Contacts of the helix formed by residues 168 - 178 (chain C) in PDB entry 5A0Q
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 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C GLN* 5.6 0.5 + - - -
163C CYS* 2.8 34.5 + - - +
164C ILE* 3.6 17.0 - - - +
165C GLY 3.2 19.3 + - - -
167C ASN* 1.4 76.7 - - - +
169C ALA* 1.4 54.3 + - - +
171C ALA* 3.7 0.2 - - - +
172C VAL* 2.8 42.3 + - - +
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Residues in contact with ALA 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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167C ASN* 3.2 1.5 - - - -
168C SER* 1.4 76.8 - - - +
170C ALA* 1.3 61.9 + - - +
172C VAL* 3.6 8.2 - - - +
173C SER* 2.9 30.8 + - - -
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Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ASN* 3.7 21.7 + - + +
168C SER 3.5 0.2 - - - -
169C ALA* 1.3 78.5 - - - +
171C ALA* 1.3 57.2 - - - +
173C SER* 3.0 8.3 + - - -
174C MET* 3.0 28.4 + - - +
200C THR* 6.6 0.2 - - - -
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Residues in contact with ALA 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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163C CYS* 3.5 26.9 - - - -
167C ASN 3.1 20.5 + - - +
168C SER 3.7 0.2 - - - +
170C ALA* 1.3 74.6 - - - +
172C VAL* 1.4 59.5 + - - +
174C MET* 3.2 7.4 + - - +
175C LEU* 3.1 29.2 + - - +
196C VAL* 3.6 22.5 - - + +
200C THR* 4.8 11.2 - - - -
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Residues in contact with VAL 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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159C TRP* 4.8 9.0 - - + -
161C ALA 4.4 0.9 - - - +
162C THR* 4.0 32.5 - - - +
163C CYS* 4.1 7.4 - - - +
168C SER* 2.8 32.8 + - - +
169C ALA* 3.6 9.6 - - - +
171C ALA* 1.4 69.6 - - - +
173C SER* 1.4 62.3 + - - +
175C LEU* 3.2 10.3 + - + +
176C LYS* 3.1 22.0 + - - +
53D LEU* 3.8 18.5 - - + +
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Residues in contact with SER 173 (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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169C ALA 2.9 22.8 + - - -
170C ALA* 3.0 15.1 + - - -
172C VAL* 1.4 76.2 - - - +
174C MET* 1.4 63.0 + - - +
176C LYS* 3.3 30.9 + - - +
177C GLN* 4.0 9.7 + - - +
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Residues in contact with MET 174 (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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170C ALA 3.0 20.8 + - - +
171C ALA* 3.2 9.8 + - - +
173C SER* 1.4 77.7 + - - +
175C LEU* 1.4 56.8 + - - +
177C GLN* 3.7 11.0 - - - +
178C ASP* 2.9 51.8 + - - +
195C LYS* 4.2 10.8 - - + -
196C VAL* 4.2 16.4 - - + -
199C LYS* 3.6 43.7 - - + -
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Residues in contact with LEU 175 (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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35C LEU* 5.1 3.8 - - + -
37C ILE* 3.9 28.0 - - + -
161C ALA* 4.0 17.7 - - + -
162C THR 4.4 16.4 - - - +
163C CYS* 5.0 3.1 - - + +
171C ALA 3.1 19.2 + - - +
172C VAL* 3.2 14.8 + - - +
174C MET* 1.4 74.4 - - - +
176C LYS* 1.3 57.2 + - - +
177C GLN 3.3 1.3 - - - -
178C ASP* 3.6 6.3 - - + +
179C TYR* 2.9 41.4 + - + +
192C LEU* 4.4 10.8 - - + -
196C VAL* 3.6 28.0 - - + -
53D LEU* 3.7 11.5 - - + +
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Residues in contact with LYS 176 (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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172C VAL 3.1 11.5 + - - +
173C SER* 3.3 25.4 - - - +
174C MET 3.3 0.8 - - - -
175C LEU* 1.3 77.6 - - - +
177C GLN* 1.3 59.3 + - + +
179C TYR 3.8 9.7 - - - +
50D VAL 4.7 2.4 + - - -
51D ALA* 3.5 46.6 - - - +
52D LYS* 5.8 1.7 - - - +
53D LEU* 4.0 13.5 - - + +
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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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173C SER 4.0 10.2 + - - +
174C MET* 3.7 16.4 + - - +
176C LYS* 1.3 73.8 - - + +
178C ASP* 1.4 80.3 + - - +
179C TYR 3.3 7.4 + - - -
180C LYS* 4.7 2.6 + - - +
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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
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174C MET* 2.9 55.1 + - + +
175C LEU* 3.5 6.3 + - + -
177C GLN* 1.4 95.4 + - - +
179C TYR* 1.3 59.6 + - - +
180C LYS 3.8 2.5 + - - -
184C MET* 4.8 0.3 - - - +
192C LEU* 3.1 27.1 - - + +
195C LYS* 3.7 27.9 + - + +
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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