Contacts of the helix formed by residues 149 - 155 (chain B) in PDB entry 2VRF
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 LEU 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B GLN* 3.2 22.4 - - - +
123B ALA 6.0 0.2 - - - +
124B GLY* 4.2 16.8 - - - +
125B GLY 5.9 0.4 - - - +
127B GLY* 3.8 27.6 - - - -
146B PHE* 3.2 28.9 + - + +
147B PRO 4.4 3.8 - - - +
148B GLY* 1.3 79.7 - - - +
150B ALA* 1.3 66.9 + - - +
151B ALA 3.4 1.8 - - - -
152B ASP 3.0 4.4 + - - -
153B GLN* 3.0 24.2 + - - +
155D ARG* 3.4 28.9 - - - +
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Residues in contact with ALA 150 (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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118B VAL* 3.6 17.6 - - + +
119B VAL 3.4 25.6 - - - +
120B LYS* 4.1 2.5 - - - -
121B GLN* 4.4 6.6 + - + +
125B GLY 4.1 13.2 + - - +
126B LEU 3.9 7.9 + - - +
149B LEU* 1.3 76.8 - - - +
151B ALA* 1.3 62.9 + - - +
153B GLN* 3.3 7.2 + - - +
154B SER* 3.2 18.9 + - - -
158D ARG* 3.7 14.9 + - - +
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Residues in contact with ALA 151 (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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118B VAL* 4.1 6.9 - - + +
126B LEU* 3.0 15.8 + - + +
127B GLY 4.3 2.5 - - - +
128B ILE* 3.1 36.6 - - + -
145B ILE* 4.3 6.2 - - + +
149B LEU 3.4 0.4 - - - -
150B ALA* 1.3 73.1 - - - +
152B ASP* 1.3 61.4 + - - +
154B SER* 2.5 28.7 + - - -
155B ARG* 3.8 0.7 + - - -
156B ALA 4.7 0.2 + - - -
157B LEU* 3.6 25.0 + - + +
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Residues in contact with ASP 152 (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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145B ILE* 3.7 17.7 - - + +
146B PHE 3.6 16.5 + - - +
147B PRO* 3.6 9.9 - - - +
148B GLY* 2.7 24.4 + - - +
149B LEU 3.0 10.6 + - - +
151B ALA* 1.3 77.2 - - - +
153B GLN* 1.3 58.0 + - - +
155B ARG* 2.9 57.8 + - - -
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Residues in contact with GLN 153 (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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121B GLN* 4.5 1.6 + - - -
148B GLY* 2.8 27.7 + - - +
149B LEU* 3.0 16.9 + - - +
150B ALA* 3.3 7.5 + - - +
152B ASP* 1.3 75.2 - - - +
154B SER* 1.3 61.4 + - - +
155B ARG* 3.3 14.4 + - - +
154D SER 5.5 0.4 - - - -
155D ARG* 2.8 28.2 + - - +
156D ALA* 3.9 9.8 - - + +
158D ARG* 2.9 31.9 + - - +
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Residues in contact with SER 154 (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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116B VAL* 4.2 4.0 - - - -
117B ARG 4.1 20.0 - - - -
118B VAL* 4.3 4.3 - - - -
150B ALA 3.2 10.1 + - - -
151B ALA* 2.5 21.9 + - - -
153B GLN* 1.3 76.6 - - - +
155B ARG* 1.3 66.7 + - - +
156B ALA* 3.0 26.2 + - - +
157B LEU* 3.8 11.6 + - - +
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Residues in contact with ARG 155 (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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151B ALA 3.8 0.4 + - - -
152B ASP* 2.9 56.7 + - - -
153B GLN* 3.5 11.7 - - - +
154B SER* 1.3 78.7 + - - +
156B ALA* 1.3 55.5 + - - +
157B LEU 3.7 4.3 - - - -
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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