Contacts of the helix formed by residues 193 - 198 (chain B) in PDB entry 3E7O
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 ALA 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B TYR 3.6 1.8 + - - -
192B ARG* 1.3 74.0 - - - +
194B PRO* 1.3 74.0 - - + +
195B GLU* 3.5 19.3 - - + +
196B VAL* 2.9 17.1 + - + +
197B ILE* 3.1 10.8 + - - +
206B VAL* 3.6 29.6 - - + +
209B TRP* 3.4 24.1 - - + -
210B SER* 5.2 0.6 + - - -
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Residues in contact with PRO 194 (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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192B ARG 3.7 0.4 - - - +
193B ALA* 1.3 84.8 - - + +
195B GLU* 1.3 60.1 + - - +
197B ILE* 3.1 14.8 + - + +
198B LEU* 3.0 34.3 + - - +
200B MET* 5.3 0.4 - - - -
209B TRP* 3.4 46.7 - - + -
234B TRP* 3.8 19.3 - - + -
237B VAL* 4.4 7.4 - - + -
248B PHE* 5.2 2.2 - - + -
304B ILE* 3.9 29.2 - - + +
309B ARG* 3.9 0.4 - - - +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA* 3.5 13.5 - - + +
194B PRO* 1.3 74.1 - - - +
196B VAL* 1.3 60.5 + - - +
198B LEU 3.7 0.2 + - - -
199B GLY 3.2 1.6 + - - -
200B MET* 2.8 63.7 + - + +
201B GLY 3.6 22.0 - - - +
202B TYR* 4.0 14.0 - - + +
203B LYS 5.2 0.7 + - - -
205B ASN* 4.3 1.7 - - - +
206B VAL* 3.8 13.8 - - + +
248B PHE* 5.8 0.4 - - - -
304B ILE 4.0 3.5 - - - +
306B PRO* 3.8 16.2 - - + +
309B ARG* 2.9 45.6 + - - -
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Residues in contact with VAL 196 (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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150B ARG* 4.3 22.0 - - + +
192B ARG* 4.1 34.3 - - + +
193B ALA* 2.9 17.0 + - + +
195B GLU* 1.3 76.7 - - + +
197B ILE* 1.3 67.7 + - - +
199B GLY* 3.1 12.9 + - - -
200B MET 4.9 2.9 - - - -
202B TYR* 4.8 7.9 - - + -
206B VAL* 3.8 27.8 - - + -
230B HIS* 4.6 9.0 - - + -
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Residues in contact with ILE 197 (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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186A VAL* 4.5 14.5 - - + +
192B ARG* 3.4 30.1 - - + +
193B ALA 3.1 9.1 + - - +
194B PRO* 3.4 14.6 - - + +
196B VAL* 1.3 77.7 - - - +
198B LEU* 1.3 63.3 + - + +
199B GLY 3.5 0.7 + - - -
230B HIS* 3.5 38.9 + - + +
231B ILE* 5.2 1.3 - - - -
233B GLN* 3.8 27.6 - - + -
234B TRP* 4.2 28.9 - - + +
237B VAL* 4.7 10.3 - - + -
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Residues in contact with LEU 198 (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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186A VAL* 4.1 30.4 - - + +
194B PRO 3.0 16.1 + - - +
195B GLU 4.4 0.2 - - - +
197B ILE* 1.3 79.3 - - + +
199B GLY* 1.3 61.7 + - - +
200B MET* 3.3 15.0 + - + +
234B TRP* 3.8 46.7 - - + -
248B PHE* 4.2 10.1 - - + -
252B LEU* 4.0 19.3 - - + -
256B VAL* 4.0 23.1 - - + +
259B TYR* 5.2 1.1 - - + -
260B VAL* 3.9 27.1 - - + -
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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