Contacts of the helix formed by residues 131 - 141 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA 3.4 9.8 - - - +
130B ASP* 1.3 88.6 - - - +
132B ALA* 1.3 54.9 + - + +
134B ALA* 3.6 1.2 - - - +
135B ALA* 2.8 35.2 + - - +
148B THR* 3.7 21.5 - - + +
151B LEU* 3.7 6.1 - - + +
152B LYS* 3.6 41.3 - - + +
155B GLN* 4.0 14.1 - - - +
190B LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP* 3.1 11.1 + - - +
131B PRO* 1.3 77.9 - - + +
133B LYS* 1.3 63.8 + - - +
135B ALA* 3.6 2.1 + - - +
136B ARG* 3.0 52.5 + - - +
148B THR* 3.6 24.7 - - + +
152B LYS* 5.8 0.7 - - - +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP* 3.0 27.6 + - + +
132B ALA* 1.3 80.5 - - - +
134B ALA* 1.3 62.3 + - - +
136B ARG* 3.4 20.8 + - - +
137B LEU* 3.2 23.3 + - + +
187B GLU* 3.6 32.9 - - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP 2.8 14.8 + - - +
131B PRO 3.6 1.3 - - - +
133B LYS* 1.3 78.2 - - - +
135B ALA* 1.3 62.0 + - - +
137B LEU* 3.3 5.2 + - - +
138B ALA* 3.0 23.6 + - - +
151B LEU* 3.5 20.2 - - + -
187B GLU* 3.7 30.0 - - + +
190B LEU* 3.6 18.8 - - + -
191B ILE* 3.6 4.2 - - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PRO 2.8 21.3 + - - +
132B ALA 4.1 3.4 - - - +
133B LYS 3.4 0.2 - - - -
134B ALA* 1.3 73.5 - - - +
136B ARG* 1.3 61.6 + - + +
138B ALA* 3.6 4.7 - - - +
139B ASN* 3.0 32.5 + - - +
146B THR* 4.2 10.3 - - + +
147B THR 3.9 7.6 - - - +
148B THR* 3.9 27.4 - - - +
151B LEU* 3.4 10.7 - - + +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP* 5.2 2.6 + - - -
132B ALA* 3.0 41.8 + - - +
133B LYS* 3.8 29.8 - - - +
134B ALA 3.2 0.2 - - - -
135B ALA* 1.3 76.6 - - + +
137B LEU* 1.3 64.1 + - - +
139B ASN* 3.3 9.0 + - - +
140B ASP* 3.1 27.1 + - - +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LYS* 3.2 14.9 + - + +
134B ALA 3.5 4.3 - - - +
136B ARG* 1.3 81.5 - - - +
138B ALA* 1.3 55.9 + - - +
140B ASP* 2.8 24.9 + - + -
141B LEU* 3.0 28.3 + - + +
187B GLU* 4.6 11.9 - - + -
188B VAL* 3.9 27.8 - - + -
191B ILE* 3.8 13.0 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA 3.0 16.8 + - - +
135B ALA* 3.6 7.2 - - - +
137B LEU* 1.3 77.0 - - - +
139B ASN* 1.3 59.2 + - - +
141B LEU* 3.2 20.6 + - - +
142B SER* 3.4 16.3 + - - +
144B LYS 4.7 1.7 - - - +
146B THR* 3.9 24.6 + - + +
151B LEU* 5.2 0.2 - - + -
191B ILE* 3.8 24.2 - - + +
195B HIS* 5.8 5.2 - - + +
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ALA* 3.0 24.7 + - - +
136B ARG* 3.6 7.9 - - - +
137B LEU 3.1 0.2 - - - -
138B ALA* 1.3 80.1 - - - +
140B ASP* 1.3 65.5 + - - +
141B LEU 3.2 1.1 - - - -
142B SER 3.3 16.7 - - - +
144B LYS 3.5 3.2 - - - +
145B LYS* 3.4 16.5 - - - +
146B THR* 2.8 47.3 + - - +
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 3.1 14.8 + - - +
137B LEU* 2.8 16.6 + - + +
139B ASN* 1.3 84.8 - - - +
141B LEU* 1.3 67.1 + - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 3.0 31.8 + - + +
138B ALA* 3.2 13.2 + - - +
140B ASP* 1.3 88.0 - - + +
142B SER* 1.3 60.7 + - - +
188B VAL* 6.4 1.6 - - + -
191B ILE* 5.1 8.7 - - + -
259B THR* 3.9 25.9 - - - +
260B ASP* 5.4 5.2 - - - +
263B 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