Contacts of the helix formed by residues 195 - 201 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B ARG* 3.1 49.4 - - - +
298B LEU* 3.6 11.2 - - + +
408B GAI 3.8 14.4 - - - +
173C GLY* 3.8 14.8 - - - +
174C VAL 3.0 6.9 + - - -
175C ARG* 3.8 21.8 - - + +
194C THR* 1.3 75.2 - - - +
196C HIS* 1.3 52.0 + - - +
198C VAL* 3.6 3.9 - - + +
199C ASP* 2.7 38.6 + - - +
244C GLY 3.4 23.6 - - - +
245C GLY* 3.8 2.0 - - - -
246C LEU* 3.5 31.2 - - + -
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Residues in contact with HIS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B LEU* 3.5 21.1 - - + +
256B GLU* 2.8 45.8 + - + +
257B MET* 4.1 5.4 - - + -
260B GLU* 4.9 0.8 + - - -
298B LEU* 3.9 4.6 - - + +
408B GAI 3.5 9.9 + - - -
194C THR* 3.0 13.1 + - - +
195C MET* 1.3 78.3 - - - +
197C GLU* 1.3 70.3 + - + +
199C ASP* 3.2 2.1 + - - +
200C ARG* 2.7 75.5 + - - +
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE 4.3 6.0 - - - +
193C TYR* 3.8 29.8 - - + -
194C THR* 2.6 49.5 + - - +
196C HIS* 1.3 92.4 - - + +
198C VAL* 1.3 61.0 + - - +
200C ARG* 4.3 6.1 - - - -
201C LEU* 2.7 45.9 + - + +
206C VAL* 4.4 1.6 - - - -
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Residues in contact with VAL 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ARG* 3.9 4.3 + - - +
172C ILE* 4.6 7.0 - - + -
173C GLY 4.5 5.4 - - - +
193C TYR* 4.4 8.5 - - + +
194C THR 3.1 18.0 + - - +
195C MET* 3.7 11.2 - - + +
197C GLU* 1.3 77.4 - - - +
199C ASP* 1.3 57.7 + - - +
202C GLY* 2.8 28.6 + - - -
203C MET* 4.1 19.0 + - + +
206C VAL* 4.1 17.3 - - + -
246C LEU* 3.8 31.6 - - + -
250C GLU* 3.9 18.1 - - - +
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Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B THR* 3.5 7.3 + - - -
249B ARG* 2.9 48.1 + - - +
250B GLU* 5.5 1.3 - - - +
253B LEU* 3.9 19.3 - - + +
408B GAI 2.6 41.2 + - - +
195C MET* 2.7 18.0 + - - +
196C HIS 3.6 3.6 - - - +
198C VAL* 1.3 76.2 - - - +
200C ARG* 1.3 60.9 + - - +
202C GLY* 4.4 2.4 + - - -
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Residues in contact with ARG 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B THR* 2.9 39.3 + - + +
208B GLU* 4.9 6.9 + - - +
253B LEU* 3.8 9.6 - - + +
257B MET* 3.7 26.1 - - - +
260B GLU* 2.8 41.7 + - - -
196C HIS* 2.7 56.1 + - - +
197C GLU* 4.0 4.7 - - - +
199C ASP* 1.3 75.7 - - - +
201C LEU* 1.3 69.9 + - + +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 4.1 28.7 - - + -
197C GLU* 2.7 31.4 + - + +
199C ASP 4.9 0.2 - - - -
200C ARG* 1.3 87.3 - - + +
202C GLY* 1.3 61.9 + - - +
205C ARG* 3.6 60.5 + - + +
206C VAL* 4.3 2.7 - - + -
209C GLU* 4.2 9.0 - - - +
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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