Contacts of the helix formed by residues 180 - 192 (chain C) in PDB entry 5AYZ
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 GLY 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C VAL* 3.0 19.0 + - - -
178C ALA* 4.1 0.7 - - - +
179C GLY* 1.3 78.5 - - - +
181C VAL* 1.3 65.4 + - - -
182C GLU* 3.3 10.3 - - - -
183C LYS* 3.3 5.7 + - - +
184C ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 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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175C VAL* 3.5 22.7 - - + +
180C GLY* 1.3 71.3 - - - -
182C GLU* 1.3 85.4 + - - +
184C ALA* 3.2 3.5 + - - +
185C VAL* 2.9 44.4 + - + +
200C VAL* 4.1 17.7 - - + -
201C GLU 5.8 0.2 - - - +
207C GLU* 4.0 33.4 - - + +
210C GLN* 3.8 22.9 - - + +
211C ALA* 4.5 2.7 - - + +
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Residues in contact with GLU 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 GLY* 3.8 6.6 - - - -
181C VAL* 1.3 91.7 + - + +
183C LYS* 1.3 65.2 + - + +
185C VAL* 4.8 3.1 - - - +
186C ARG* 3.1 37.8 + - - +
210C GLN* 2.6 36.9 - - + +
214C ALA* 4.8 11.2 - - + +
287J ALA* 3.7 31.9 - - + +
288J LYS 5.4 0.2 - - - +
289J GLU 3.3 26.5 - - - +
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Residues in contact with LYS 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 ALA* 3.5 28.5 + - + +
179C GLY* 3.6 23.9 + - - +
180C GLY* 3.3 4.2 + - - +
181C VAL 3.3 0.4 - - - -
182C GLU* 1.3 77.9 - - + +
184C ALA* 1.3 59.6 + - - +
186C ARG* 3.6 5.0 + - - +
187C ALA* 3.0 30.5 + - - +
289J GLU 5.8 5.4 - - - +
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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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170C VAL* 3.8 25.1 - - + -
175C VAL* 4.2 9.6 - - - -
178C ALA* 3.7 19.4 - - + +
180C GLY 3.0 17.9 + - - +
181C VAL* 3.2 5.8 + - - +
183C LYS* 1.3 77.1 - - - +
185C VAL* 1.3 57.6 + - - +
187C ALA* 3.3 1.3 + - - -
188C ALA* 2.8 28.3 + - - +
36D VAL* 3.5 14.3 - - + +
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Residues in contact with VAL 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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170C VAL* 4.5 1.6 - - + -
181C VAL* 2.9 32.0 + - + +
184C ALA* 1.3 73.6 - - + +
186C ARG* 1.3 62.4 + - - +
188C ALA* 3.5 6.8 - - - +
189C ARG* 2.7 35.7 + - - +
198C VAL* 4.8 3.8 - - + -
200C VAL* 3.9 28.7 - - + -
211C ALA* 4.2 13.7 - - - +
214C ALA* 3.2 40.8 - - + +
215C GLY* 4.4 1.3 - - - +
216C ALA* 4.6 5.4 - - - +
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Residues in contact with ARG 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 GLU* 3.1 29.2 + - - +
183C LYS* 3.8 6.1 - - - +
185C VAL* 1.3 81.2 - - - +
187C ALA* 1.3 61.7 + - - +
189C ARG* 3.3 7.4 + - + +
190C GLN* 3.2 25.0 + - + +
214C ALA* 5.0 16.8 + - - +
289J GLU* 3.0 49.1 + - - +
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 3.8 29.6 - - + +
183C LYS 3.0 18.9 + - - +
184C ALA* 3.6 4.3 - - - +
186C ARG* 1.3 75.8 - - - +
188C ALA* 1.3 63.6 + - - +
190C GLN* 3.1 15.2 + - - +
191C ALA* 3.1 13.7 + - - +
35D LEU* 3.9 18.3 - - - +
36D VAL* 3.9 13.0 - - + +
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Residues in contact with ALA 188 (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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168C VAL* 3.8 15.4 - - + +
170C VAL* 3.5 26.0 - - + -
184C ALA 2.8 20.6 + - - +
185C VAL* 3.2 6.9 + - - +
187C ALA* 1.3 71.8 - - - +
189C ARG* 1.3 61.4 + - - +
191C ALA* 3.2 16.8 + - - +
192C ALA 3.5 5.4 + - - -
198C VAL* 3.8 19.4 - - + +
36D VAL* 3.6 13.6 - - + +
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Residues in contact with ARG 189 (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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197B LYS* 4.8 3.8 - - - +
185C VAL* 2.7 21.0 + - - +
186C ARG* 3.5 9.2 - - + +
188C ALA* 1.3 69.5 - - - +
190C GLN* 1.2 64.9 + - + +
192C ALA 3.9 0.6 + - - -
193C ASP* 3.1 69.0 + - + +
196C LEU 3.6 12.5 + - - -
198C VAL* 3.7 19.5 - - - +
214C ALA 4.4 6.1 - - - +
215C GLY* 3.4 37.0 + - - -
217C ASP* 3.6 21.2 + - - -
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Residues in contact with GLN 190 (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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1B MET* 3.8 38.4 + - + -
186C ARG* 3.2 14.2 + - + +
187C ALA* 3.1 12.6 + - - +
189C ARG* 1.2 79.4 - - + +
191C ALA* 1.3 66.6 + - - +
192C ALA* 3.3 2.8 + - - -
193C ASP* 3.9 5.2 + - - +
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Residues in contact with ALA 191 (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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153B LEU* 5.9 2.9 - - - +
168C VAL* 4.7 3.6 - - + -
187C ALA 3.1 11.3 + - - +
188C ALA* 3.2 13.7 + - - +
190C GLN* 1.3 75.4 - - - +
192C ALA* 1.3 65.2 + - - +
32D TYR* 3.9 46.0 - - + +
35D LEU* 4.3 21.7 - - + +
36D VAL* 5.4 0.4 - - + -
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Residues in contact with ALA 192 (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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168C VAL* 4.8 5.0 - - + +
188C ALA 3.5 7.6 + - - -
189C ARG* 3.9 2.9 - - - -
190C GLN 3.3 1.3 - - - -
191C ALA* 1.3 84.5 - - - +
193C ASP* 1.3 67.2 + - - +
194C PHE 3.1 16.8 + - - +
195C ALA 4.9 0.2 - - - +
196C LEU* 3.4 47.1 + - + +
198C VAL* 6.1 0.9 - - - -
32D TYR* 4.7 7.9 - - + -
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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