Contacts of the helix formed by residues 180 - 187 (chain C) in PDB entry 4C1M
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 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.6 5.8 - - - +
11A THR* 4.3 6.1 - - + -
25A SER* 4.5 1.1 - - - +
26A ASN* 3.5 33.0 + - - +
166C ALA* 4.4 10.8 - - - +
178C GLY* 4.5 0.2 - - - -
179C SER* 1.3 84.3 + - - +
181C GLU* 1.3 59.8 + - - +
182C PRO* 3.6 12.7 - - + +
183C LEU* 3.6 14.1 + - + +
184C ALA* 3.0 26.9 + - - +
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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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10A ILE* 4.2 12.9 - - + +
11A THR* 4.7 10.9 - - + +
180C GLU* 1.3 67.6 - - - +
182C PRO* 1.4 72.9 - - + +
184C ALA* 3.5 6.3 + - + +
185C ARG* 3.2 51.4 + - - +
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Residues in contact with PRO 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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180C GLU* 3.7 12.6 - - + +
181C GLU* 1.4 91.2 - - + +
183C LEU* 1.3 59.2 + - + +
185C ARG* 3.2 22.5 + - - +
186C ASN* 2.9 39.9 + - - +
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Residues in contact with LEU 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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178C GLY* 4.1 12.6 - - - -
179C SER 4.7 4.5 - - - +
180C GLU* 3.9 14.4 - - + +
181C GLU 3.5 0.2 - - - -
182C PRO* 1.3 81.7 - - + +
184C ALA* 1.3 56.9 + - - +
186C ASN* 3.2 10.3 + - + +
187C LEU* 2.9 43.1 + - + +
234C LEU* 3.8 30.3 - - + -
235C ALA 3.8 12.6 - - - +
236C GLY 3.7 23.3 - - - +
238C THR* 6.2 4.3 - - + -
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Residues in contact with ALA 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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10A ILE* 3.6 30.7 - - + -
177C TYR 3.4 26.3 - - - +
178C GLY* 4.8 0.2 - - - -
180C GLU 3.0 19.1 + - - +
181C GLU* 3.8 4.7 - - - +
182C PRO 3.3 0.6 - - - -
183C LEU* 1.3 76.3 - - - +
185C ARG* 1.3 61.3 + - - +
187C LEU* 3.4 11.0 + - - +
188C ARG* 3.5 21.4 + - - +
277C TYR* 4.7 2.7 + - - +
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Residues in contact with ARG 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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181C GLU* 3.2 57.7 + - - +
182C PRO* 3.4 27.4 - - - +
184C ALA* 1.3 75.8 - - - +
186C ASN* 1.3 65.9 + - - +
188C ARG* 3.2 30.5 + - - +
190C MET* 5.4 15.4 - - + +
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Residues in contact with ASN 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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182C PRO* 2.9 30.1 + - - +
183C LEU* 3.2 10.6 + - + +
185C ARG* 1.3 79.4 + - - +
187C LEU* 1.3 59.5 + - - +
188C ARG 3.2 6.2 + - - +
198C ALA* 4.7 6.6 - - - +
212C PRO* 5.9 0.9 - - - +
234C LEU* 4.5 16.2 - - + +
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Residues in contact with LEU 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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176C VAL 3.6 7.6 - - - +
177C TYR 3.6 18.2 - - - +
183C LEU* 2.9 28.6 + - + +
184C ALA* 3.7 7.4 - - - +
185C ARG 3.2 0.6 - - - -
186C ASN* 1.3 74.1 - - - +
188C ARG* 1.3 59.6 + - - +
197C LEU* 3.4 19.2 - - + +
198C ALA* 2.9 25.0 + - - +
212C PRO* 5.3 5.5 - - + +
234C LEU* 3.8 35.9 - - + +
235C ALA* 3.7 16.2 - - - +
236C GLY* 3.5 32.8 - - - +
254C LEU* 5.7 0.2 - - - +
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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