Contacts of the helix formed by residues 53 - 65 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10L VAL 5.2 1.3 - - - -
11L VAL* 3.7 8.0 - - - +
12L ASP 3.7 28.7 - - - -
13L PRO* 2.8 23.6 + - - +
174L TYR* 4.8 0.7 - - - -
52S ALA* 1.3 71.4 - - - +
54S HIS* 1.3 62.2 + - - -
56S VAL* 3.0 22.1 + - - +
57S GLU* 3.5 3.1 + - - +
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Residues in contact with HIS 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G PHE* 4.5 18.3 - + - -
195G GLU* 3.6 49.1 + - + +
10L VAL* 4.4 23.1 + - + +
12L ASP 5.2 7.0 + - - -
52S ALA 3.5 0.4 + - - -
53S GLY* 1.3 69.5 - - - -
55S ALA* 1.3 62.9 + - - +
56S VAL 3.2 0.2 - - - -
57S GLU* 3.9 11.6 - - + +
58S GLU* 3.1 41.8 + - - +
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Residues in contact with ALA 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L ASN* 2.5 62.2 + - + +
174L TYR* 4.4 12.1 - - + -
51S GLY* 4.6 1.8 - - - -
52S ALA 3.3 15.9 + - - +
53S GLY 3.2 2.0 + - - -
54S HIS* 1.3 76.3 - - - +
56S VAL* 1.3 59.0 + - - +
58S GLU* 3.7 4.8 + - - -
59S ALA* 3.4 7.1 + - - +
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Residues in contact with VAL 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L PRO* 3.7 17.3 - - + -
15L THR* 3.9 9.4 - - + -
171L THR 5.1 3.8 - - - +
44S TYR* 3.5 18.7 - - + -
49S MET* 3.8 25.1 - - + -
51S GLY* 3.2 33.0 - - - +
53S GLY 3.0 26.9 - - - +
55S ALA* 1.3 76.7 - - - +
57S GLU* 1.3 73.4 + - - +
58S GLU 3.3 0.4 - - - -
59S ALA* 3.1 8.2 - - - +
60S LEU 2.9 23.6 + - - -
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Residues in contact with GLU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ASP 4.4 4.7 - - - +
13L PRO* 3.4 30.4 - - + +
44S TYR* 2.8 30.9 + - - -
53S GLY 3.5 4.4 + - - +
54S HIS* 3.3 15.2 + - + +
56S VAL* 1.3 74.8 - - - +
58S GLU* 1.3 60.0 + - - +
60S LEU* 4.0 15.9 - - - +
61S HIS* 3.0 27.2 + - - +
87S VAL* 4.3 11.3 - - - +
88S GLY* 5.8 4.4 - - - -
90S ARG* 6.0 2.6 + - - -
95S ILE* 5.7 4.9 - - - +
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Residues in contact with GLU 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L ASN* 4.0 9.0 + - - +
54S HIS* 3.1 35.1 + - - +
55S ALA* 3.8 8.6 - - - +
57S GLU* 1.3 75.5 - - - +
59S ALA* 1.3 57.3 - - - +
61S HIS* 3.4 7.1 + - - +
62S GLU* 3.1 36.6 + - + +
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Residues in contact with ALA 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171L THR* 4.2 20.2 - - + +
172L ASN* 3.8 8.7 - - - +
43S ASP 4.5 15.3 - - - +
44S TYR* 4.8 1.1 - - + -
49S MET* 4.6 5.6 - - + -
55S ALA 3.4 12.1 + - - +
56S VAL* 3.1 14.6 + - - +
58S GLU* 1.3 76.5 - - - +
60S LEU* 1.3 67.7 + - - +
62S GLU* 4.1 3.9 - - - +
63S ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S VAL* 3.2 35.4 - - + -
12S LEU* 4.2 13.7 - - + -
44S TYR* 3.6 45.1 - - + +
56S VAL 2.9 11.3 + - - +
57S GLU* 4.1 19.3 - - - +
59S ALA* 1.3 79.7 - - - +
61S HIS* 1.3 63.9 + - - +
63S ALA* 3.0 9.4 + - - +
64S ILE* 3.1 30.3 + - + +
90S ARG* 6.1 1.1 - - - +
95S ILE* 4.3 15.5 - - + -
98S GLU* 6.5 0.2 - - - -
99S VAL* 4.4 7.0 - - + -
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Residues in contact with HIS 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G TYR* 3.9 23.1 + + - -
222G PRO* 4.2 23.4 + - + +
223G ASP* 2.7 38.7 + - - -
57S GLU 3.0 18.8 + - - +
58S GLU* 3.5 8.3 - - - +
60S LEU* 1.3 77.7 - - - +
62S GLU* 1.3 84.4 + - - +
64S ILE* 3.6 18.7 - - - +
65S LYS* 3.5 18.3 - - - +
98S GLU* 4.8 3.8 + - - -
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Residues in contact with GLU 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58S GLU* 3.1 18.7 + - + +
59S ALA* 4.2 4.3 - - - +
61S HIS* 1.3 87.6 - - - +
63S ALA* 1.3 66.9 + - - +
64S ILE 3.2 0.4 - - - -
65S LYS* 2.9 51.7 + - - +
66S GLY 4.2 1.2 + - - -
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Residues in contact with ALA 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8S SER* 4.7 3.4 + - - +
10S VAL* 3.7 24.0 - - + -
43S ASP* 4.0 23.1 - - + +
59S ALA 2.9 19.6 + - - +
60S LEU* 3.0 4.2 + - - +
62S GLU* 1.3 79.1 - - - +
64S ILE* 1.3 57.6 + - - +
65S LYS 3.1 4.4 + - - -
66S GLY* 3.2 12.1 + - - -
68S PHE* 3.8 13.9 - - - +
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Residues in contact with ILE 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S VAL* 4.2 5.8 - - + -
60S LEU* 3.1 36.3 + - + +
61S HIS* 3.6 23.1 - - - +
62S GLU 3.2 0.4 - - - -
63S ALA* 1.3 75.3 - - - +
65S LYS* 1.3 63.2 + - + +
66S GLY 3.2 2.4 + - - +
68S PHE* 3.5 36.6 - - + -
98S GLU* 3.7 28.7 - - + +
99S VAL* 3.9 25.1 - - + -
102S LYS* 3.9 29.5 - - + +
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Residues in contact with LYS 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G PRO 5.5 0.4 + - - -
223G ASP* 2.7 33.7 + - - +
258G TYR* 5.2 4.2 + - - -
61S HIS* 3.5 28.2 + - - +
62S GLU* 2.9 41.8 + - - +
63S ALA 3.1 1.0 - - - -
64S ILE* 1.3 80.7 - - + +
66S GLY* 1.3 56.7 + - - +
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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