Contacts of the helix formed by residues 184 - 193 (chain B) in PDB entry 6GR2
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 ILE 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 3.7 4.8 + - + +
167B ALA* 5.0 2.9 - - + +
168B GLN* 3.9 23.3 - - - +
171B GLN* 2.9 31.2 - - + +
183B GLY* 1.3 73.0 - - - -
185B MET* 1.3 73.6 + - - +
186B ASP 3.4 0.8 + - - -
187B GLN* 3.5 9.2 - - - +
188B PHE* 3.1 31.9 + - + +
201B ILE* 4.4 9.9 - - + -
203B CYS* 3.6 36.1 - - + +
206B LEU* 4.3 20.4 - - + -
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.9 7.2 - - - -
39B ASN* 3.0 47.3 - - + +
42B GLY 5.2 0.4 - - - +
43B GLU* 4.9 3.4 - - - +
46B ASP* 3.5 25.3 + - + +
52B VAL* 3.9 22.4 - - + -
54B PRO* 3.1 36.3 - - + -
183B GLY 3.3 2.2 - - - -
184B ILE* 1.3 86.8 - - - +
186B ASP* 1.3 78.0 + - - +
188B PHE* 3.1 5.7 + - - +
189B ILE* 3.0 24.3 + - - +
201B ILE* 4.4 3.8 - - + +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 2.3 34.2 + - - +
140B SER* 3.1 19.9 + - - +
142B SER* 5.3 2.9 + - - -
143B ALA* 3.6 21.7 - - + +
174B GLU* 5.7 1.6 - - - +
182B CYS* 5.3 9.3 - - - +
183B GLY 4.6 2.6 + - - +
184B ILE 3.4 0.2 - - - -
185B MET* 1.3 81.8 - - - +
187B GLN* 1.3 71.9 + - - +
189B ILE* 3.1 21.7 - - - +
190B SER* 3.1 12.3 + - - -
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 4.1 9.6 - - + +
146B GLU* 3.2 10.8 + - - +
147B VAL* 3.9 10.5 - - + +
167B ALA* 3.8 22.4 - - - +
170B CYS* 3.4 28.0 - - + -
171B GLN* 4.1 13.2 - - - +
174B GLU* 3.1 26.1 + - - -
182B CYS* 3.7 12.5 - - - -
183B GLY 3.2 20.0 - - - +
184B ILE* 3.5 10.3 - - - +
186B ASP* 1.3 77.2 + - - +
188B PHE* 1.3 63.1 + - - +
190B SER* 3.5 1.9 + - - -
191B LEU* 3.1 29.4 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 5.5 0.9 - - + -
164B ALA* 4.4 28.5 - - + -
167B ALA* 3.9 18.2 - - + -
168B GLN* 5.3 1.8 - - - -
184B ILE* 3.1 31.2 + - + +
185B MET* 3.1 5.5 + - - +
187B GLN* 1.3 77.9 - - - +
189B ILE* 1.3 58.9 + - - +
191B LEU* 3.3 2.3 + - - -
192B MET* 2.8 70.1 + - + +
199B LEU* 4.2 4.5 - - + -
201B ILE* 4.0 13.9 - - + -
206B LEU* 3.9 34.3 - - + -
208B THR* 3.2 27.8 - - + -
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.8 31.2 - - + -
54B PRO* 3.7 31.4 - - + +
55B MET* 4.0 2.2 - - - +
56B ALA* 3.9 29.7 - - - +
185B MET 3.0 11.3 + - - +
186B ASP 3.1 16.4 - - - +
188B PHE* 1.3 74.4 - - - +
190B SER* 1.3 66.4 + - - +
193B GLY* 3.0 35.3 + - - -
197B HIS 5.9 0.7 - - - +
198B ALA 5.6 0.4 - - - -
199B LEU* 3.7 33.0 - - + +
201B ILE* 4.5 1.0 - - + +
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.8 10.9 - - - +
35B PRO* 2.8 40.4 + - - +
36B GLY 5.4 1.8 - - - -
37B ARG* 6.2 0.7 - - - -
140B SER* 6.5 0.4 - - - -
143B ALA* 4.6 6.5 - - - -
144B SER* 4.0 3.7 - - - -
147B VAL* 3.9 15.3 - - - +
186B ASP 3.1 17.7 + - - -
187B GLN* 3.8 4.5 - - - -
189B ILE* 1.3 78.3 - - - +
191B LEU* 1.3 57.8 + - - +
386B GLY* 3.2 6.6 - - - -
387B ALA* 2.8 24.6 + - - -
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 3.4 29.6 - - + -
150B TYR* 5.5 3.8 - - + -
151B THR* 4.9 3.4 - - - +
154B GLN* 5.5 0.9 - - - +
163B ILE* 3.8 36.8 - - + +
166B ARG* 3.8 25.4 - - + +
167B ALA* 3.4 37.0 - - + +
170B CYS* 5.5 0.9 - - - -
187B GLN 3.1 20.5 + - - +
188B PHE* 3.7 3.8 - - - +
190B SER* 1.3 79.7 - - - +
192B MET* 1.3 58.9 + - - +
193B GLY 3.6 1.3 + - - +
386B GLY* 4.2 2.3 - - - -
387B ALA* 4.0 21.2 + - + +
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Residues in contact with MET 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 3.3 39.5 - - + -
188B PHE* 2.8 50.6 + - + +
189B ILE 3.3 0.2 + - - -
191B LEU* 1.3 73.1 - - - +
193B GLY* 1.3 66.5 + - - +
194B GLN* 3.6 7.5 + - - +
199B LEU* 3.5 18.8 - - + -
208B THR* 3.4 26.7 - - - +
210B LEU* 4.0 15.1 - - + +
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Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA* 4.7 2.0 - - - -
189B ILE* 3.0 30.2 + - - +
191B LEU 3.6 2.3 - - - +
192B MET* 1.3 80.8 - - - +
194B GLN* 1.3 68.6 + - - +
197B HIS 5.8 1.8 - - - -
199B LEU* 5.3 0.4 - - - -
210B LEU* 5.1 2.9 - - - -
384B ALA 3.9 6.5 - - - -
385B ASP* 3.8 0.6 - - - +
386B GLY* 2.8 28.6 + - - -
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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