Contacts of the helix formed by residues 192 - 198 (chain C) in PDB entry 5AYR
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 LEU 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C LEU* 4.3 3.4 - - - -
157C CYS 3.8 21.8 - - - +
158C PHE* 3.8 23.6 - - + +
159C SER* 2.8 15.8 + - - +
170C LEU* 4.3 9.4 - - + -
174C TYR* 4.0 19.3 - - - +
190C GLY 4.1 3.4 - - - +
191C ASP* 1.3 73.4 + - - +
193C SER* 1.3 65.4 + - - +
194C GLY 3.1 3.6 - - - -
195C TRP* 2.8 55.4 + - + +
196C ALA 3.2 6.9 + - - -
202C LEU* 3.6 20.4 - - + +
304C LEU* 3.9 14.6 - - + -
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Residues in contact with SER 193 (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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131C MET* 3.3 28.5 - - - +
154C HIS* 4.0 5.9 - - - -
156C LEU* 4.0 10.7 - - - +
191C ASP* 2.4 34.4 + - - -
192C LEU* 1.3 76.7 - - - +
194C GLY* 1.3 61.9 + - - +
196C ALA* 2.9 13.6 + - - +
197C LYS* 2.9 32.2 + - - +
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Residues in contact with GLY 194 (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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191C ASP 4.7 0.6 + - - -
192C LEU 3.0 2.0 + - - -
193C SER* 1.3 79.0 - - - +
195C TRP* 1.3 62.9 + - - +
197C LYS* 4.0 16.8 + - - +
198C GLN* 3.0 31.2 + - - +
303C GLU* 3.5 22.3 - - - +
304C LEU* 4.4 6.6 - - - +
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Residues in contact with TRP 195 (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 ILE* 5.2 6.1 - - + -
170C LEU* 5.1 0.2 - - + -
173C ILE* 4.1 18.4 - - + -
174C TYR* 4.7 2.9 - + - -
177C LEU* 3.7 29.6 - - + -
192C LEU* 2.8 44.8 + - + +
194C GLY* 1.3 79.6 - - - +
196C ALA* 1.3 66.7 + - - +
197C LYS 3.2 0.4 - - - -
198C GLN* 3.1 15.4 + - - +
200C VAL* 3.2 36.5 + - + +
202C LEU* 4.6 12.1 - - + -
245C TRP* 6.2 0.9 - + - -
284C PHE* 4.9 3.4 - + - -
299C ILE* 4.7 0.9 - - + -
300C ASP 4.1 12.8 - - - -
301C TRP* 3.0 60.6 + + - +
304C LEU* 3.6 29.2 - - + +
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Residues in contact with ALA 196 (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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128C TRP* 6.1 0.4 - - - -
131C MET* 3.4 28.7 - - + -
132C CYS* 3.5 16.5 - - - +
156C LEU* 4.0 20.0 - - + -
192C LEU 3.2 4.5 + - - +
193C SER* 2.9 11.3 + - - +
195C TRP* 1.3 80.4 - - - +
197C LYS* 1.3 56.2 - - - +
199C GLY* 2.9 19.4 + - - -
200C VAL 3.5 16.0 + - - +
202C LEU* 4.6 2.6 - - + +
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Residues in contact with LYS 197 (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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131C MET* 3.5 31.0 - - - +
132C CYS* 3.9 9.5 - - - +
136C ASP* 5.6 1.9 - - - +
193C SER* 2.9 34.4 + - - +
194C GLY* 4.0 15.8 - - - +
195C TRP 3.2 0.4 - - - -
196C ALA* 1.3 75.9 - - - +
198C GLN* 1.3 60.4 + - + +
199C GLY 3.2 1.3 + - - -
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Residues in contact with GLN 198 (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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136C ASP* 4.1 4.8 - - - +
138C LYS* 3.6 22.5 + - - +
194C GLY 3.0 24.1 + - - +
195C TRP* 3.1 10.7 + - - +
196C ALA 3.1 0.8 - - - -
197C LYS* 1.3 78.1 - - + +
199C GLY* 1.3 61.2 + - - +
200C VAL 3.5 0.4 + - - -
298C PRO 4.4 2.3 - - - +
299C ILE* 3.6 21.4 - - + +
300C ASP* 2.7 56.7 + - - +
303C GLU* 3.5 16.7 - - + +
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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