Contacts of the helix formed by residues 165 - 174 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A CYS* 1.3 78.2 - - - +
166A GLY* 1.3 70.4 + - - +
167A ALA 3.5 0.2 + - - -
168A THR* 3.2 18.6 + - - -
169A LEU* 3.4 9.0 + - - -
188A GLU* 3.8 37.2 + - - -
191A GLN* 5.1 3.4 - - - -
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Residues in contact with GLY 166 (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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165A SER* 1.3 76.0 - - - +
167A ALA* 1.3 62.8 + - - -
169A LEU* 3.2 4.4 + - - +
170A GLN* 3.0 19.6 + - - -
188A GLU 5.5 3.8 + - - -
191A GLN* 5.0 12.1 + - - +
192A LEU* 3.5 21.4 - - - +
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Residues in contact with ALA 167 (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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143A GLN* 6.2 1.6 - - - +
165A SER 3.5 0.4 + - - -
166A GLY* 1.3 68.7 - - - -
168A THR* 1.3 64.7 + - - +
170A GLN* 3.6 12.4 - - - +
171A THR* 3.0 30.1 + - - +
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Residues in contact with THR 168 (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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136A SER* 4.0 23.9 - - - -
137A LEU* 4.7 10.7 + - + +
146A TYR* 3.7 35.2 - - + -
164A CYS* 3.8 13.7 - - + -
165A SER 3.2 10.2 + - - -
166A GLY 3.2 0.8 - - - -
167A ALA* 1.3 81.0 - - - +
169A LEU* 1.3 61.2 + - - +
171A THR* 3.6 5.2 + - - -
172A VAL* 3.5 20.3 + - - +
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Residues in contact with LEU 169 (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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162A LEU* 4.1 23.6 - - + +
164A CYS* 3.5 33.1 - - - +
165A SER* 3.4 8.1 + - - -
166A GLY 3.2 8.6 + - - +
168A THR* 1.3 75.1 - - - +
170A GLN* 1.3 66.1 + - - +
172A VAL* 3.0 12.7 + - + +
173A LEU* 3.1 35.2 + - + +
182A ILE* 4.2 22.2 - - + -
184A PRO* 4.9 13.9 - - + -
188A GLU* 5.5 2.9 - - + +
192A LEU* 3.7 28.0 - - + -
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Residues in contact with GLN 170 (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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166A GLY 3.0 14.2 + - - +
167A ALA* 3.6 13.8 - - + +
168A THR 3.3 0.4 - - - -
169A LEU* 1.3 76.9 - - - +
171A THR* 1.3 61.9 + - - +
173A LEU* 3.2 8.5 + - - +
174A GLU* 3.2 49.6 + - + +
192A LEU* 3.8 34.9 + - + +
194A ASN* 5.0 10.2 + - - +
212A LEU* 5.3 8.3 - - + -
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Residues in contact with THR 171 (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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143A GLN* 3.4 53.4 + - + +
144A ASP* 4.5 7.0 - - + -
147A ALA* 5.1 4.2 - - + +
167A ALA* 3.0 18.5 + - - +
168A THR* 3.8 6.5 - - - -
169A LEU 3.3 0.2 - - - -
170A GLN* 1.3 75.7 - - - +
172A VAL* 1.3 64.2 + - + +
174A GLU* 3.8 11.5 + - - +
175A ASN* 3.5 19.5 + - + +
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Residues in contact with VAL 172 (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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146A TYR* 3.9 29.6 - - + -
147A ALA* 4.7 5.8 - - + +
150A ILE* 3.7 11.4 - - + -
162A LEU* 3.7 31.0 - - + -
164A CYS* 4.9 0.4 - - - -
168A THR 3.5 13.7 + - - +
169A LEU* 3.0 9.6 + - + +
171A THR* 1.3 80.5 - - + +
173A LEU* 1.3 61.5 + - + +
175A ASN* 2.8 39.5 + - - +
177A TYR 4.4 0.5 - - - +
178A LYS* 4.6 1.6 + - - +
179A PRO* 3.7 24.5 - - + -
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Residues in contact with LEU 173 (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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169A LEU* 3.1 34.6 + - + +
170A GLN* 3.2 5.1 + - - +
172A VAL* 1.3 79.8 - - + +
174A GLU* 1.3 57.6 + - - +
178A LYS* 2.7 29.8 + - - +
179A PRO* 6.2 0.2 - - - -
182A ILE* 4.7 4.5 - - + -
192A LEU* 3.6 33.4 - - + -
212A LEU* 3.6 40.3 - - + +
213A PHE* 3.7 19.3 - - + -
216A ILE* 3.5 31.4 - - + -
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Residues in contact with GLU 174 (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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170A GLN* 3.2 39.6 + - + +
171A THR* 4.2 10.6 + - - +
172A VAL 3.2 0.2 - - - -
173A LEU* 1.3 75.1 - - - +
175A ASN* 1.3 61.1 + - - +
176A PRO* 4.1 2.3 - - - +
178A LYS* 4.8 0.4 - - - -
212A LEU* 4.5 13.6 - - + +
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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