Contacts of the helix formed by residues 54 - 64 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F ARG 3.5 4.9 - - - +
53F ASP* 1.3 88.0 - - - +
55F ARG* 1.3 58.1 + - - +
56F ASP 3.4 0.7 + - - -
57F ALA* 3.4 17.8 + - + +
58F GLN 4.6 0.9 + - - -
80F VAL* 3.9 25.5 - - + +
225F VAL* 4.9 1.7 - - - +
449F TYR* 3.5 19.5 - - + +
470F ILE* 3.7 22.9 - - + -
472F GLN* 4.3 7.9 - - + -
475F GLY 3.1 26.9 - - - +
476F LYS 3.8 2.2 - - - +
477F ILE* 3.8 22.7 - - + -
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Residues in contact with ARG 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E PHE* 3.9 18.6 - - - -
217E LEU* 5.4 3.6 - - - +
262E TYR* 3.4 73.4 + - + +
53F ASP* 2.8 19.3 + - - +
54F PRO* 1.3 75.8 - - - +
56F ASP* 1.3 60.0 + - - +
58F GLN* 4.3 8.7 + - - +
59F HIS* 3.9 6.2 + - - -
224F VAL* 5.4 3.4 - - - +
225F VAL* 4.7 15.6 - - + +
444F TYR* 4.7 8.0 + - - -
447F TRP* 3.8 32.3 - - + +
449F TYR* 3.7 12.3 - - - +
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Residues in contact with ASP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E SER* 3.7 7.3 - - - -
260E PRO* 3.2 24.6 - - - +
261E PHE* 3.0 38.1 + - + +
262E TYR* 4.6 2.1 + - - -
52F ARG* 5.2 6.8 - - + +
53F ASP* 2.8 26.0 + - + +
55F ARG* 1.3 79.7 - - - +
57F ALA* 1.3 66.1 + - - +
58F GLN 3.2 2.7 - - - -
59F HIS* 2.8 23.8 + - - +
60F PHE* 3.5 22.9 + - + -
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 4.4 14.6 - - + -
52F ARG* 6.0 0.6 - - - +
53F ASP 3.5 3.4 + - - -
54F PRO* 3.4 17.8 + - + +
56F ASP* 1.3 76.2 - - - +
58F GLN* 1.3 64.6 + - - +
60F PHE* 3.1 3.3 + - - +
61F THR* 2.8 29.1 + - + +
76F SER* 4.3 2.9 - - - +
80F VAL* 5.1 2.2 - - + -
477F ILE* 4.4 8.4 - - + +
480F PHE* 3.6 35.7 - - + -
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Residues in contact with GLN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E TYR* 3.3 16.0 + - - -
54F PRO 4.6 1.8 + - - -
55F ARG 4.3 6.8 + - - +
56F ASP 3.0 1.6 + - - -
57F ALA* 1.3 79.0 - - - +
59F HIS* 1.3 78.5 + - + +
61F THR* 3.2 7.2 + - - -
62F GLN* 3.1 31.1 + - - +
73F ALA* 3.9 27.6 - - - +
76F SER* 3.8 8.4 - - - -
77F VAL* 3.5 13.5 - - + +
223F THR* 2.7 52.1 + - - +
224F VAL* 3.5 9.7 - - - +
225F VAL* 4.5 2.8 - - + +
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Residues in contact with HIS 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E HIS* 3.5 21.9 - + - -
247E ILE* 4.3 23.2 - - + +
255E TRP* 3.4 5.8 - - + -
261E PHE* 3.7 38.9 - + + +
262E TYR* 2.8 32.1 + + - -
55F ARG 3.9 11.4 - - - -
56F ASP 2.8 15.3 + - - +
58F GLN* 1.3 85.9 + - + +
60F PHE* 1.3 65.5 + - - +
62F GLN* 3.9 4.7 + - - +
63F ARG* 3.3 35.8 + - - +
221F GLN* 4.7 9.9 - - + +
223F THR 5.0 0.2 - - - -
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Residues in contact with PHE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL* 4.0 12.3 - - + +
121E ALA* 3.8 13.5 - - + -
255E TRP* 3.5 51.4 - + - -
259E SER* 4.8 1.6 - - - -
261E PHE* 4.1 15.3 - + - -
45F LEU* 3.8 14.5 - - + +
48F ILE* 3.7 31.4 - - + -
49F LEU* 3.5 25.1 - - + -
52F ARG* 3.6 24.5 - - + -
56F ASP* 3.6 23.3 - - + -
57F ALA 3.1 2.8 + - - +
59F HIS* 1.3 78.0 - - - +
61F THR* 1.3 63.8 + - - +
63F ARG* 3.2 19.8 + - - +
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Residues in contact with THR 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 4.5 8.3 - - + -
49F LEU* 3.8 26.9 - - + -
57F ALA 2.8 22.0 + - - +
58F GLN* 3.2 7.4 + - - -
60F PHE* 1.3 68.1 - - - +
62F GLN* 1.3 70.3 + - - +
63F ARG 3.0 2.0 - - - -
64F ALA* 2.9 22.4 + - - +
72F HIS* 3.3 13.5 + - - +
76F SER* 3.0 24.8 + - - +
468F HIS* 3.8 11.9 - - - -
480F PHE* 4.0 11.0 - - + -
482F LEU* 4.0 12.1 - - + -
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Residues in contact with GLN 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F GLN* 3.1 15.5 + - - +
59F HIS* 4.0 10.2 + - - +
60F PHE 3.2 0.6 - - - -
61F THR* 1.3 85.3 + - - +
63F ARG* 1.3 72.8 + - - +
64F ALA 3.2 1.6 + - - -
65F CYS 3.1 23.7 + - - +
69F THR* 5.1 0.3 - - - -
70F TYR 2.9 30.7 + - - +
72F HIS* 3.8 12.3 - - + -
73F ALA* 3.7 21.9 - - + +
219F HIS* 3.4 15.1 - - - +
220F THR* 3.0 43.8 + - - -
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Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E CYS* 3.2 7.8 - - - +
118E VAL* 4.0 11.9 - - + +
148E CYS* 3.0 38.3 + - - +
247E ILE* 4.3 17.5 - - - +
249E CYS* 4.8 3.8 - - - +
255E TRP* 3.7 20.2 - - + -
267E SF4 3.6 26.5 - - - -
43F ARG* 2.8 21.3 + - - -
45F LEU* 4.3 2.0 - - - +
59F HIS* 3.3 28.8 + - - +
60F PHE 3.2 11.6 + - - +
61F THR 3.0 1.2 - - - -
62F GLN* 1.3 95.4 - - - +
64F ALA* 1.3 61.8 + - - +
65F CYS 3.0 2.2 - - - +
216F LYS* 4.3 6.9 - - - +
219F HIS* 3.5 28.0 + - - +
220F THR 5.0 1.6 + - - -
221F GLN* 4.6 5.3 + - - -
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Residues in contact with ALA 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ARG* 2.7 27.4 + - - +
45F LEU* 3.6 18.5 - - + +
61F THR 2.9 17.4 + - - +
63F ARG* 1.3 80.0 - - - +
65F CYS* 1.3 59.6 + - - +
72F HIS* 4.1 21.3 - - + +
482F LEU* 4.4 3.4 - - + -
532F ALA* 3.1 19.1 - - - +
533F CYS* 5.0 1.3 - - - -
536F 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