Contacts of the helix formed by residues 193 - 198 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ARG 5.7 1.8 + - - -
191A TYR 3.4 3.0 + - - -
192A ARG* 1.3 74.0 - - - +
194A PRO* 1.3 73.6 - - + +
195A GLU* 3.5 18.6 - - + +
196A VAL* 3.0 19.0 + - + +
197A ILE* 3.1 11.0 + - - +
206A VAL* 3.6 39.5 - - + +
209A TRP* 3.5 10.3 - - + -
210A SER* 5.3 1.2 + - - +
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Residues in contact with PRO 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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192A ARG 3.7 0.8 - - - +
193A ALA* 1.3 84.3 - - + +
195A GLU* 1.3 55.8 + - - +
197A ILE* 3.3 12.5 + - + +
198A LEU* 2.8 44.3 + - + +
209A TRP* 3.3 51.1 - - + -
234A TRP* 4.3 10.3 - - + -
237A VAL* 4.9 4.9 - - + -
248A PHE* 5.5 0.2 - - + -
304A ILE* 3.9 35.2 - - + +
309A ARG* 3.9 0.2 - - - +
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Residues in contact with GLU 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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193A ALA* 3.5 12.6 - - - +
194A PRO* 1.3 73.9 - - - +
196A VAL* 1.3 60.0 + - - +
199A GLY 3.4 1.4 + - - -
200A MET* 2.8 56.4 + - + +
201A GLY 3.6 22.2 - - - +
202A TYR* 4.5 7.2 - - + -
203A LYS 5.2 1.9 + - - +
205A ASN* 4.4 0.5 - - - +
206A VAL* 3.4 25.9 + - + +
304A ILE 5.1 0.2 + - - -
306A PRO* 3.6 22.6 - - + +
309A ARG* 2.8 43.2 + - - -
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Residues in contact with VAL 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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150A ARG* 4.3 25.4 - - + +
178A THR* 3.6 28.9 + - + +
179A ASN 4.3 0.3 - - - +
180A PHE* 3.8 11.8 + - - -
192A ARG* 3.6 37.7 - - - +
193A ALA* 3.0 16.4 + - + +
195A GLU* 1.3 77.2 - - + +
197A ILE* 1.3 64.4 + - - +
198A LEU 3.3 0.9 + - - -
199A GLY* 3.3 10.2 + - - -
200A MET 5.3 1.3 - - - -
202A TYR* 5.3 2.9 - - + -
206A VAL* 4.2 24.5 - - + -
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Residues in contact with ILE 197 (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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179A ASN 5.4 0.7 - - - -
180A PHE* 3.3 4.9 - - - +
181A MET* 2.8 61.8 + - + +
185A TYR* 6.0 1.1 - - - +
192A ARG* 3.4 39.0 - - + +
193A ALA 3.1 12.5 + - - +
194A PRO* 3.5 11.7 - - + +
196A VAL* 1.3 77.7 - - - +
198A LEU* 1.3 64.8 + - + +
209A TRP* 6.4 0.2 - - + -
230A HIS 5.1 3.1 - - - +
233A GLN* 3.9 29.2 - - + -
234A TRP* 4.6 13.2 - - + -
237A VAL* 5.2 10.8 - - + -
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Residues in contact with LEU 198 (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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181A MET* 3.8 15.3 - - + -
194A PRO* 2.8 29.1 + - + +
196A VAL 3.2 0.2 - - - -
197A ILE* 1.3 74.7 - - + +
199A GLY* 1.3 59.7 + - - +
200A MET* 3.4 5.8 + - + -
234A TRP* 3.7 36.1 - - + -
248A PHE* 3.6 37.2 - - + -
252A LEU* 3.9 23.7 - - + +
253A GLN* 4.6 3.1 + - - -
256A VAL* 3.4 45.4 - - + +
260A VAL* 3.9 8.3 - - + -
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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