Contacts of the helix formed by residues 185 - 195 (chain C) in PDB entry 4GCK
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 ASP 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C THR 3.1 1.6 + - - -
184C ASP* 1.3 79.4 - - - +
186C PHE* 1.3 54.0 + - - +
187C GLU* 3.2 2.9 - - - -
188C ALA* 3.0 11.9 + - + +
189C ARG* 2.7 50.4 + - - +
157D LEU* 4.2 15.2 - - + +
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Residues in contact with PHE 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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89C ARG* 3.7 50.3 - - + -
92C VAL* 4.0 22.9 - - + -
93C LEU* 3.7 31.0 - - + -
96C LEU* 4.1 17.0 - - + -
165C PHE* 5.3 4.5 - + - -
182C PRO 5.5 0.7 - - - -
183C THR* 3.1 24.7 + - - +
184C ASP 3.2 2.1 - - - -
185C ASP* 1.3 76.9 - - - +
187C GLU* 1.3 71.7 + - + +
189C ARG* 3.0 7.9 + - + +
190C TRP* 2.6 58.1 + + + +
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Residues in contact with GLU 187 (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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89C ARG* 2.6 34.8 + - - -
93C LEU* 5.6 0.3 - - - +
185C ASP* 3.2 1.2 - - - +
186C PHE* 1.3 95.4 - - + +
188C ALA* 1.3 56.6 + - - +
190C TRP* 5.0 1.8 - - - -
191C PRO* 3.0 24.8 - - - +
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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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185C ASP* 3.0 19.3 + - + +
187C GLU* 1.3 79.0 - - - +
189C ARG* 1.3 62.0 + - - +
190C TRP 3.5 0.2 - - - -
191C PRO* 3.5 6.7 - - - +
192C LEU* 3.5 19.9 - - - +
153D LEU* 5.6 3.1 - - + +
157D LEU* 3.9 26.4 - - + +
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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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165C PHE* 4.2 14.8 - - + -
169C MET* 3.6 31.6 - - - +
172C ARG* 6.0 0.4 - - - -
182C PRO 5.4 0.4 - - - -
184C ASP* 3.5 19.7 + - - +
185C ASP* 2.7 25.0 + - - +
186C PHE* 3.7 7.0 - - + +
188C ALA* 1.3 77.4 - - - +
190C TRP* 1.3 66.3 + - - +
192C LEU* 3.0 20.3 + - - +
193C VAL* 3.0 15.0 + - - +
157D LEU* 3.6 27.9 + - + +
160D SER* 2.9 33.6 + - - -
161D GLN* 2.9 33.5 + - - +
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Residues in contact with TRP 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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85C THR* 3.9 18.2 - - + +
88C LEU* 3.8 12.3 - - + -
89C ARG* 3.4 66.6 - - + +
92C VAL* 4.0 20.6 - - + -
162C LEU* 4.2 9.2 - - + -
186C PHE* 2.6 47.3 + + + +
187C GLU* 4.8 1.8 - - - +
189C ARG* 1.3 73.0 - - - +
191C PRO* 1.3 65.1 - - + +
193C VAL* 2.7 29.9 + - + -
194C ALA* 2.6 57.7 + - + +
197C LEU* 4.6 6.5 - - + -
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Residues in contact with PRO 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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187C GLU 3.0 23.8 - - - +
188C ALA* 3.5 7.6 - - - +
189C ARG 3.5 3.6 - - - -
190C TRP* 1.3 101.0 - - + +
192C LEU* 1.3 66.8 + - + +
194C ALA* 3.9 5.8 - - + +
195C ALA* 3.0 22.3 + - - +
198D GLN* 4.5 2.3 + - - +
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Residues in contact with LEU 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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188C ALA 3.5 20.9 - - - +
189C ARG* 3.0 7.5 + - - +
191C PRO* 1.3 80.3 - - + +
193C VAL* 1.3 66.9 + - - +
195C ALA* 3.2 17.1 + - - +
196C GLN 3.8 0.9 + - - -
153D LEU* 3.3 26.9 - - + -
157D LEU* 4.1 17.3 - - + -
158D LEU* 3.9 16.4 - - + -
161D GLN* 4.3 14.6 - - + +
196D GLN* 3.1 48.0 - - + +
198D GLN* 3.9 16.4 - - - +
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Residues in contact with VAL 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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162C LEU* 3.3 31.6 - - + +
165C PHE* 3.9 34.3 - - + -
189C ARG 3.0 15.4 + - - +
190C TRP* 2.7 23.8 + - + +
192C LEU* 1.3 78.4 - - - +
194C ALA* 1.3 61.8 + - - +
196C GLN* 3.0 28.9 + - - +
197C LEU* 4.0 3.8 + - - +
161D GLN* 3.3 20.9 - - - +
196D GLN* 4.0 6.7 - - - +
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Residues in contact with ALA 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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85C THR* 4.7 10.8 - - + -
190C TRP* 2.6 46.7 + - + +
191C PRO* 3.9 7.9 - - + +
193C VAL* 1.3 67.7 - - - +
195C ALA* 1.3 56.2 + - - +
196C GLN 3.0 5.8 - - - -
197C LEU* 2.9 38.1 + - + +
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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 PRO 3.0 12.9 + - - +
192C LEU 3.2 15.9 - - - +
193C VAL 3.1 0.2 - - - -
194C ALA* 1.3 77.0 - - - +
196C GLN* 1.3 57.7 + - - +
197C LEU 3.4 0.6 - - - +
198C GLN* 3.0 25.5 + - - +
195D ALA* 3.8 16.0 - - + +
198D GLN* 3.6 21.5 - - - +
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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