Contacts of the helix formed by residues 195 - 201 (chain E) in PDB entry 4CEV
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 MET 195 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D ARG* 3.1 49.4 - - - +
298D LEU* 3.6 12.0 - - + +
410D GAI 3.9 14.1 - - - +
173E GLY* 3.7 25.1 - - - +
174E VAL 3.0 9.1 + - - -
175E ARG* 3.9 12.8 - - + +
194E THR* 1.3 71.3 - - - +
196E HIS* 1.3 56.1 + - - +
198E VAL* 3.6 5.0 - - + +
199E ASP* 2.8 33.6 + - - +
244E GLY 3.5 23.6 - - - +
245E GLY* 3.7 4.0 - - - -
246E LEU* 3.6 30.7 - - + -
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Residues in contact with HIS 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D LEU* 3.6 20.7 - - + +
256D GLU* 2.8 47.5 + - + +
257D MET* 4.4 2.9 - - + -
260D GLU* 5.1 0.6 + - - -
298D LEU* 4.0 5.4 - - + +
410D GAI 3.8 8.3 - - - -
194E THR* 3.0 13.8 + - - +
195E MET* 1.3 78.8 - - - +
197E GLU* 1.3 76.5 + - + +
199E ASP* 3.4 1.9 + - - +
200E ARG* 2.8 68.6 + - - +
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Residues in contact with GLU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ILE 4.5 7.2 - - - +
193E TYR* 3.8 28.7 - - + -
194E THR* 2.8 45.5 + - - +
196E HIS* 1.3 92.0 - - + +
198E VAL* 1.3 58.9 + - - +
200E ARG* 4.3 5.8 - - - -
201E LEU* 2.7 46.9 + - + +
206E VAL* 4.4 1.6 - - - -
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Residues in contact with VAL 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ARG* 3.8 15.0 + - - +
172E ILE* 4.7 5.4 - - + -
173E GLY 4.5 7.0 - - - +
193E TYR* 4.3 10.5 - - + +
194E THR 3.1 18.6 + - - +
195E MET* 3.7 11.4 - - + +
197E GLU* 1.3 75.9 - - - +
199E ASP* 1.3 58.2 + - - +
202E GLY* 2.9 27.9 + - - -
203E MET* 4.1 16.3 + - + +
206E VAL* 4.2 16.2 - - + -
246E LEU* 3.7 31.6 - - + -
250E GLU* 3.9 8.4 - - - +
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Residues in contact with ASP 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D THR* 3.6 7.6 + - - -
249D ARG* 2.8 52.2 + - - +
250D GLU* 4.9 1.9 + - - +
253D LEU* 3.7 19.3 - - + +
410D GAI 2.7 38.6 + - - +
195E MET* 2.8 14.3 + - - +
196E HIS 3.8 4.0 - - - +
198E VAL* 1.3 78.0 - - - +
200E ARG* 1.3 61.7 + - - +
202E GLY* 4.5 1.6 + - - -
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Residues in contact with ARG 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D THR* 3.0 39.9 + - + +
208D GLU* 5.0 7.5 + - - +
253D LEU* 3.7 9.0 - - + -
257D MET* 3.7 23.9 - - + +
260D GLU* 3.0 41.1 + - - -
196E HIS* 2.8 53.4 + - - +
197E GLU* 4.1 4.9 - - - +
199E ASP* 1.3 79.8 - - - +
201E LEU* 1.3 69.7 + - + +
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Residues in contact with LEU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E TYR* 4.1 28.0 - - + -
197E GLU* 2.7 34.3 + - + +
200E ARG* 1.3 86.7 - - + +
202E GLY* 1.3 62.8 + - - +
205E ARG* 3.5 48.5 + - + +
206E VAL* 4.2 3.6 - - + -
209E GLU* 4.1 13.5 - - - +
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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