Contacts of the helix formed by residues 131 - 138 (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 VAL 131 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72S ILE* 3.6 46.9 - - + -
74S GLY 4.6 1.1 - - - +
76S ILE* 4.3 13.7 - - + -
106S VAL* 4.4 1.3 - - + -
108S ALA* 4.2 7.4 - - + -
113S ALA* 2.8 29.0 + - + +
114S THR* 4.4 0.4 + - - -
130S GLY* 1.3 67.2 - - - -
132S ASN* 1.3 70.6 + - - +
134S ALA* 3.0 1.6 + - - -
135S LEU* 2.8 31.6 + - + +
140S VAL* 4.1 13.9 - - + -
142S ALA* 3.7 23.8 - - + -
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Residues in contact with ASN 132 (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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114S THR 5.0 5.7 + - - +
130S GLY 3.6 0.2 - - - -
131S VAL* 1.3 78.6 - - - +
133S GLU* 1.3 56.6 + - - +
136S GLY* 3.1 27.3 + - - +
140S VAL 3.5 11.2 - - - +
141S LYS* 4.3 5.7 - - - +
142S ALA* 2.7 51.2 + - - +
144S ASN* 3.7 22.6 + - - +
174S GLY* 5.7 1.4 - - - -
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Residues in contact with GLU 133 (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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115S TYR 5.4 2.4 - - - +
129S VAL* 3.8 30.7 - - + +
130S GLY 3.2 12.6 + - - +
131S VAL 3.1 1.0 - - - -
132S ASN* 1.3 78.0 - - - +
134S ALA* 1.3 63.3 + - - +
136S GLY 4.5 1.6 + - - -
137S LYS* 5.6 1.7 + - - +
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Residues in contact with ALA 134 (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* 4.1 13.5 - - + -
78S MET* 3.6 19.2 - - - +
93S TYR* 3.7 1.8 - - + -
129S VAL* 3.5 17.4 - - + +
130S GLY 2.9 16.5 + - - +
131S VAL 3.8 1.6 - - - +
133S GLU* 1.3 80.0 - - - +
135S LEU* 1.3 75.1 + - + +
136S GLY 3.7 0.2 - - - -
137S LYS* 3.3 29.5 + - - +
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Residues in contact with LEU 135 (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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72S ILE* 4.3 8.7 - - + -
76S ILE* 3.8 11.9 - - + -
93S TYR* 3.3 35.9 - - + -
96S CYS* 3.7 23.8 - - + +
97S ALA* 4.4 6.5 - - - +
100S ALA* 4.0 20.4 - - + -
131S VAL* 2.8 21.4 + - + +
134S ALA* 1.3 78.1 - - + +
136S GLY* 1.3 61.8 + - - +
137S LYS 3.1 3.1 - - - -
138S LEU* 2.9 34.9 + - + +
140S VAL* 3.1 30.0 + - + -
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Residues in contact with GLY 136 (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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132S ASN* 3.1 21.2 + - - -
133S GLU 4.5 1.4 + - - -
134S ALA 3.7 1.2 - - - -
135S LEU* 1.3 74.1 - - - +
137S LYS* 1.3 56.0 + - - +
139S GLY* 3.0 22.0 + - - -
140S VAL 3.3 18.3 + - - +
141S LYS* 6.0 0.3 - - - +
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Residues in contact with LYS 137 (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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78S MET* 4.6 8.7 - - - +
93S TYR* 2.8 35.3 + - - -
133S GLU 5.6 1.9 + - - +
134S ALA 3.3 19.9 + - - +
135S LEU 3.1 0.8 - - - -
136S GLY* 1.3 72.6 - - - +
138S LEU* 1.3 71.4 + - + +
139S GLY 3.1 5.7 + - - -
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Residues in contact with LEU 138 (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* 3.9 9.2 - - - +
97S ALA* 3.4 45.5 - - + +
101S PRO* 4.0 27.4 - - + +
135S LEU* 2.9 27.6 + - + +
137S LYS* 1.3 95.0 - - + +
139S GLY* 1.3 61.1 - - - +
140S VAL* 3.4 2.1 + - + -
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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