Contacts of the helix formed by residues 210 - 214 (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 GLN 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C LEU* 4.0 21.7 - - - +
195C GLN* 4.3 11.4 + - - -
206C GLN 3.5 10.3 + - - +
207C ALA* 3.4 14.7 - - - +
208C VAL 3.3 1.0 - - - -
209C SER* 1.3 80.3 - - - +
211C PRO* 1.4 73.3 - - + +
212C LEU* 3.0 30.3 - - - +
213C PHE* 2.9 28.6 + - + +
214C GLU* 3.9 2.6 + - - +
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Residues in contact with PRO 211 (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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173C LEU 5.5 0.2 - - - +
209C SER 3.8 4.0 - - - +
210C GLN* 1.4 91.6 - - + +
212C LEU* 1.3 60.4 + - - +
213C PHE 3.1 0.2 - - - -
214C GLU* 2.7 40.8 - - + +
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Residues in contact with LEU 212 (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* 4.9 4.9 - - + +
173C LEU* 3.5 57.9 - - + +
174C GLU* 4.7 13.7 - - + +
178C LYS* 5.1 0.5 + - - -
192C LEU* 4.2 21.3 - - + +
193C LEU* 3.8 27.6 - - + -
210C GLN* 2.9 22.2 + - - +
211C PRO* 1.3 78.4 - - - +
213C PHE* 1.3 65.9 + - + +
214C GLU 3.8 1.9 + - - +
216C ILE* 5.1 0.5 - - - +
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Residues in contact with PHE 213 (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* 5.5 0.4 - - + -
173C LEU* 3.7 24.7 - - + -
182C ILE* 3.7 28.0 - - + -
184C PRO* 5.8 0.4 - - + -
189C LEU* 3.6 21.1 - - + -
192C LEU* 3.7 11.4 - - + -
193C LEU* 3.6 31.0 - - + -
207C ALA 3.2 30.3 - - - -
208C VAL* 3.6 13.0 - - - +
210C GLN* 2.9 12.4 + - + +
212C LEU* 1.3 85.7 - - + +
214C GLU* 1.3 62.9 + - - +
216C ILE* 3.5 26.4 + - + +
219C ILE* 3.6 24.4 - - + +
231C LYS* 4.8 4.0 + - - -
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Residues in contact with GLU 214 (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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178C LYS* 3.3 31.5 + - - +
210C GLN 3.9 2.1 + - - +
211C PRO* 2.7 38.7 + - + +
212C LEU 3.5 1.5 - - - +
213C PHE* 1.3 79.2 - - - +
215C GLY* 1.3 61.8 + - - +
216C ILE* 3.6 1.2 + - - +
231C LYS* 5.8 2.5 - - - +
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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