Contacts of the helix formed by residues 176 - 185 (chain C) in PDB entry 3I54
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 THR 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C LEU* 1.3 76.8 - - - +
177C GLN* 1.3 65.8 + - - +
178C GLU* 3.5 8.3 + - - +
179C GLU* 2.9 41.1 + - - +
180C ILE* 3.1 22.2 + - - +
209C LYS* 3.2 28.9 - - - +
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Residues in contact with GLN 177 (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 THR* 1.3 72.4 - - - +
178C GLU* 1.3 66.9 + - - +
180C ILE* 3.5 10.9 + - - +
181C ALA* 3.1 22.0 + - - +
188C ARG* 3.7 27.0 + - - +
191C VAL* 5.0 3.5 - - - +
192C ASN* 2.7 44.7 + - - +
195C LEU* 6.5 0.7 - - - -
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Residues in contact with GLU 178 (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 THR* 3.3 8.1 + - - +
177C GLN* 1.3 78.3 - - - +
179C GLU* 1.3 59.1 + - + +
181C ALA* 3.1 11.6 + - - +
182C GLN* 2.9 56.6 + - - +
186C ALA 5.2 0.7 - - - +
188C ARG* 4.2 27.6 + - - +
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Residues in contact with GLU 179 (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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56C LYS* 2.5 41.8 + - - +
68C LEU* 3.6 11.4 - - + +
96C ILE* 4.3 6.6 - - - +
174C ASP 4.2 3.3 - - - +
175C LEU* 3.4 25.9 - - + +
176C THR* 2.9 42.0 + - - +
178C GLU* 1.3 73.4 - - + +
180C ILE* 1.3 65.4 + - - +
182C GLN* 3.3 15.9 + - - +
183C LEU* 3.0 24.1 + - - +
209C LYS* 4.7 1.2 + - - -
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Residues in contact with ILE 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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150C VAL* 5.4 4.5 - - + -
153C GLN* 5.2 8.1 - - + -
154C LEU* 5.8 9.2 - - + -
157C LEU* 5.3 5.2 - - + -
173C HIS* 3.7 30.7 - - + +
175C LEU* 4.0 19.7 - - + +
176C THR 3.1 17.1 + - - +
177C GLN* 3.9 9.9 - - - +
178C GLU 3.4 0.2 - - - -
179C GLU* 1.3 75.7 - - - +
181C ALA* 1.3 51.6 + - - +
183C LEU* 3.1 9.2 + - + +
184C VAL* 2.8 42.8 + - + +
191C VAL* 4.0 18.6 - - + -
195C LEU* 4.7 17.5 - - + -
206C LEU* 6.5 0.4 - - + -
211C VAL* 6.1 1.1 - - + -
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Residues in contact with ALA 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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177C GLN 3.1 9.5 + - - +
178C GLU* 3.1 14.6 + - - +
180C ILE* 1.3 75.0 - - - +
182C GLN* 1.3 57.0 + - - +
184C VAL* 3.3 0.9 + - - +
185C GLY 2.8 23.6 + - - -
186C ALA 3.0 29.8 + - - +
187C SER 3.9 1.6 - - - +
188C ARG* 3.5 30.5 - - + +
191C VAL* 3.8 13.8 - - + +
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Residues in contact with GLN 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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56C LYS* 5.1 1.6 + - - -
66C GLU* 3.6 54.3 + - - +
67C ASN* 3.9 8.7 + - - +
68C LEU* 3.2 41.2 + - + +
178C GLU* 2.9 44.1 + - - +
179C GLU* 3.7 19.9 - - - +
181C ALA* 1.3 74.6 - - - +
183C LEU* 1.3 61.2 + - - +
185C GLY* 3.6 8.0 + - - +
186C ALA 5.0 0.4 - - - -
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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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68C LEU* 3.6 36.0 - - + +
69C LEU 4.3 2.2 - - - +
70C THR* 4.0 20.6 - - - +
71C ILE* 3.9 15.3 - - + -
153C GLN* 3.8 42.3 + - + +
157C LEU* 4.7 3.1 - - + -
175C LEU* 3.6 31.9 - - + -
179C GLU 3.0 15.0 + - - +
180C ILE* 3.4 7.0 - - + +
182C GLN* 1.3 77.9 - - - +
184C VAL* 1.3 63.0 + - - +
185C GLY 3.2 0.7 + - - -
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Residues in contact with VAL 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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141C LEU* 3.7 7.0 - - - +
146C VAL* 4.2 3.8 - - + -
149C ARG* 3.4 41.5 + - + +
150C VAL* 4.1 30.3 - - + -
153C GLN* 4.2 15.9 - - + +
180C ILE* 2.8 38.4 + - + +
181C ALA 3.3 4.9 + - - +
183C LEU* 1.3 71.5 - - - +
185C GLY* 1.3 58.6 + - - +
186C ALA* 4.0 19.1 - - + -
191C VAL* 4.1 9.6 - - + -
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Residues in contact with GLY 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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67C ASN* 6.0 2.7 - - - -
141C LEU* 4.2 13.8 - - - +
149C ARG* 3.2 12.7 + - - -
181C ALA 2.8 8.9 + - - -
182C GLN* 3.6 9.0 + - - -
183C LEU 3.2 4.4 - - - -
184C VAL* 1.3 79.6 - - - +
186C ALA* 1.3 57.0 + - - -
142D ILE* 6.3 2.7 - - - -
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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