Contacts of the helix formed by residues 191 - 198 (chain C) in PDB entry 4GTU
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 GLU 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C GLY 3.3 5.3 + - - -
190C LEU* 1.3 69.5 - - - +
192C LYS* 1.3 82.3 + - + +
194C SER* 2.9 19.1 + - - -
195C ALA* 3.0 18.4 + - + +
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Residues in contact with LYS 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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21C GLU* 4.0 18.9 - - - +
22C TYR* 3.3 34.8 - - - +
24C ASP* 3.2 25.4 - - - +
190C LEU* 3.4 4.2 - - - +
191C GLU* 1.3 98.0 + - + +
193C ILE* 1.3 68.1 + - + +
195C ALA* 3.2 7.7 + - + +
196C TYR* 2.9 29.6 + - - +
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Residues in contact with ILE 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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18C LEU* 4.9 11.7 - - + +
21C GLU* 6.1 1.1 - - + -
22C TYR* 3.7 34.8 - - + +
157C PHE* 4.6 3.1 - - + -
187C PHE* 3.5 37.9 - - + +
188C GLU* 3.8 13.0 - - - -
190C LEU* 3.1 37.4 + - + +
192C LYS* 1.3 77.5 - - + +
194C SER* 1.3 68.0 + - - +
196C TYR* 3.1 9.6 + - - +
197C MET* 2.9 37.6 + - + +
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Residues in contact with SER 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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188C GLU 3.4 17.3 - - - -
189C GLY* 4.5 3.3 + - - -
190C LEU 2.8 18.1 + - - -
191C GLU* 2.9 16.1 + - - -
193C ILE* 1.3 74.1 - - - +
195C ALA* 1.3 55.4 + - - +
197C MET* 3.0 14.9 - - - +
198C LYS* 2.9 34.8 + - - +
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Residues in contact with ALA 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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191C GLU* 3.0 16.8 + - + +
192C LYS* 3.3 14.4 - - + +
194C SER* 1.3 77.0 + - - +
196C TYR* 1.3 58.3 + - - +
198C LYS* 2.8 31.5 + - - +
199C SER* 3.5 3.2 + - - -
201C ARG* 5.0 1.3 - - - -
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Residues in contact with TYR 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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14C HIS* 5.9 1.6 - + - -
17C ARG* 3.8 38.7 - - + +
18C LEU* 4.7 13.0 - - + -
21C GLU* 3.4 33.6 + - + +
27C TYR* 4.1 4.9 + - - -
29C GLU* 5.5 1.6 + - - -
192C LYS 2.9 12.4 + - - +
193C ILE* 3.6 9.6 - - + +
195C ALA* 1.3 76.0 - - - +
197C MET* 1.3 64.0 + - + +
199C SER* 2.7 36.3 + - - -
201C ARG* 2.8 46.6 + - + +
202C PHE* 3.4 51.4 - + - +
203C LEU 3.7 4.6 + - - -
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Residues in contact with MET 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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18C LEU* 5.3 4.7 - - + -
160C TYR* 3.6 26.9 - - + +
188C GLU* 4.1 27.1 - - + +
193C ILE* 2.9 30.1 + - + +
194C SER* 3.0 23.8 - - - +
196C TYR* 1.3 78.2 - - + +
198C LYS* 1.3 59.4 + - + +
199C SER 3.2 4.6 + - - +
202C PHE* 3.8 50.0 - - + +
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Residues in contact with LYS 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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194C SER* 2.9 16.8 + - - +
195C ALA* 2.8 17.2 + - - +
197C MET* 1.3 78.1 - - + +
199C SER* 1.3 55.9 + - - +
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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