Contacts of the helix formed by residues 131 - 141 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129J ALA 3.4 10.5 - - - +
130J ASP* 1.3 89.0 - - - +
132J ALA* 1.3 53.2 + - + +
134J ALA* 3.6 1.2 - - - +
135J ALA* 2.8 35.3 + - - +
148J THR* 3.7 22.1 - - + +
151J LEU* 3.7 6.1 - - + +
152J LYS* 3.6 39.7 - - + +
155J GLN* 4.0 13.9 - - - +
190J LEU* 4.1 13.9 - - + -
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Residues in contact with ALA 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ASP* 3.1 10.6 + - - +
131J PRO* 1.3 78.4 - - + +
133J LYS* 1.3 63.5 + - - +
135J ALA* 3.9 1.9 - - - +
136J ARG* 3.0 53.5 + - - +
148J THR* 3.6 25.3 - - + +
152J LYS* 5.8 0.2 - - - +
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Residues in contact with LYS 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ASP* 3.0 27.6 + - + +
132J ALA* 1.3 80.0 - - - +
134J ALA* 1.3 62.1 + - - +
136J ARG* 3.4 21.3 + - - +
137J LEU* 3.2 23.3 + - + +
187J GLU* 3.6 32.2 - - + +
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Residues in contact with ALA 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ASP 2.8 15.4 + - - +
131J PRO 3.6 1.1 - - - +
132J ALA 3.3 0.2 - - - -
133J LYS* 1.3 78.4 - - - +
135J ALA* 1.3 62.4 + - - +
137J LEU* 3.3 5.5 + - - +
138J ALA* 3.0 23.4 + - - +
151J LEU* 3.5 19.7 - - + -
187J GLU* 3.7 29.4 - - + +
190J LEU* 3.6 19.1 - - + -
191J ILE* 3.6 3.6 - - + +
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Residues in contact with ALA 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J PRO 2.8 21.9 + - - +
132J ALA* 4.1 3.1 - - - +
133J LYS 3.4 0.2 - - - -
134J ALA* 1.3 72.8 - - - +
136J ARG* 1.3 63.2 + - + +
138J ALA* 3.6 5.7 - - - +
139J ASN* 3.0 32.1 + - - +
146J THR* 4.2 10.5 - - + +
147J THR 3.9 7.0 - - - +
148J THR* 3.9 27.8 - - - +
151J LEU* 3.4 10.7 - - + +
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Residues in contact with ARG 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ASP* 5.2 2.6 + - - -
132J ALA* 3.0 41.9 + - - +
133J LYS* 3.4 29.9 + - - +
134J ALA 3.2 0.2 - - - -
135J ALA* 1.3 76.0 - - - +
137J LEU* 1.3 63.9 + - - +
139J ASN* 3.3 9.9 + - - +
140J ASP* 3.1 27.1 + - - +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J LYS* 3.2 15.3 + - + +
134J ALA 3.5 4.3 - - - +
136J ARG* 1.3 81.0 - - - +
138J ALA* 1.3 56.0 + - - +
140J ASP* 2.8 25.1 + - + -
141J LEU* 3.0 28.5 + - + +
185J PRO* 6.3 0.4 - - + -
187J GLU* 4.6 11.2 - - + -
188J VAL* 3.9 28.7 - - + -
191J ILE* 3.8 12.8 - - + -
267J PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J ALA 3.0 17.4 + - - +
135J ALA* 3.6 7.4 - - - +
137J LEU* 1.3 76.1 - - - +
139J ASN* 1.3 58.8 + - - +
141J LEU* 3.2 20.0 + - - +
142J SER* 3.4 16.3 + - - +
144J LYS 4.7 1.7 - - - +
146J THR* 3.9 24.8 + - + +
191J ILE* 3.9 24.5 - - + -
195J HIS* 5.8 5.6 - - + +
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Residues in contact with ASN 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ALA* 3.0 23.3 + - - +
136J ARG* 3.6 8.1 - - - +
137J LEU 3.1 0.2 - - - -
138J ALA* 1.3 81.4 - - - +
140J ASP* 1.3 65.6 + - - +
141J LEU 3.2 0.9 - - - -
142J SER 3.3 16.8 - - - +
144J LYS 3.5 2.9 - - - +
145J LYS* 3.4 15.6 - - - +
146J THR* 2.8 47.7 + - - -
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Residues in contact with ASP 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ARG* 3.1 15.0 + - - +
137J LEU* 2.8 16.9 + - + +
139J ASN* 1.3 85.4 - - - +
141J LEU* 1.3 67.1 + - + +
142J SER 4.9 0.2 - - - -
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Residues in contact with LEU 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J LEU* 3.0 33.1 + - + +
138J ALA* 3.2 13.6 + - - +
140J ASP* 1.3 89.2 - - + +
142J SER* 1.3 60.0 + - - +
188J VAL* 6.4 1.6 - - + -
191J ILE* 5.1 8.7 - - + -
259J THR* 3.9 27.1 - - - +
260J ASP* 5.4 5.4 - - - +
263J ALA* 3.7 30.5 - - + -
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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