Contacts of the helix formed by residues 54 - 64 (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 PRO 54 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ARG 3.5 4.7 - - - +
53J ASP* 1.3 88.1 - - - +
55J ARG* 1.3 58.9 + - - +
56J ASP 3.4 1.0 + - - -
57J ALA* 3.4 17.5 + - + +
58J GLN 4.6 0.7 + - - -
80J VAL* 3.9 26.3 - - + +
225J VAL* 4.9 1.7 - - - +
449J TYR* 3.5 19.1 - - + +
470J ILE* 3.7 22.9 - - + -
472J GLN* 4.3 8.7 - - + -
475J GLY 3.1 27.4 - - - +
476J LYS 4.2 1.6 - - - +
477J ILE* 3.8 22.2 - - + -
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Residues in contact with ARG 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I PHE* 3.9 17.8 - - - -
217I LEU* 5.4 4.0 - - - +
262I TYR* 3.4 72.8 + - + +
53J ASP* 2.8 19.5 + - - +
54J PRO* 1.3 76.2 - - - +
56J ASP* 1.3 60.1 + - - +
57J ALA 3.5 0.2 - - - -
58J GLN* 4.3 9.1 + - - +
59J HIS* 3.9 5.9 + - - -
80J VAL* 5.9 0.2 - - + -
224J VAL* 5.4 3.2 - - - +
225J VAL* 4.7 14.6 - - + +
444J TYR* 4.7 7.3 + - - -
447J TRP* 3.8 33.3 - - + +
449J TYR* 3.7 12.6 - - - +
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Residues in contact with ASP 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259I SER* 3.7 8.1 + - - -
260I PRO* 3.2 23.6 - - - +
261I PHE* 3.0 38.3 + - + +
262I TYR* 4.6 2.3 + - - -
52J ARG* 5.2 6.3 - - + +
53J ASP* 2.8 28.3 + - - +
55J ARG* 1.3 77.3 - - - +
57J ALA* 1.3 66.7 + - - +
58J GLN 3.2 2.5 - - - -
59J HIS* 2.8 24.3 + - - +
60J PHE* 3.5 22.3 + - + -
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Residues in contact with ALA 57 (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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49J LEU* 4.4 14.1 - - + -
52J ARG* 6.0 0.8 - - - +
53J ASP 3.5 3.6 + - - -
54J PRO* 3.4 17.8 + - + +
56J ASP* 1.3 76.0 - - - +
58J GLN* 1.3 64.0 + - - +
60J PHE* 3.1 3.0 + - - -
61J THR* 2.8 29.1 + - + +
76J SER* 4.3 3.1 - - - +
80J VAL* 5.1 2.0 - - + -
477J ILE* 4.4 7.8 - - + +
480J PHE* 3.6 36.8 - - + -
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Residues in contact with GLN 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I TYR* 3.3 16.6 + - - -
54J PRO 4.6 1.8 + - - -
55J ARG 4.3 7.0 + - - +
56J ASP 3.0 1.6 + - - -
57J ALA* 1.3 77.9 - - - +
59J HIS* 1.3 77.1 + - + +
61J THR* 3.2 8.0 + - - -
62J GLN* 3.1 30.3 + - - +
73J ALA* 3.9 27.4 - - - +
76J SER* 3.8 8.7 - - - -
77J VAL* 3.5 14.8 - - + +
223J THR* 2.7 50.5 + - - +
224J VAL* 3.5 9.1 - - - +
225J VAL* 4.5 3.0 - - + +
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Residues in contact with HIS 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I HIS* 3.5 22.3 - + - -
247I ILE* 4.3 22.2 - - + +
255I TRP* 3.4 6.1 - - + -
261I PHE* 3.7 38.7 - + + +
262I TYR* 2.8 33.4 + + - -
55J ARG 3.9 10.5 - - - -
56J ASP 2.8 15.7 + - - +
58J GLN* 1.3 86.8 - - + +
60J PHE* 1.3 63.9 + - - +
62J GLN* 3.9 4.5 + - - +
63J ARG* 3.3 36.9 + - - +
220J THR 5.8 0.8 + - - -
221J GLN* 4.7 8.8 + - + +
223J THR 5.0 0.2 - - - -
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Residues in contact with PHE 60 (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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118I VAL* 4.0 11.9 - - + +
121I ALA* 3.8 13.2 - - + -
255I TRP* 3.5 52.5 - + - -
259I SER* 4.8 1.3 - - - -
261I PHE* 4.1 15.7 - + - -
45J LEU* 3.8 14.2 - - + +
48J ILE* 3.7 32.5 - - + -
49J LEU* 3.5 25.4 - - + -
52J ARG* 3.6 24.5 - - + -
56J ASP* 3.6 23.1 - - + -
57J ALA 3.1 2.8 + - - +
59J HIS* 1.3 77.2 - - - +
61J THR* 1.3 63.2 + - - +
63J ARG* 3.2 19.9 + - - +
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Residues in contact with THR 61 (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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45J LEU* 4.5 7.4 - - + -
49J LEU* 3.8 26.9 - - + -
57J ALA 2.8 21.7 + - - +
58J GLN* 3.2 7.1 + - - -
60J PHE* 1.3 66.3 - - - +
62J GLN* 1.3 70.8 + - - +
63J ARG 3.0 2.0 - - - -
64J ALA* 2.9 22.7 + - - +
72J HIS* 3.3 12.6 + - - +
76J SER* 3.0 25.9 + - - +
468J HIS* 3.8 11.2 - - + -
480J PHE* 4.0 10.8 - - + -
482J LEU* 4.0 11.9 - - + -
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Residues in contact with GLN 62 (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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58J GLN* 3.1 16.1 + - - +
59J HIS* 4.0 10.4 + - - +
60J PHE 3.2 0.4 - - - -
61J THR* 1.3 84.4 + - - +
63J ARG* 1.3 71.3 + - - +
64J ALA 3.1 2.3 + - - -
65J CYS 3.1 23.2 + - - +
69J THR* 5.1 0.2 - - - -
70J TYR 2.9 29.8 + - - +
72J HIS* 3.8 11.7 - - + -
73J ALA* 3.7 22.4 - - + +
219J HIS* 3.4 14.3 - - - +
220J THR* 3.0 45.0 + - - +
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Residues in contact with ARG 63 (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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17I CYS* 3.2 7.7 - - - +
118I VAL* 4.0 11.1 - - + +
148I CYS* 3.0 39.1 + - - +
247I ILE* 4.3 18.3 - - - +
249I CYS* 4.8 3.4 - - - +
255I TRP* 3.7 18.0 - - + -
267I SF4 3.6 27.1 - - - -
43J ARG* 2.8 21.8 + - - -
45J LEU* 4.3 1.7 - - - +
59J HIS* 3.3 28.1 + - - +
60J PHE 3.2 12.3 + - - +
61J THR 3.0 1.6 - - - -
62J GLN* 1.3 95.1 - - - +
64J ALA* 1.3 61.6 + - - +
65J CYS 3.0 1.8 - - - -
216J LYS* 4.3 7.1 - - - +
219J HIS* 3.5 27.7 - - - +
220J THR 5.0 1.4 + - - -
221J GLN* 4.6 4.8 + - - -
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Residues in contact with ALA 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J ARG* 2.7 27.3 + - - +
45J LEU* 3.6 18.1 - - + +
61J THR 2.9 17.5 + - - +
63J ARG* 1.3 79.1 - - - +
65J CYS* 1.3 57.9 + - - +
72J HIS* 4.1 20.0 - - + +
482J LEU* 4.4 4.0 - - + -
532J ALA* 3.1 19.4 - - - +
533J CYS* 5.0 2.2 - - - -
536J HIS* 4.3 14.4 - - + -
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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