Contacts of the helix formed by residues 185 - 195 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A THR 3.2 1.4 + - - -
184A ASP* 1.3 79.0 - - - +
186A PHE* 1.3 66.5 + - - +
187A GLU* 3.2 4.9 - - - -
188A ALA* 2.8 15.3 + - + +
189A ARG* 2.7 35.9 + - - +
157B LEU* 4.1 15.7 - - + +
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Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 3.7 47.3 - - + -
92A VAL* 3.8 23.8 - - + -
93A LEU* 3.6 31.2 - - + -
96A LEU* 4.0 17.5 - - + -
165A PHE* 5.0 6.1 - + - -
182A PRO 5.4 1.1 - - - -
183A THR* 2.9 25.0 + - - +
184A ASP 3.1 2.6 - - - -
185A ASP* 1.3 75.9 - - - +
187A GLU* 1.3 72.3 + - - +
189A ARG* 3.0 7.9 + - + +
190A TRP* 2.6 63.0 + + + +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG* 2.9 30.6 + - - -
93A LEU* 5.7 0.9 - - - +
185A ASP* 4.8 1.8 - - - -
186A PHE* 1.3 91.9 + - - +
188A ALA* 1.3 58.4 + - + +
190A TRP* 5.1 1.1 - - - -
191A PRO* 2.9 25.4 - - - +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASP* 2.8 22.6 + - + +
187A GLU* 1.3 81.2 - - + +
189A ARG* 1.3 63.7 + - - +
191A PRO* 3.5 8.9 - - - +
192A LEU* 3.7 19.9 - - - +
153B LEU* 5.5 2.8 - - + +
157B LEU* 3.9 21.8 - - + +
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 4.3 16.2 - - + -
169A MET* 3.9 28.6 - - - +
182A PRO 5.5 0.4 - - - -
184A ASP* 3.3 24.1 + - - +
185A ASP* 2.7 21.6 + - - +
186A PHE* 3.7 7.2 - - + +
188A ALA* 1.3 76.8 - - - +
190A TRP* 1.3 66.2 + - - +
192A LEU* 3.0 20.7 + - - +
193A VAL* 3.0 14.9 + - - +
157B LEU* 3.5 29.2 + - + +
160B SER* 2.9 35.5 + - - -
161B GLN* 2.9 34.0 + - - +
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Residues in contact with TRP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 4.1 13.5 - - + +
88A LEU* 3.8 13.2 - - + -
89A ARG* 3.5 58.8 - - + +
92A VAL* 3.8 24.9 - - + -
162A LEU* 4.7 4.3 - - + -
165A PHE* 6.2 0.2 - - - -
186A PHE* 2.6 50.6 + + + +
187A GLU* 4.8 1.3 - - - +
189A ARG* 1.3 72.8 - - - +
191A PRO* 1.3 62.8 - - + +
193A VAL* 2.9 31.0 + - + -
194A ALA* 2.7 54.5 + - + +
197A LEU* 4.4 10.3 - - + -
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Residues in contact with PRO 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU 2.9 25.6 - - - +
188A ALA* 3.5 7.9 - - - +
189A ARG 3.4 3.1 - - - -
190A TRP* 1.3 98.4 - - + +
192A LEU* 1.3 67.1 + - + +
194A ALA* 3.5 7.7 + - + +
195A ALA* 3.1 22.3 + - - +
198B GLN* 4.7 2.2 + - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA 3.7 19.5 - - - +
189A ARG* 3.0 11.1 + - - +
191A PRO* 1.3 79.6 - - + +
193A VAL* 1.3 64.4 + - - +
195A ALA* 3.3 19.4 - - - +
196A GLN 3.9 0.7 + - - -
153B LEU* 3.4 22.7 - - + -
157B LEU* 3.9 23.8 - - + -
158B LEU* 4.1 11.2 - - + -
161B GLN* 4.2 16.6 - - + +
196B GLN* 3.2 44.7 + - + +
198B GLN* 3.8 19.5 - - - +
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.5 29.4 - - + -
165A PHE* 4.0 34.3 - - + -
189A ARG 3.0 9.6 + - - +
190A TRP* 2.9 27.5 + - + +
192A LEU* 1.3 76.8 - - - +
194A ALA* 1.3 57.1 + - - +
196A GLN* 3.0 34.2 + - - +
197A LEU* 4.0 3.1 + - - +
161B GLN* 3.5 23.3 - - - +
196B GLN* 3.1 9.4 - - - +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 4.7 7.9 - - + -
190A TRP* 2.7 43.7 + - + +
191A PRO* 3.8 7.0 - - + +
193A VAL* 1.3 67.8 - - - +
195A ALA* 1.3 57.4 + - - +
196A GLN 3.0 5.4 - - - -
197A LEU* 2.9 41.6 + - + +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PRO 3.1 12.9 + - - +
192A LEU 3.3 14.6 - - - +
193A VAL 3.1 0.4 - - - -
194A ALA* 1.3 76.1 - - - +
196A GLN* 1.3 57.4 + - - +
197A LEU 3.3 0.6 + - - -
198A GLN* 3.0 25.6 + - - +
195B ALA* 4.0 15.1 - - + +
198B GLN* 3.7 21.1 - - - +
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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