 - 527 (chain H) 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 VAL 518 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ARG* 5.8 0.4 - - - +
119H ASP* 3.8 29.8 - - + +
174H TYR* 3.8 21.5 - - + -
179H HIS* 4.1 10.5 - - + +
181H ALA* 3.9 28.0 - - + -
182H TYR* 3.4 32.3 - - + +
516H ARG 3.3 3.1 + - - +
517H PRO* 1.3 71.3 - - - +
519H GLU* 1.3 72.0 + - - +
520H ILE 3.1 1.3 - - - -
521H LEU* 3.1 5.7 + - + -
522H ARG* 2.9 30.8 + - - +
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Residues in contact with GLU 519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H HIS* 4.7 1.1 - - - -
181H ALA* 4.0 11.8 - - + +
271H TRP* 3.6 34.2 - - + -
509H THR* 3.6 16.3 - - + +
510H PRO* 3.3 26.5 - - + +
511H ILE* 3.6 7.4 - - + +
512H ALA* 2.7 40.9 + - - +
513H ASP 4.7 0.5 - - - +
516H ARG 4.4 1.7 - - - +
517H PRO* 3.1 9.7 - - - +
518H VAL* 1.3 99.6 + - + +
520H ILE* 1.3 59.9 + - - +
522H ARG* 3.6 1.0 + - - +
523H THR* 3.6 14.0 + - - -
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Residues in contact with ILE 520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 4.0 18.8 - - + +
11H VAL* 4.2 11.9 - - + -
14H ILE* 4.6 7.4 - - + -
23H ILE* 4.0 19.5 - - + -
25H VAL* 3.8 32.8 - - + -
32H ILE* 3.7 22.0 - - + -
506H LEU* 4.3 10.3 - - + +
511H ILE* 3.8 11.7 - - + -
517H PRO* 3.2 11.7 + - + +
518H VAL 3.1 1.0 - - - -
519H GLU* 1.3 78.8 - - - +
521H LEU* 1.3 58.0 + - + +
523H THR* 3.4 2.9 + - - -
524H VAL* 2.9 41.5 + - + +
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Residues in contact with LEU 521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ALA 4.5 0.4 - - - +
52G ALA* 3.9 28.0 - - + -
11H VAL* 4.3 14.1 - - + -
14H ILE* 4.6 11.0 - - + -
15H THR* 4.7 0.9 - - - +
16H ARG* 3.4 28.7 - - - +
119H ASP* 3.6 11.7 - - - +
174H TYR* 4.1 22.0 - - + -
517H PRO 3.6 15.9 - - - +
518H VAL* 3.5 9.4 - - + +
520H ILE* 1.3 78.1 - - + +
522H ARG* 1.3 62.3 + - - +
524H VAL* 4.4 5.4 - - - +
525H HIS* 2.7 50.3 + - + +
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Residues in contact with ARG 522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H HIS* 3.5 6.6 + - - -
119H ASP* 2.4 50.6 + - + -
120H TRP* 3.4 40.5 - - + +
181H ALA* 2.9 44.4 + - - +
182H TYR* 4.1 7.1 - - - +
268H TYR* 3.4 17.2 + - - -
271H TRP* 3.7 38.5 - - + +
407H THR* 3.6 5.0 - - - +
518H VAL* 2.9 27.9 + - - +
519H GLU* 4.0 4.9 - - - +
520H ILE 3.3 0.4 - - - -
521H LEU* 1.3 76.6 - - - +
523H THR* 1.3 61.9 + - - +
526H SER* 3.2 23.7 + - - -
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Residues in contact with THR 523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H TRP* 4.0 9.9 - - - -
274H ILE* 4.5 2.1 - - - +
407H THR* 3.5 19.7 + - - +
502H VAL* 4.8 2.2 - - + +
505H ALA* 3.6 33.4 + - + +
506H LEU* 3.9 26.0 - - + -
509H THR* 4.0 10.2 + - - -
519H GLU 3.6 9.1 + - - -
520H ILE 3.4 3.0 + - - -
521H LEU 3.2 0.2 - - - -
522H ARG* 1.3 77.3 - - - +
524H VAL* 1.3 66.8 + - - +
526H SER* 2.7 23.5 + - - -
527H TYR* 3.5 10.9 - - + -
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Residues in contact with VAL 524 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H ILE* 4.2 17.5 - - + -
17H ILE* 4.6 0.7 - - + -
21H LEU* 4.1 16.4 - - + -
23H ILE* 3.7 26.7 - - + -
490H LEU* 4.8 2.0 - - + -
502H VAL* 4.2 16.3 - - + +
506H LEU* 4.6 5.8 - - + -
520H ILE* 2.9 32.3 + - + +
521H LEU* 4.2 4.5 - - - +
523H THR* 1.3 77.2 - - - +
525H HIS* 1.3 64.2 + - + +
527H TYR* 3.3 8.7 + - - +
529H PRO* 3.2 34.6 - - + +
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Residues in contact with HIS 525 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ILE* 4.6 4.2 - - + +
15H THR 2.9 28.0 + - - -
16H ARG* 3.0 44.0 + - + +
17H ILE* 3.8 13.1 - - + +
111H HIS* 2.9 31.3 + - - +
115H LEU 4.1 6.7 - - - -
116H HIS* 3.5 19.5 - - + -
119H ASP* 2.8 17.4 + - - -
521H LEU* 2.7 45.7 + - + +
524H VAL* 1.3 70.0 - - - +
526H SER* 1.3 58.0 + - - +
527H TYR 3.0 2.9 - - - -
528H ASP 2.9 9.6 + - - -
529H PRO* 4.2 3.4 - - + -
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Residues in contact with SER 526 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H HIS* 4.0 9.2 - - - -
407H THR* 3.7 16.5 - - - +
410H ARG* 3.3 36.9 + - - +
411H THR* 3.7 12.8 - - - -
414H ARG* 2.6 34.5 + - - +
522H ARG 3.2 16.6 + - - -
523H THR 2.7 18.7 + - - -
525H HIS* 1.3 77.3 - - - +
527H TYR* 1.3 50.2 + - - +
528H ASP 3.2 0.7 - - - -
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Residues in contact with TYR 527 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277H THR* 3.3 3.5 - - - +
368H GLU* 3.1 41.6 + - + -
369H VAL 5.2 0.9 - - - -
410H ARG* 3.3 34.2 + - - +
414H ARG* 3.8 4.5 + - - +
463H ARG* 4.8 4.5 - - - +
486H SER* 5.2 0.7 + - - -
489H ASN* 3.6 38.6 + - + -
490H LEU* 4.6 9.4 - - + +
501H ALA* 3.1 29.0 + - + -
502H VAL* 4.1 17.3 - - + -
505H ALA* 3.5 14.3 - - + +
523H THR 3.5 14.4 - - - -
524H VAL 3.3 8.9 + - - +
525H HIS 3.0 0.6 - - - -
526H SER* 1.3 79.2 + - - +
528H ASP* 1.3 71.0 + - - +
529H PRO* 4.2 7.1 - - + +
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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