Contacts of the helix formed by residues 190 - 196 (chain A) in PDB entry 3J0A
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 LEU 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.6 22.7 - - + -
162A LEU* 4.3 5.4 - - + -
185A VAL* 4.8 4.7 - - + -
186A CYS 4.2 8.1 - - - +
187A GLU 2.9 11.4 + - - +
189A GLU* 1.3 95.0 - - - +
191A GLU* 1.3 64.0 + - - +
192A PRO* 3.6 3.8 - - - -
193A LEU* 3.4 42.1 - - + +
194A GLN* 4.0 4.9 + - - +
203A LEU* 5.8 4.0 - - + -
222A PRO* 3.0 45.8 - - + +
223A PHE* 3.8 23.8 - - + -
226A MET* 4.1 8.3 - - + +
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Residues in contact with GLU 191 (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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161A TYR* 3.9 16.5 + - + -
187A GLU 4.5 1.1 - - - +
188A HIS* 3.0 43.5 - - - +
190A LEU* 1.3 73.6 - - - +
192A PRO* 1.4 73.0 - - + +
193A LEU 2.9 6.3 + - - -
194A GLN* 3.0 32.5 + - + +
195A GLY* 3.5 3.3 + - - -
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Residues in contact with PRO 192 (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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161A TYR* 5.8 1.1 - - + -
162A LEU* 3.5 39.9 - - + +
163A HIS 4.0 16.8 - - - +
164A PRO* 4.4 8.7 - - + -
166A PHE* 4.5 12.8 - - + -
167A GLY* 4.9 9.4 - - - +
188A HIS 5.2 0.9 - - - +
189A GLU 5.2 0.9 - - - -
190A LEU* 3.8 2.0 - - - +
191A GLU* 1.4 92.8 - - + +
193A LEU* 1.3 61.5 + - - +
194A GLN 3.4 0.2 - - - -
195A GLY* 3.2 14.7 + - - +
196A LYS* 3.8 12.6 + - - +
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Residues in contact with LEU 193 (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* 3.6 23.6 - - + -
190A LEU* 3.4 45.3 - - + +
191A GLU 2.9 0.6 + - - -
192A PRO* 1.3 79.4 - - - +
194A GLN* 1.3 62.7 - - - +
195A GLY 3.0 1.3 + - - -
196A LYS* 3.3 21.1 + - - +
199A SER* 5.4 0.5 + - - -
201A PHE* 4.2 29.6 - - + -
203A LEU* 6.0 2.0 - - + -
223A PHE* 5.5 4.7 - - + -
226A MET* 3.6 26.3 - - + +
228A LEU* 5.6 10.1 - - + -
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Residues in contact with GLN 194 (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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187A GLU* 6.1 1.2 - - - +
190A LEU 4.0 6.2 + - - +
191A GLU* 3.0 27.0 + - - +
193A LEU* 1.3 78.5 - - - +
195A GLY* 1.3 63.1 + - - +
196A LYS 3.3 5.6 + - - +
220A MET* 5.7 7.7 - - - +
224A ARG 5.8 0.2 - - - +
225A ASN* 5.0 14.0 + - - +
226A MET* 4.4 24.6 - - + +
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Residues in contact with GLY 195 (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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191A GLU 3.5 2.7 + - - -
192A PRO* 3.2 10.2 + - - -
193A LEU 3.0 2.4 - - - -
194A GLN* 1.3 84.6 - - - +
196A LYS* 1.3 64.6 + - - +
197A THR 3.9 1.4 + - - -
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Residues in contact with LYS 196 (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 PHE 5.2 3.1 - - - +
167A GLY* 3.7 24.7 - - - +
169A LEU 4.7 2.9 - - - +
170A ASN* 3.3 33.3 + - - +
192A PRO 4.1 10.8 - - - +
193A LEU 3.3 15.2 + - - +
194A GLN* 3.3 5.6 - - - +
195A GLY* 1.3 80.4 - - - +
197A THR* 1.3 65.8 + - - +
198A LEU 3.6 21.4 + - - +
199A SER* 3.2 26.7 + - - +
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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