Contacts of the helix formed by residues 179 - 188 (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 GLU 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C LEU 3.9 0.9 + - - +
178C ASP* 1.3 72.2 - - - +
180C GLY* 1.3 64.4 + - - +
182C LYS* 3.0 44.1 + - - +
183C LYS* 3.1 13.7 + - - +
186C ARG* 5.2 4.7 + - - -
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Residues in contact with GLY 180 (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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127C VAL 5.5 0.4 - - - -
132C THR* 4.1 32.9 + - - +
178C ASP* 3.2 3.2 - - - +
179C GLU* 1.3 77.7 - - - +
181C GLU* 1.3 56.7 + - - +
183C LYS* 3.4 12.5 + - - +
184C PHE* 2.9 26.6 + - - +
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Residues in contact with GLU 181 (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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403A ORN 3.3 9.7 + - - -
125C GLY* 3.7 2.4 + - - -
126C ASP* 3.1 14.6 + - - -
127C VAL* 3.0 43.7 + - + +
128C ASN* 3.3 30.4 + - - +
176C SER 4.4 1.0 - - - +
177C LEU* 3.8 15.4 - - + +
178C ASP* 2.9 40.8 + - + +
180C GLY* 1.3 76.3 - - - +
182C LYS* 1.3 59.6 + - - +
184C PHE* 3.4 3.4 - - - +
185C ILE* 2.9 35.9 + - - +
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Residues in contact with LYS 182 (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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297B LYS* 2.9 23.4 + - - +
298B LEU 3.2 24.2 - - - -
299B MET* 3.2 41.1 + - - +
177C LEU* 3.7 27.1 - - + +
178C ASP 2.9 16.2 + - - +
179C GLU* 3.0 36.1 + - - +
181C GLU* 1.3 75.2 - - - +
183C LYS* 1.3 63.1 + - - +
186C ARG* 3.1 31.1 + - - +
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Residues in contact with LYS 183 (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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179C GLU 3.1 10.7 + - - +
180C GLY* 3.4 13.5 - - - +
182C LYS* 1.3 75.1 - - - +
184C PHE* 1.3 59.5 + - - +
186C ARG* 3.2 23.0 + - - +
187C GLU* 2.8 72.7 + - + +
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Residues in contact with PHE 184 (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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127C VAL* 3.7 29.4 - - + +
129C THR* 5.6 4.5 - - + -
144C ALA* 4.0 12.3 - - + -
147C LEU* 3.6 14.6 - - + -
149C PHE* 3.7 36.6 - + + -
180C GLY 2.9 14.7 + - - +
181C GLU* 3.4 12.8 - - - +
183C LYS* 1.3 76.1 - - - +
185C ILE* 1.3 56.2 + - - +
187C GLU* 3.7 4.4 - - - -
188C LYS* 2.7 77.4 + - + +
190C ILE* 3.5 22.2 - - + -
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Residues in contact with ILE 185 (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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299B MET* 3.4 19.5 - - + -
125C GLY* 5.0 0.2 - - - -
127C VAL* 4.1 14.6 - - + -
171C LEU* 3.8 22.2 - - + -
177C LEU* 3.6 42.8 - - + -
181C GLU 2.9 17.4 + - - +
184C PHE* 1.3 78.9 - - + +
186C ARG* 1.3 63.1 + - - +
189C GLY* 3.0 18.4 + - - -
190C ILE* 3.2 42.3 + - + +
192C ILE* 3.8 16.6 - - + -
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Residues in contact with ARG 186 (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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299B MET* 3.1 45.4 + - + -
179C GLU* 5.2 4.9 + - - -
182C LYS* 3.1 29.4 + - - +
183C LYS* 3.5 27.8 - - - +
185C ILE* 1.3 79.1 - - - +
187C GLU* 1.3 65.0 + - + +
189C GLY* 3.5 9.2 + - - -
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Residues in contact with GLU 187 (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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183C LYS* 2.8 68.0 + - + +
184C PHE* 4.0 3.6 - - - +
186C ARG* 1.3 75.1 - - + +
188C LYS* 1.3 71.4 + - + +
189C GLY* 3.0 5.7 + - - -
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Residues in contact with LYS 188 (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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149C PHE* 3.1 38.9 - - + -
166C PRO* 3.3 25.6 - - + +
167C GLU 5.0 0.3 + - - -
184C PHE* 2.7 72.0 + - + +
187C GLU* 1.3 81.0 + - + +
189C GLY* 1.3 63.4 + - - +
190C ILE* 4.0 17.0 - - + -
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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