Contacts of the helix formed by residues 92 - 102 (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 MET 92 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L HIS* 3.6 43.3 - - + +
41L LEU* 4.0 7.4 - - + -
13S HIS 4.7 0.7 - - - +
14S ASN* 2.9 46.2 - - - +
15S ALA 3.8 2.5 - - - -
76S ILE* 4.3 1.6 - - + -
77S PRO* 4.1 16.2 - - + -
82S GLY 4.6 0.6 + - - +
85S GLY* 3.0 43.6 + - - +
86S LYS* 3.7 6.3 - - - +
87S VAL* 4.6 11.2 - - + -
90S ARG 3.4 0.2 + - - -
91S ASN* 1.3 67.9 - - - +
93S TYR* 1.3 67.4 + - - +
94S ASP 3.3 0.2 + - - -
95S ILE* 3.3 9.7 + - + +
96S CYS* 3.1 27.4 + - - -
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Residues in contact with TYR 93 (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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76S ILE* 3.5 24.2 - - + +
77S PRO 4.2 11.8 + - - +
78S MET* 3.7 26.7 - - + -
81S GLY 5.8 1.8 - - - +
82S GLY* 5.7 1.8 - - - -
91S ASN* 3.2 6.5 - - + +
92S MET* 1.3 79.5 - - - +
94S ASP* 1.3 71.2 + - - +
96S CYS* 3.8 1.5 - - - +
97S ALA* 2.9 39.9 + - + +
134S ALA* 3.7 10.3 - - + -
135S LEU* 3.3 26.7 - - + -
137S LYS* 2.8 33.9 + - - -
138S LEU* 3.9 10.0 - - - +
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Residues in contact with ASP 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G THR* 3.8 22.0 - - - +
216G GLU* 3.5 31.2 - - - +
90S ARG* 3.8 4.6 + - - -
91S ASN* 2.8 33.6 + - - +
93S TYR* 1.3 87.4 - - - +
95S ILE* 1.3 64.8 + - - +
97S ALA* 3.3 5.0 + - - +
98S GLU* 3.1 23.2 + - - +
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Residues in contact with ILE 95 (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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12S LEU* 4.3 17.7 - - + -
57S GLU* 5.7 4.0 - - - +
60S LEU* 4.3 11.7 - - + -
87S VAL* 3.6 37.2 - - + +
90S ARG* 3.4 57.2 - - + +
91S ASN 3.1 10.3 + - - +
92S MET* 3.3 8.2 + - + +
94S ASP* 1.3 76.8 - - - +
96S CYS* 1.3 56.6 + - - +
98S GLU* 3.2 2.0 + - - +
99S VAL* 2.9 42.4 + - + +
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Residues in contact with CYS 96 (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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12S LEU* 4.0 20.6 - - - -
14S ASN* 3.4 32.1 - - - -
72S ILE* 4.4 7.2 - - + -
76S ILE* 3.9 16.4 - - + -
92S MET 3.1 19.9 + - - +
93S TYR 3.8 3.4 - - - +
95S ILE* 1.3 72.9 - - - +
97S ALA* 1.3 63.3 - - - +
99S VAL 4.4 0.2 - - - +
100S ALA* 2.9 37.0 + - - +
135S LEU* 3.7 19.7 - - + +
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Residues in contact with ALA 97 (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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93S TYR* 2.9 36.0 + - + +
94S ASP* 3.3 6.3 + - - +
96S CYS* 1.3 77.4 - - - +
98S GLU* 1.3 56.4 + - - +
101S PRO* 2.9 25.3 - - - +
135S LEU* 4.4 2.4 - - + +
138S LEU* 3.4 30.1 - - + +
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Residues in contact with GLU 98 (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* 2.7 24.6 + - - -
264G ALA* 4.2 31.9 - - + +
60S LEU* 6.5 0.4 - - - -
61S HIS* 4.8 2.9 + - - -
64S ILE* 3.7 25.5 - - + +
90S ARG* 2.7 35.3 + - - +
94S ASP 3.1 10.3 + - - +
95S ILE* 3.5 8.0 - - - +
96S CYS 3.1 0.4 - - - -
97S ALA* 1.3 78.6 - - - +
99S VAL* 1.3 65.9 + - + +
101S PRO* 3.8 2.3 - - - +
102S LYS* 3.1 31.8 + - - +
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Residues in contact with VAL 99 (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 6.5 - - + -
12S LEU* 4.1 13.0 - - + -
60S LEU* 4.4 10.8 - - + -
64S ILE* 3.9 30.7 - - + -
68S PHE* 3.7 17.5 - - + -
70S CYS* 4.0 20.9 - - - -
95S ILE* 2.9 36.2 + - + +
98S GLU* 1.3 79.3 - - + +
100S ALA* 1.3 67.5 + - - +
102S LYS* 3.0 22.8 + - - +
103S ALA 3.6 3.6 + - - -
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Residues in contact with ALA 100 (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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70S CYS* 4.3 8.7 - - - -
72S ILE* 4.1 17.3 - - + -
96S CYS* 2.9 20.4 + - - +
99S VAL* 1.3 76.7 - - - +
101S PRO* 1.3 64.5 - - + +
103S ALA* 3.2 20.8 + - - +
106S VAL* 3.6 14.2 - - + +
135S LEU* 4.0 12.8 - - + -
140S VAL* 3.9 18.3 - - + +
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Residues in contact with PRO 101 (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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96S CYS 3.4 1.6 - - - +
97S ALA 2.9 29.4 - - - +
98S GLU 3.8 2.7 - - - +
99S VAL 3.4 3.1 - - - -
100S ALA* 1.3 94.9 - - + +
102S LYS* 1.3 61.0 + - + +
103S ALA 3.5 4.3 + - - +
138S LEU* 4.0 36.3 - - + +
139S GLY 6.3 0.4 - - - -
140S VAL* 4.1 9.6 - - + -
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Residues in contact with LYS 102 (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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264G ALA 3.7 25.1 + - - -
64S ILE* 3.9 42.2 - - + +
66S GLY 4.4 5.2 - - - +
68S PHE* 3.6 17.1 - - + -
98S GLU* 3.1 25.1 + - - +
99S VAL 3.0 6.7 + - - +
101S PRO* 1.3 78.1 - - + +
103S ALA* 1.3 61.2 + - - +
104S LYS* 4.5 7.4 - - - -
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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