Contacts of the helix formed by residues 165 - 175 (chain B) in PDB entry 2JG1
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 SER 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B CYS* 1.3 78.8 - - - +
166B GLY* 1.3 70.2 + - - +
168B THR* 3.3 12.5 + - - -
169B LEU* 3.3 18.1 + - - -
188B GLU* 3.7 35.7 + - - -
191B GLN* 6.0 1.8 - - - -
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Residues in contact with GLY 166 (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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165B SER* 1.3 76.6 - - - +
167B ALA* 1.3 58.1 + - - -
169B LEU* 3.2 3.1 + - - +
170B GLN* 3.0 27.0 + - - +
188B GLU 5.8 2.2 + - - -
191B GLN* 5.6 6.1 + - - -
192B LEU* 3.7 14.8 - - - +
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Residues in contact with ALA 167 (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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166B GLY* 1.3 69.6 - - - -
168B THR* 1.3 58.9 + - - +
170B GLN* 3.6 9.7 - - + +
171B THR* 2.8 39.1 + - - +
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Residues in contact with THR 168 (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 GLY 4.5 3.4 - - - +
136B SER* 4.3 18.7 - - - -
137B LEU* 4.7 10.0 + - + +
146B TYR* 3.7 33.3 - - + -
164B CYS* 3.8 15.9 - - + -
165B SER 3.3 12.1 + - - -
166B GLY 3.2 0.2 - - - -
167B ALA* 1.3 80.5 - - - +
169B LEU* 1.3 60.1 + - - +
171B THR* 3.6 4.9 + - - -
172B VAL* 3.5 21.3 + - - +
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Residues in contact with LEU 169 (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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162B LEU* 4.0 25.6 - - + +
164B CYS* 3.3 34.7 - - - +
165B SER* 3.3 8.6 + - - -
166B GLY 3.2 7.9 + - - +
168B THR* 1.3 75.9 - - - +
170B GLN* 1.3 68.6 + - - +
172B VAL* 3.0 6.6 + - + +
173B LEU* 2.9 48.0 + - + +
182B ILE* 4.3 17.9 - - + -
184B PRO* 4.9 15.5 - - + -
188B GLU* 5.7 3.6 - - + +
192B LEU* 3.9 23.3 - - + -
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Residues in contact with GLN 170 (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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166B GLY 3.0 17.5 + - - +
167B ALA* 3.6 12.3 - - + +
169B LEU* 1.3 75.2 - - - +
171B THR* 1.3 61.5 + - - +
173B LEU* 3.3 5.5 + - - +
174B GLU* 2.7 63.9 + - - +
192B LEU* 3.6 27.3 - - + +
212B LEU* 3.7 25.6 - - - +
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Residues in contact with THR 171 (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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143B GLN* 3.5 39.5 + - + +
144B ASP* 4.7 7.0 - - + -
147B ALA* 5.2 4.4 - - + +
167B ALA* 2.8 24.0 + - - +
168B THR* 3.9 6.5 - - - -
169B LEU 3.2 0.4 - - - -
170B GLN* 1.3 77.9 - - - +
172B VAL* 1.3 63.8 + - + +
174B GLU* 3.6 12.9 + - - +
175B ASN* 3.5 19.2 + - - +
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Residues in contact with VAL 172 (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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146B TYR* 3.9 30.5 - - + -
147B ALA* 4.5 6.3 - - + +
150B ILE* 3.8 11.7 - - + -
162B LEU* 3.8 24.5 - - + -
164B CYS* 5.0 0.4 - - - -
168B THR 3.5 13.0 + - - +
169B LEU 3.0 8.8 + - - +
171B THR* 1.3 78.2 - - + +
173B LEU* 1.3 60.0 + - + +
175B ASN* 2.7 40.4 + - - +
178B LYS* 4.3 1.9 + - - +
179B PRO* 3.7 29.4 - - + -
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Residues in contact with LEU 173 (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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169B LEU* 2.9 37.4 + - + +
170B GLN* 3.3 4.5 + - - +
172B VAL* 1.3 79.5 - - + +
174B GLU* 1.3 55.0 + - - +
178B LYS* 2.8 27.1 + - - +
179B PRO* 5.3 0.2 - - + -
182B ILE* 4.3 4.5 - - + -
192B LEU* 3.6 33.0 - - + -
212B LEU* 3.5 40.2 - - + +
213B PHE* 3.8 14.6 - - + -
216B ILE* 3.4 33.4 - - + -
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Residues in contact with GLU 174 (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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170B GLN* 2.7 49.4 + - - +
171B THR* 3.9 12.2 + - - +
172B VAL 3.2 0.2 - - - -
173B LEU* 1.3 76.9 - - - +
175B ASN* 1.3 59.7 + - - +
176B PRO* 4.7 1.0 - - - +
178B LYS* 4.6 0.9 - - - -
212B LEU* 4.6 6.1 - - + -
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Residues in contact with ASN 175 (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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147B ALA* 3.5 28.9 - - + +
171B THR 3.5 10.7 + - - +
172B VAL* 2.7 31.4 + - - +
174B GLU* 1.3 79.8 - - - +
176B PRO* 1.4 67.2 - - + +
177B TYR* 2.8 50.7 + - - +
178B LYS* 2.7 33.5 + - - -
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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