Contacts of the helix formed by residues 152 - 157 (chain B) in PDB entry 2G98
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 ARG 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLU* 5.8 5.4 - - + -
96B ASP* 5.9 0.7 - - - -
121B HIS* 3.3 14.8 - - + -
150B TYR 3.2 2.6 + - - +
151B ARG* 1.3 80.7 - - - +
153B TYR* 1.4 59.7 + - + +
154B GLN* 3.3 46.6 - - - +
155B ASP* 3.2 44.4 + - - +
156B TRP* 4.1 11.7 - - - -
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Residues in contact with TYR 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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120B ILE 4.6 1.1 - - - +
121B HIS* 3.8 32.9 + + + -
152B ARG* 1.4 69.8 - - - +
154B GLN* 1.3 99.4 + - - +
155B ASP 3.0 2.7 + - - -
156B TRP* 3.2 45.9 + - + -
158B ALA 3.0 36.7 + - - -
159B THR* 2.9 35.5 + - - -
160B ASN* 3.2 18.6 - - - +
161B ALA* 4.1 7.4 - - - -
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Residues in contact with GLN 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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152B ARG* 3.3 49.0 - - - +
153B TYR* 1.3 125.4 + - - +
155B ASP* 1.3 62.0 + - - +
157B GLY* 3.2 14.9 + - - -
158B ALA 3.9 11.4 - - - +
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Residues in contact with ASP 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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149B ASP 5.0 3.4 - - - +
150B TYR* 3.3 27.8 - - + -
151B ARG* 3.6 19.2 + - - +
152B ARG* 3.2 36.1 + - - +
153B TYR 3.0 2.0 - - - -
154B GLN* 1.3 77.3 - - - +
156B TRP* 1.3 55.9 + - - +
157B GLY 3.4 1.3 - - - -
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Residues in contact with TRP 156 (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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54B GLN* 3.4 10.9 + - - -
120B ILE* 2.9 39.0 - - + -
121B HIS 3.9 0.2 - - - -
122B SER* 3.6 20.2 - - - -
123B LEU* 3.4 34.5 - - + -
132B LEU* 4.4 7.0 - - + +
143B TYR* 3.3 38.4 - + + +
144B LEU 4.7 5.6 - - - +
145B LEU* 3.3 29.2 - - + -
150B TYR* 3.6 13.2 - + + -
152B ARG 4.1 15.0 - - - -
153B TYR* 3.2 27.1 + - + -
155B ASP* 1.3 74.2 - - - +
157B GLY* 1.3 65.3 + - - +
158B ALA* 3.2 29.7 - - + +
160B ASN 4.0 1.2 + - - -
161B ALA* 4.5 2.9 - - - -
162B ARG 5.5 0.4 + - - -
163B VAL* 4.4 11.1 - - + +
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Residues in contact with GLY 157 (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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54B GLN* 4.0 12.1 + - - -
143B TYR* 3.0 19.1 - - - -
154B GLN 3.2 11.3 + - - -
155B ASP 3.4 1.4 - - - -
156B TRP* 1.3 86.0 - - - +
158B ALA* 1.3 57.4 + - - +
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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