Contacts of the helix formed by residues 165 - 172 (chain C) in PDB entry 1SMV
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 SER 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C GLN* 2.7 34.8 + - - +
50C GLY 4.0 11.1 + - - -
51C ALA* 3.8 25.3 - - - +
120C ILE* 4.5 2.5 - - - -
121C PRO* 3.9 8.3 - - - +
163C SER 3.6 0.6 - - - -
164C GLY* 1.3 76.3 - - - +
166C ALA* 1.3 63.9 + - - +
167C GLY 3.0 1.1 - - - -
168C LEU* 3.0 23.7 + - - +
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Residues in contact with ALA 166 (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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164C GLY 2.9 1.0 - - - -
165C SER* 1.3 82.7 + - - +
167C GLY* 1.3 57.9 + - - +
168C LEU 3.1 2.0 + - - -
169C CYS* 4.0 6.8 + - - -
178C ASP 3.8 18.2 - - - +
179C THR* 4.0 17.4 - - - +
181C THR* 3.6 25.6 - - - +
182C ALA* 3.9 13.5 - - + +
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Residues in contact with GLY 167 (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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118C THR* 3.6 16.8 - - - +
120C ILE* 4.5 0.7 - - - -
164C GLY 2.9 12.4 + - - -
166C ALA* 1.3 77.0 - - - +
168C LEU* 1.3 64.6 + - - +
169C CYS 3.2 2.0 - - - -
170C PHE* 3.0 35.0 + - - +
171C ILE* 4.0 1.2 + - - +
182C ALA* 3.5 19.3 - - - +
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Residues in contact with LEU 168 (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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51C ALA* 4.2 13.0 - - + -
52C MET* 3.7 22.2 - - + +
53C VAL* 3.7 25.8 - - + -
120C ILE* 4.1 8.5 - - + +
165C SER 3.0 17.9 + - - +
166C ALA 3.1 1.0 - - - -
167C GLY* 1.3 76.9 - - - +
169C CYS* 1.3 64.8 + - - +
171C ILE* 2.9 20.3 + - + -
172C ASN* 2.9 52.0 + - + +
174C SER* 5.7 0.7 - - - +
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Residues in contact with CYS 169 (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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166C ALA 4.0 7.9 + - - +
168C LEU* 1.3 77.7 - - - +
170C PHE* 1.3 67.4 + - - +
173C ASN* 3.0 23.6 + - - -
174C SER* 3.4 22.6 + - - +
175C ARG 4.1 4.3 - - - +
176C CYS* 2.0 64.5 - - - +
177C SER 4.8 0.9 - - - +
179C THR* 3.8 14.8 - - - -
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Residues in contact with PHE 170 (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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72C CYS* 4.4 0.2 - - - -
116C ARG* 3.6 55.0 - - - -
118C THR* 4.1 6.5 - - + +
167C GLY* 3.0 36.2 + - - +
168C LEU 2.9 0.2 + - - -
169C CYS* 1.3 79.1 - - - +
171C ILE* 1.3 61.0 + - - +
173C ASN* 4.1 4.3 + - - -
176C CYS* 3.9 16.8 - - - -
179C THR* 3.8 28.5 - - + -
182C ALA* 4.3 5.4 - - + -
184C SER* 3.8 18.4 - - - -
245C THR* 3.9 20.0 - - - +
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Residues in contact with ILE 171 (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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53C VAL* 4.1 22.0 - - + -
54C ARG 4.7 2.6 - - - +
55C ILE* 4.3 14.9 - - + +
56C ARG 5.4 1.0 + - - -
72C CYS* 3.8 28.6 - - + +
118C THR* 4.3 19.3 - - + +
120C ILE* 3.7 36.1 - - + -
167C GLY 4.4 1.6 - - - +
168C LEU* 2.9 11.1 + - + +
170C PHE* 1.3 78.5 - - - +
172C ASN* 1.3 64.1 + - - +
173C ASN* 3.1 8.1 + - - +
243C TYR* 3.7 34.1 - - + -
245C THR* 4.3 4.0 - - - +
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Residues in contact with ASN 172 (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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52C MET 2.9 22.0 + - - -
53C VAL* 3.4 8.5 - - - +
54C ARG* 2.7 45.6 + - - +
56C ARG* 5.3 5.5 - - - +
168C LEU* 2.9 32.8 + - + +
171C ILE* 1.3 76.0 - - - +
173C ASN* 1.3 68.7 + - - +
174C SER* 3.5 19.9 + - - +
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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