Contacts of the helix formed by residues 165 - 175 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ARG* 3.9 20.3 + - - -
38C LYS* 6.0 0.7 - - - -
164C CYS* 1.3 79.4 - - - +
166C GLY* 1.3 68.9 + - - +
167C ALA 3.7 0.2 + - - -
168C THR* 3.4 12.2 + - - -
169C LEU* 3.4 17.6 + - - -
188C GLU* 3.8 36.7 + - - -
1312C TA6 4.9 1.6 + - - -
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C SER* 1.3 73.1 - - - +
167C ALA* 1.3 61.3 + - - -
168C THR 3.2 0.3 + - - -
169C LEU* 3.2 2.6 + - - +
170C GLN* 2.9 28.3 + - - +
188C GLU* 5.5 2.2 + - - +
191C GLN 6.4 0.4 - - - -
192C LEU* 3.5 19.8 - - - +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C SER 3.7 0.2 + - - -
166C GLY* 1.3 71.2 - - - -
168C THR* 1.3 50.9 + - - +
170C GLN* 3.4 9.8 - - - +
171C THR* 2.8 43.1 + - - +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C GLY 5.0 0.2 - - - +
136C SER* 5.3 3.7 - - - -
137C LEU* 3.9 30.9 + - + +
146C TYR* 3.8 33.0 - - + -
164C CYS* 3.9 9.6 - - + -
165C SER 3.4 11.0 + - - -
167C ALA* 1.3 77.6 - - - +
169C LEU* 1.3 65.3 + - - +
171C THR* 3.6 5.9 + - - -
172C VAL* 3.4 21.3 + - - +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LEU* 4.2 20.9 - - + -
164C CYS* 3.3 29.1 - - - +
165C SER* 3.4 15.7 + - - +
166C GLY 3.2 8.4 + - - +
168C THR* 1.3 76.1 - - - +
170C GLN* 1.3 66.5 + - - +
172C VAL* 3.0 12.6 + - - +
173C LEU* 3.0 40.5 + - + +
182C ILE* 4.6 15.9 - - + -
184C PRO* 4.9 15.9 - - + -
188C GLU* 5.5 3.8 - - + +
192C LEU* 3.8 27.1 - - + -
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Residues in contact with GLN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLY 2.9 14.6 + - - +
167C ALA* 3.4 14.8 - - - +
169C LEU* 1.3 76.2 - - - +
171C THR* 1.3 62.4 + - - +
173C LEU* 3.3 8.3 + - - +
174C GLU* 3.1 37.7 + - + +
192C LEU* 3.8 15.1 - - + +
212C LEU* 4.9 4.8 - - + +
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Residues in contact with THR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLN* 3.4 59.8 + - - +
144C ASP* 4.6 6.7 - - + -
147C ALA* 5.3 5.2 - - + +
167C ALA* 2.8 29.1 + - - +
168C THR* 3.7 7.7 - - - -
170C GLN* 1.3 71.5 - - - +
172C VAL* 1.3 63.6 + - + +
174C GLU* 3.5 11.5 + - - +
175C ASN* 3.3 21.1 + - + +
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 3.8 30.5 - - + -
147C ALA* 4.5 7.2 - - + +
150C ILE* 3.8 22.2 - - + -
162C LEU* 3.8 24.7 - - + -
168C THR 3.4 14.1 + - - +
169C LEU* 3.0 9.2 + - + +
171C THR* 1.3 78.4 - - + +
173C LEU* 1.3 59.4 + - + +
175C ASN* 2.6 42.2 + - - +
177C TYR 4.6 0.2 - - - +
178C LYS* 4.5 2.1 + - - +
179C PRO* 3.8 17.0 - - + -
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LEU* 3.0 34.6 + - + +
170C GLN* 3.8 5.8 - - - +
172C VAL* 1.3 78.8 - - + +
174C GLU* 1.3 57.9 + - - +
175C ASN 3.3 0.2 - - - -
178C LYS* 3.0 23.8 + - - +
182C ILE* 4.6 5.4 - - + -
192C LEU* 3.7 30.7 - - + -
211C PRO 5.5 0.3 - - - +
212C LEU* 3.5 38.3 - - + +
213C PHE* 3.7 18.2 - - + -
216C ILE* 3.5 31.2 - - + -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLN* 3.1 28.3 + - - +
171C THR* 3.8 9.5 - - - +
172C VAL 3.2 0.4 - - - -
173C LEU* 1.3 75.7 - - - +
175C ASN* 1.3 62.4 + - - +
176C PRO* 4.1 2.1 - - - +
178C LYS* 4.6 0.7 - - - -
212C LEU* 4.7 13.7 - - + +
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ALA* 3.8 26.5 - - + +
171C THR* 3.3 11.4 + - + +
172C VAL* 2.6 32.0 + - - +
174C GLU* 1.3 80.5 - - - +
176C PRO* 1.3 67.3 - - + +
177C TYR* 2.8 53.0 + - - +
178C LYS* 2.7 27.6 + - - -
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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