Contacts of the helix formed by residues 53 - 65 (chain I) 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 GLY 53 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I ALA* 1.3 71.3 - - - +
54I HIS* 1.3 62.1 + - - -
56I VAL* 3.0 21.4 - - - +
57I GLU* 3.5 3.5 + - - +
10J VAL 5.2 1.8 - - - -
11J VAL* 3.7 8.2 - - - +
12J ASP 3.7 28.7 - - - -
13J PRO* 2.8 23.7 + - - +
174J TYR* 4.8 0.7 - - - -
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Residues in contact with HIS 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I ALA 3.5 0.4 + - - -
53I GLY* 1.3 70.9 - - - -
55I ALA* 1.3 61.9 + - - +
56I VAL 3.2 0.2 - - - -
57I GLU* 3.8 12.4 - - + +
58I GLU* 3.1 42.1 + - - +
10J VAL* 4.4 29.2 + - + +
12J ASP 5.2 6.6 + - - -
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Residues in contact with ALA 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I GLY* 4.6 1.1 - - - -
52I ALA 3.3 15.1 + - - +
53I GLY 3.2 1.8 + - - -
54I HIS* 1.3 76.1 - - - +
56I VAL* 1.3 60.9 + - - +
58I GLU* 3.7 5.6 + - - -
59I ALA* 3.4 5.7 + - - +
171J THR 4.8 0.2 - - - +
172J ASN* 2.5 63.2 + - + +
174J TYR* 4.4 12.1 - - + -
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Residues in contact with VAL 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I TYR* 3.5 18.4 - - + -
49I MET* 3.8 24.5 - - + -
51I GLY* 3.2 33.0 - - - +
52I ALA 4.1 0.2 + - - -
53I GLY 3.0 26.9 - - - +
55I ALA* 1.3 76.1 - - - +
57I GLU* 1.3 72.6 + - - +
58I GLU 3.3 0.2 - - - -
59I ALA* 3.1 7.8 - - - +
60I LEU 2.9 23.7 + - - -
13J PRO* 3.7 17.9 - - + -
15J THR* 3.9 9.9 - - + -
171J THR 5.1 4.3 - - - +
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I TYR* 2.8 31.6 + - - -
53I GLY 3.5 4.5 + - - +
54I HIS* 3.3 16.5 + - + +
56I VAL* 1.3 75.4 - - - +
58I GLU* 1.3 59.1 + - + +
60I LEU* 3.6 16.2 + - - +
61I HIS* 3.0 27.9 + - - +
87I VAL* 4.3 11.9 - - - +
88I GLY* 5.8 4.0 - - - -
90I ARG* 6.0 3.1 + - - -
95I ILE* 5.7 4.5 - - - +
12J ASP 4.4 4.7 - - - +
13J PRO* 3.4 29.5 - - + +
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Residues in contact with GLU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I HIS* 3.1 34.7 + - - +
55I ALA* 3.8 9.3 - - - +
57I GLU* 1.3 75.5 - - + +
59I ALA* 1.3 57.2 - - - +
61I HIS* 3.4 7.7 + - - +
62I GLU* 3.1 36.5 + - + +
172J ASN* 4.0 9.3 + - - +
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Residues in contact with ALA 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ASP 4.5 14.7 - - - +
44I TYR* 4.8 0.4 - - + -
49I MET* 4.6 6.1 - - + -
55I ALA 3.4 12.2 + - - +
56I VAL* 3.1 14.1 - - - +
58I GLU* 1.3 76.5 - - - +
60I LEU* 1.3 67.9 + - - +
61I HIS 3.2 0.2 - - - -
62I GLU* 4.2 3.7 - - - +
63I ALA* 2.9 27.0 + - - +
171J THR* 4.2 21.1 - - + +
172J ASN* 3.8 8.4 - - - +
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I VAL* 3.2 36.1 - - + -
12I LEU* 4.2 13.2 - - + -
44I TYR* 3.6 44.1 - - + +
56I VAL 2.9 11.1 + - - +
57I GLU* 4.1 18.8 - - - +
58I GLU 3.4 0.2 - - - -
59I ALA* 1.3 81.1 - - - +
61I HIS* 1.3 62.9 + - - +
63I ALA* 3.0 8.7 + - - +
64I ILE* 3.1 29.6 + - + +
90I ARG* 6.1 1.6 - - - +
95I ILE* 4.3 15.0 - - + -
98I GLU* 6.5 0.2 - - - -
99I VAL* 4.4 7.4 - - + -
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Residues in contact with HIS 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I GLU 3.0 19.7 + - - +
58I GLU* 3.5 7.4 - - - +
59I ALA 3.2 0.2 - - - -
60I LEU* 1.3 78.4 - - - +
62I GLU* 1.3 82.5 + - - +
64I ILE* 3.6 17.9 - - - +
65I LYS* 3.5 33.4 + - - +
98I GLU* 4.8 10.7 + - - -
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Residues in contact with GLU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I GLU* 3.1 19.6 + - + +
59I ALA* 4.2 4.5 - - - +
61I HIS* 1.3 87.1 - - - +
63I ALA* 1.3 69.2 + - - +
64I ILE 3.2 0.7 - - - -
65I LYS* 2.9 52.1 + - - +
66I GLY 4.2 1.7 + - - -
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Residues in contact with ALA 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I SER* 4.7 3.4 + - - +
10I VAL* 3.7 24.0 - - + -
43I ASP* 4.0 22.9 - - + +
59I ALA 2.9 19.4 + - - +
60I LEU* 3.6 3.6 - - - +
62I GLU* 1.3 80.0 - - - +
64I ILE* 1.3 58.1 + - - +
65I LYS 3.1 4.4 + - - -
66I GLY* 3.2 12.5 + - - -
68I PHE* 3.8 14.2 - - - +
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Residues in contact with ILE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I VAL* 4.2 6.3 - - + -
60I LEU* 3.1 36.8 + - + +
61I HIS* 3.6 22.7 - - - +
62I GLU 3.2 0.2 - - - -
63I ALA* 1.3 74.0 - - - +
65I LYS* 1.3 62.3 + - + +
66I GLY 3.2 2.8 + - - +
68I PHE* 3.5 36.1 - - + -
98I GLU* 3.7 28.5 - - + +
99I VAL* 3.9 25.4 - - + -
102I LYS* 3.9 28.8 - - + +
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Residues in contact with LYS 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I HIS* 3.5 40.8 + - - +
62I GLU* 2.9 42.0 + - - +
63I ALA 3.1 1.2 - - - -
64I ILE* 1.3 79.6 - - + +
66I GLY* 1.3 56.6 + - - +
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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