Contacts of the helix formed by residues 176 - 183 (chain C) in PDB entry 4I5L
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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174C ILE* 3.4 12.5 - - - +
175C ASP* 1.3 87.7 - - + +
177C LEU* 1.3 65.8 + - - +
178C ASP* 3.5 12.0 + - + +
179C HIS* 3.0 50.9 + - + +
180C ILE 3.4 1.4 + - - -
228C PHE* 4.9 0.9 - - - -
231C ALA* 5.7 4.7 - - + +
232C ASN* 3.1 11.0 - - - +
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Residues in contact with LEU 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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45C VAL* 3.8 8.0 - - + +
158C LEU* 3.7 30.3 - - + -
161C GLY 5.8 0.2 - - - +
164C PHE* 3.7 39.3 - - + -
176C THR* 1.3 71.5 - - - +
178C ASP* 1.3 57.6 + - - +
180C ILE* 2.9 28.7 + - + +
181C ARG* 3.0 37.9 + - - +
228C PHE* 4.3 12.1 - - + -
232C ASN* 3.0 27.2 + - + +
234C LEU* 4.4 14.8 - - + -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C THR* 3.1 10.8 - - - +
177C LEU* 1.3 77.2 - - - +
179C HIS* 1.3 63.2 + - + +
181C ARG* 2.9 46.0 + - - +
182C ALA* 3.0 14.5 + - - +
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Residues in contact with HIS 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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173C SER 4.8 4.8 + - - +
174C ILE* 4.1 17.7 - - + +
175C ASP* 3.3 39.7 + - + -
176C THR* 3.0 33.2 + - + +
178C ASP* 1.3 75.8 - - + +
180C ILE* 1.3 61.3 + - - +
182C ALA* 3.6 12.3 + - + +
183C LEU* 3.5 20.5 + - - +
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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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44C ASN* 3.0 36.8 + - + +
45C VAL* 3.7 17.3 - - + -
155C LEU* 5.0 2.0 - - + -
156C THR* 4.0 4.5 - - + +
164C PHE* 3.5 35.9 - - + -
174C ILE* 3.7 30.3 - - + -
176C THR 3.4 1.5 + - - +
177C LEU* 2.9 21.0 + - + +
179C HIS* 1.3 75.8 - - - +
181C ARG* 1.3 62.1 + - - +
183C LEU* 3.2 15.2 + - + +
198C LEU* 4.1 30.5 - - + -
228C PHE* 4.7 2.0 - - + -
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Residues in contact with ARG 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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43C SER* 4.2 15.3 - - - +
44C ASN* 3.8 14.3 + - - +
45C VAL* 3.7 29.1 - - + +
47C GLU* 3.8 21.6 + - - -
158C LEU* 5.0 2.8 - - - +
177C LEU* 3.0 37.5 + - - +
178C ASP* 2.9 37.3 + - - +
180C ILE* 1.3 75.8 - - - +
182C ALA* 1.3 59.8 + - - +
183C LEU 3.7 2.3 + - - +
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Residues in contact with ALA 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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178C ASP 3.0 13.2 + - - +
179C HIS* 3.9 9.9 - - + +
180C ILE 3.2 0.6 - - - -
181C ARG* 1.3 75.7 - - - +
183C LEU* 1.3 66.5 + - - +
184C ASP* 3.8 0.5 + - - +
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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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44C ASN* 2.9 19.4 + - - +
155C LEU* 4.1 12.3 - - + -
174C ILE* 4.8 2.2 - - + -
179C HIS 3.5 11.9 - - - +
180C ILE* 3.2 21.2 + - - +
181C ARG 3.9 2.8 - - - +
182C ALA* 1.3 83.3 - - + +
184C ASP* 1.3 64.1 + - - +
185C ARG 3.8 0.2 + - - -
194C PRO* 3.6 36.3 - - + -
195C MET* 4.2 9.9 - - + +
198C LEU* 3.9 27.8 - - + -
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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