Contacts of the helix formed by residues 53 - 65 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52G ALA* 1.3 71.6 - - - +
54G HIS* 1.3 61.5 + - - -
56G VAL* 3.0 21.7 + - - +
57G GLU* 3.5 3.3 + - - +
10H VAL 5.2 1.6 - - - -
11H VAL* 3.7 7.8 - - - +
12H ASP 3.7 28.9 - - - -
13H PRO* 2.8 23.2 + - - +
174H TYR* 4.8 0.7 - - - -
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Residues in contact with HIS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E PHE* 4.6 18.7 - + - -
195E GLU* 3.7 44.6 + - + +
52G ALA 3.5 0.6 + - - -
53G GLY* 1.3 70.1 - - - -
55G ALA* 1.3 62.4 + - - +
56G VAL 3.2 0.2 - - - -
57G GLU* 3.8 12.1 - - - +
58G GLU* 3.1 42.6 + - - +
10H VAL* 4.4 23.8 + - + +
12H ASP 5.2 7.0 + - - -
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G GLY* 4.6 1.1 - - - -
52G ALA 3.3 16.1 + - - +
53G GLY 3.2 1.8 + - - -
54G HIS* 1.3 76.7 - - - +
56G VAL* 1.3 59.7 + - - +
58G GLU* 3.7 5.5 + - - +
59G ALA* 3.4 6.8 + - - +
172H ASN* 2.5 60.6 + - + +
174H TYR* 4.4 12.1 - - + -
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Residues in contact with VAL 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G TYR* 3.5 17.6 - - + -
49G MET* 3.8 24.9 - - + -
51G GLY* 3.2 33.4 - - - +
53G GLY 3.0 26.7 - - - +
55G ALA* 1.3 76.1 - - - +
57G GLU* 1.3 71.9 + - - +
58G GLU 3.3 0.2 - - - -
59G ALA* 3.1 8.6 - - - +
60G LEU 2.9 23.7 + - - -
13H PRO* 3.7 18.2 - - + -
15H THR* 3.9 9.4 - - + -
171H THR 5.1 3.4 - - - +
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G TYR* 2.8 31.6 + - - -
53G GLY 3.5 5.1 + - - +
54G HIS* 3.3 15.9 + - + +
56G VAL* 1.3 76.0 - - - +
58G GLU* 1.3 60.0 + - + +
60G LEU* 4.1 16.1 - - - +
61G HIS* 3.0 27.7 + - - +
87G VAL* 4.3 12.2 - - - +
88G GLY* 5.8 4.2 - - - -
90G ARG* 6.0 2.6 + - - -
95G ILE* 5.7 4.5 - - - +
12H ASP 4.4 4.5 - - - +
13H PRO* 3.4 29.4 - - + +
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Residues in contact with GLU 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G HIS* 3.1 34.2 + - - +
55G ALA* 3.8 8.9 - - - +
56G VAL 3.3 0.2 - - - -
57G GLU* 1.3 75.5 - - - +
59G ALA* 1.3 56.0 + - - +
61G HIS* 3.4 7.0 + - - +
62G GLU* 3.1 36.9 + - + +
172H ASN* 4.0 8.6 + - - +
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Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ASP 4.5 14.3 - - - +
44G TYR* 4.8 0.9 - - + -
49G MET* 4.6 6.1 - - + -
55G ALA 3.4 12.2 + - - +
56G VAL* 3.1 13.9 + - - +
58G GLU* 1.3 77.7 - - - +
60G LEU* 1.3 68.8 + - - +
62G GLU* 4.2 3.7 - - - +
63G ALA* 2.9 26.5 + - - +
171H THR* 4.2 20.6 - - + +
172H ASN* 3.8 8.9 - - - +
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.2 36.8 - - + -
12G LEU* 4.2 13.2 - - + -
44G TYR* 3.6 43.7 - - + -
56G VAL 2.9 10.7 + - - +
57G GLU* 3.6 20.2 + - - +
59G ALA* 1.3 79.1 - - - +
61G HIS* 1.3 63.8 + - - +
63G ALA* 3.0 9.0 + - - +
64G ILE* 3.1 30.0 + - + +
90G ARG* 6.1 1.1 - - - +
95G ILE* 4.3 15.3 - - + -
98G GLU* 6.5 0.4 - - - -
99G VAL* 4.4 6.5 - - + -
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Residues in contact with HIS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E TYR* 4.0 22.6 + + - -
222E PRO* 4.3 21.4 + - + +
223E ASP* 2.7 39.9 + - - -
57G GLU 3.0 19.9 + - - +
58G GLU* 3.5 7.6 - - - +
59G ALA 3.2 0.2 - - - -
60G LEU* 1.3 77.3 - - - +
62G GLU* 1.3 85.3 + - + +
64G ILE* 3.6 18.1 - - - +
65G LYS* 3.5 19.5 - - - +
98G GLU* 4.8 4.2 + - - -
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Residues in contact with GLU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLU* 3.1 19.0 + - + +
59G ALA* 4.2 3.8 - - - +
61G HIS* 1.3 87.6 - - - +
63G ALA* 1.3 67.5 + - - +
64G ILE 3.2 0.4 - - - -
65G LYS* 2.9 51.1 + - - +
66G GLY 4.2 1.2 + - - -
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Residues in contact with ALA 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER* 4.7 3.3 + - - +
10G VAL* 3.7 24.0 - - + -
43G ASP* 4.0 23.1 - - + +
59G ALA 2.9 19.4 + - - +
60G LEU* 3.6 4.3 - - - +
62G GLU* 1.3 79.2 - - - +
64G ILE* 1.3 57.6 + - - +
65G LYS 3.1 4.4 + - - -
66G GLY* 3.2 12.3 + - - -
68G PHE* 3.8 13.4 - - - +
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 4.2 5.6 - - + -
60G LEU* 3.1 36.6 + - + +
61G HIS* 3.6 22.7 - - - +
63G ALA* 1.3 74.5 - - - +
65G LYS* 1.3 63.8 + - + +
66G GLY 3.2 2.4 + - - +
68G PHE* 3.5 35.3 - - + -
98G GLU* 3.7 28.5 - - + +
99G VAL* 3.9 25.4 - - + -
102G LYS* 3.9 28.8 - - + +
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Residues in contact with LYS 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E PRO 5.6 0.2 + - - -
223E ASP* 2.8 32.4 + - - +
258E TYR* 5.3 4.1 + - - -
61G HIS* 3.5 27.7 + - - +
62G GLU* 2.9 41.8 + - - +
63G ALA 3.1 1.2 - - - -
64G ILE* 1.3 81.6 - - + +
66G GLY* 1.3 55.5 + - - +
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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