Contacts of the helix formed by residues 131 - 141 (chain F) 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 PRO 131 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ALA 3.4 10.0 - - - +
130F ASP* 1.3 88.8 - - - +
132F ALA* 1.3 53.9 + - + +
134F ALA* 3.6 1.0 - - - +
135F ALA* 2.8 34.7 + - - +
148F THR* 3.7 21.2 - - + +
151F LEU* 3.7 6.5 - - + +
152F LYS* 3.6 41.3 - - + +
155F GLN* 4.0 13.0 - - - +
190F LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ASP* 3.1 10.7 + - - +
131F PRO* 1.3 77.9 - - + +
133F LYS* 1.3 62.4 + - - +
135F ALA* 3.9 1.9 - - - +
136F ARG* 3.0 52.8 + - - +
148F THR* 3.6 25.7 - - + +
152F LYS* 5.8 0.2 - - - +
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Residues in contact with LYS 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ASP* 3.0 26.4 + - + +
132F ALA* 1.3 80.5 - - - +
134F ALA* 1.3 62.9 + - - +
136F ARG* 3.4 21.6 + - - +
137F LEU* 3.2 23.1 + - + +
187F GLU* 3.6 32.0 - - + +
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ASP 2.8 15.0 + - - +
131F PRO 3.6 1.1 - - - +
133F LYS* 1.3 78.2 - - - +
135F ALA* 1.3 61.6 + - - +
137F LEU* 3.3 5.0 + - - +
138F ALA* 3.0 24.3 + - - +
151F LEU* 3.5 20.9 - - + -
187F GLU* 3.7 30.3 - - + +
190F LEU* 3.6 18.6 - - + -
191F ILE* 3.6 3.6 - - + +
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Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F PRO 2.8 20.9 + - - +
132F ALA 4.1 3.8 - - - +
133F LYS 3.4 0.2 - - - -
134F ALA* 1.3 73.6 - - - +
136F ARG* 1.3 62.9 + - + +
138F ALA* 3.5 5.5 + - - +
139F ASN* 3.0 32.1 + - - +
146F THR* 4.2 11.4 - - + +
147F THR* 3.9 7.2 - - - +
148F THR* 3.9 26.7 - - - +
151F LEU* 3.4 10.7 - - + +
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Residues in contact with ARG 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ASP* 5.2 2.0 + - - -
132F ALA* 3.0 39.2 + - - +
133F LYS* 3.8 29.8 - - - +
134F ALA 3.2 0.4 - - - -
135F ALA* 1.3 77.8 - - + +
137F LEU* 1.3 63.1 + - - +
139F ASN* 3.3 10.0 + - - +
140F ASP* 3.1 28.0 + - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LYS* 3.2 14.9 + - + +
134F ALA 3.5 4.3 - - - +
136F ARG* 1.3 81.7 - - - +
138F ALA* 1.3 55.6 + - - +
140F ASP* 2.8 26.2 + - + +
141F LEU* 3.0 29.2 + - + +
185F PRO* 6.3 0.2 - - + -
187F GLU* 4.6 12.6 - - + -
188F VAL* 3.9 28.3 - - + -
191F ILE* 3.8 13.0 - - + -
267F PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F ALA 3.0 16.8 + - - +
135F ALA* 3.6 6.5 - - - +
137F LEU* 1.3 77.8 - - - +
139F ASN* 1.3 58.4 + - - +
141F LEU* 3.2 21.7 + - - +
142F SER* 3.4 16.3 + - - +
144F LYS 4.7 1.2 - - - +
146F THR* 3.9 25.2 + - + +
151F LEU* 5.2 0.2 - - + -
191F ILE* 3.9 24.0 - - + -
195F HIS* 5.8 5.4 - - + +
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Residues in contact with ASN 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ALA* 3.0 23.9 + - - +
136F ARG* 3.6 9.0 - - - +
138F ALA* 1.3 81.5 - - - +
140F ASP* 1.3 65.4 + - - +
141F LEU 3.2 1.1 - - - -
142F SER 3.3 16.4 - - - +
144F LYS 3.5 2.6 - - - +
145F LYS* 3.4 17.2 - - - +
146F THR* 2.8 47.9 + - - -
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Residues in contact with ASP 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ARG* 3.1 15.2 + - - +
137F LEU* 2.8 16.0 + - + +
139F ASN* 1.3 84.9 - - - +
141F LEU* 1.3 67.7 + - + +
142F SER 3.8 0.4 - - - -
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F LEU* 3.0 31.9 + - + +
138F ALA* 3.2 13.0 + - - +
140F ASP* 1.3 88.5 - - - +
142F SER* 1.3 59.6 + - - +
188F VAL* 6.4 1.6 - - + -
191F ILE* 5.1 8.5 - - + -
259F THR* 3.9 26.3 - - - +
260F ASP* 5.4 5.8 - - - +
263F ALA* 3.7 31.2 - - + -
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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