Contacts of the helix formed by residues 195 - 201 (chain F) in PDB entry 5CEV
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249E ARG* 3.3 43.1 - - - +
298E LEU* 3.5 11.8 - - + +
173F GLY* 3.8 17.0 - - - +
174F VAL 3.0 6.9 + - - -
175F ARG* 3.6 22.4 - - + -
194F THR* 1.3 73.7 - - - +
196F HIS* 1.3 57.0 + - - +
198F VAL* 3.8 5.3 - - + +
199F ASP* 2.9 33.6 + - - +
244F GLY 3.3 26.2 - - - +
245F GLY* 3.6 6.5 - - - -
246F LEU* 3.7 28.3 - - + +
411F GAI 3.7 13.7 - - - +
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Residues in contact with HIS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E LEU* 3.7 19.8 - - + +
256E GLU* 2.8 47.0 + - + +
257E MET* 4.5 2.9 - - + -
260E GLU* 4.5 3.4 + - - -
297E LYS* 6.4 2.0 - - - -
298E LEU* 3.7 6.6 - - + +
194F THR* 3.0 13.1 + - - +
195F MET* 1.3 80.0 - - - +
197F GLU* 1.3 77.2 + - + +
199F ASP* 3.8 1.4 - - - +
200F ARG* 2.8 69.5 + - - +
411F GAI 3.4 10.6 + - - +
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Residues in contact with GLU 197 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192F ILE 4.2 5.4 - - - +
193F TYR* 3.7 32.9 - - + -
194F THR* 2.8 44.3 + - - +
196F HIS* 1.3 96.7 - - + +
198F VAL* 1.3 59.8 + - - +
200F ARG* 4.3 5.6 - - + -
201F LEU* 2.7 47.2 + - + +
206F VAL* 4.0 2.0 - - - +
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Residues in contact with VAL 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ARG* 3.8 8.6 + - - +
172F ILE* 4.8 4.5 - - + -
173F GLY 4.5 6.5 - - - +
193F TYR* 4.4 8.7 - - + +
194F THR 3.1 17.0 + - - +
195F MET* 3.9 9.0 - - + +
197F GLU* 1.3 76.6 - - - +
199F ASP* 1.3 56.0 + - - +
202F GLY* 2.7 31.5 + - - -
203F MET* 4.1 20.9 - - + +
206F VAL* 4.1 17.0 - - + -
246F LEU* 3.8 26.5 - - + -
250F GLU* 3.7 23.0 - - - +
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Residues in contact with ASP 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E THR* 3.6 7.8 + - - -
249E ARG* 2.8 52.4 + - - +
250E GLU* 5.5 1.2 - - - +
253E LEU* 3.6 18.8 - - + +
195F MET 2.9 14.4 + - - +
196F HIS 3.8 2.9 - - - +
198F VAL* 1.3 76.8 - - - +
200F ARG* 1.3 62.0 + - - +
202F GLY* 4.2 2.4 + - - -
411F GAI 2.7 40.1 + - - +
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Residues in contact with ARG 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E THR* 2.8 41.6 + - + +
208E GLU* 4.9 6.9 + - - +
253E LEU* 3.7 12.1 - - + +
257E MET* 3.9 28.6 - - - +
260E GLU* 2.8 39.6 + - - -
196F HIS* 2.8 55.8 + - - +
197F GLU* 3.9 5.4 - - - +
199F ASP* 1.3 75.7 - - - +
201F LEU* 1.3 70.6 + - + +
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F TYR* 4.1 26.9 - - + -
197F GLU* 2.7 34.2 + - + +
200F ARG* 1.3 89.8 - - + +
202F GLY* 1.3 61.1 + - - +
205F ARG* 3.4 30.2 + - + +
206F VAL* 4.2 3.8 - - + -
209F GLU* 4.2 16.4 - - - +
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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