Contacts of the helix formed by residues 151 - 159 (chain A) in PDB entry 2VRB
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 GLY 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASN* 2.9 14.8 + - - -
150A GLU* 1.3 77.5 - - - +
152A LEU* 1.3 60.8 + - - +
153A ARG 3.0 7.9 + - - -
154A ALA* 3.2 22.1 + - - +
155A SER* 4.1 2.4 + - - -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE 3.8 18.8 - - - +
148A VAL* 3.8 31.9 - - + -
149A ASN* 3.1 18.3 + - - +
151A GLY* 1.3 76.6 - - - +
153A ARG* 1.3 57.8 + - - +
154A ALA 3.3 0.2 - - - -
155A SER* 3.2 16.6 + - - +
156A THR* 3.1 27.5 + - - -
161A ILE* 4.6 17.5 - - + -
209A LEU* 4.7 14.6 - - + -
213A LEU* 4.2 26.8 - - + +
281A VAL* 4.8 7.0 - - + -
284A ALA* 5.0 2.5 - - + -
285A LEU* 4.1 11.9 - - + -
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.2 35.7 + - - +
151A GLY 3.0 1.8 - - - -
152A LEU* 1.3 75.4 - - - +
154A ALA* 1.3 59.6 + - - +
156A THR* 3.2 9.5 + - - +
157A GLU* 2.9 30.7 + - - +
284A ALA 3.2 19.6 + - - -
285A LEU* 2.7 48.6 + - + +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLY* 3.2 14.1 + - - +
153A ARG* 1.3 77.1 - - - +
155A SER* 1.3 58.9 + - - +
157A GLU* 2.4 32.3 - - - +
158A SER* 3.0 14.0 + - - -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLY 4.1 1.9 + - - -
152A LEU* 3.2 19.0 + - - +
153A ARG 3.1 0.6 - - - -
154A ALA* 1.3 76.2 - - - +
156A THR* 1.3 60.3 + - - +
158A SER* 3.9 0.4 - - - -
159A GLY* 2.8 27.9 + - - -
160A ALA 3.1 34.6 + - - -
161A ILE* 3.6 16.3 - - - +
162A VAL 4.8 0.9 + - - -
213A LEU* 4.1 15.0 - - - -
221A VAL* 3.8 3.2 - - - +
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU 3.1 13.1 + - - -
153A ARG* 3.2 12.5 + - - -
155A SER* 1.3 77.1 - - - +
157A GLU* 1.3 63.0 + - - +
159A GLY* 3.3 1.9 + - - -
213A LEU* 3.5 21.7 - - - +
217A SER* 4.1 14.5 - - - +
219A LYS* 3.0 51.1 - - + +
221A VAL* 3.9 9.1 - - - +
285A LEU* 5.2 3.3 - - - +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG 2.9 13.1 + - - +
154A ALA* 2.4 36.2 - - - +
156A THR* 1.3 79.1 - - - +
158A SER* 1.3 80.8 + - - +
219A LYS* 3.9 11.1 - - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA 3.0 12.1 + - - -
155A SER* 3.9 0.2 - - - -
156A THR 3.3 0.2 - - - -
157A GLU* 1.3 96.6 - - - +
159A GLY* 1.3 58.6 + - - +
160A ALA* 3.1 31.6 + - - +
162A VAL* 5.8 1.0 - - - +
219A LYS* 5.1 0.4 - - - -
234A PHE* 6.0 2.3 - - - -
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A SER 2.8 8.8 + - - -
156A THR 3.3 9.0 + - - -
157A GLU 3.5 0.2 + - - -
158A SER* 1.3 76.0 - - - +
160A ALA* 1.3 61.8 + - - +
219A LYS* 4.0 6.3 - - - -
220A LYS 3.6 18.8 - - - +
221A VAL* 3.3 9.0 - - - -
222A VAL* 3.0 25.3 + - - +
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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