Contacts of the helix formed by residues 180 - 190 (chain B) in PDB entry 6CQE
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 ALA 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A CYS* 4.0 14.7 + - + +
199A TRP* 3.5 30.5 - - + -
200A SER* 4.7 2.4 + - - -
262A ARG* 3.8 3.6 - - - +
178B TRP 3.6 1.0 + - - -
179B MET* 1.3 74.7 - - - +
181B PRO* 1.3 69.4 - - + +
182B GLU* 3.3 25.8 - - - +
183B VAL* 3.0 8.8 + - + +
184B ALA* 2.9 25.3 + - - +
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Residues in contact with PRO 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TRP* 3.7 40.6 - - + -
227A MET* 3.7 24.9 - - + +
228A THR* 3.9 4.6 - - - +
232A TYR* 4.9 2.5 - - + -
257A LYS* 4.4 20.4 - - + +
262A ARG* 4.0 1.1 - - - +
179B MET 4.4 0.7 - - - +
180B ALA* 1.3 84.0 - - + +
182B GLU* 1.3 66.1 + - - +
184B ALA* 3.5 8.5 - - + +
185B ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLY 4.3 4.9 - - - +
193A ASN* 2.9 29.8 + - - +
196A CYS* 4.1 2.1 - - - +
257A LYS 3.8 2.8 - - - +
259A PRO* 3.4 29.6 - - + +
262A ARG* 2.7 44.2 + - - -
180B ALA* 3.3 14.1 - - - +
181B PRO* 1.3 74.4 - - - +
183B VAL* 1.3 59.9 + - - +
185B ALA* 3.6 6.5 + - - +
186B VAL* 3.3 27.9 + - + +
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Residues in contact with VAL 183 (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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190A GLY 4.1 10.1 - - - +
191A GLY 3.5 21.1 - - - +
192A TYR* 3.8 31.0 - - + -
196A CYS* 3.6 29.2 - - + -
179B MET* 3.6 23.3 - - + -
180B ALA* 3.0 16.5 + - + +
182B GLU* 1.3 76.2 - - + +
184B ALA* 1.3 67.2 + - - +
186B VAL* 3.2 4.9 + - - +
187B ALA* 3.0 22.0 + - + +
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Residues in contact with ALA 184 (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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224A LEU* 3.7 8.5 - - + +
227A MET* 3.6 39.0 - - + -
228A THR* 3.6 7.0 - - + -
179B MET* 3.2 14.9 - - + +
180B ALA 2.9 12.7 + - - +
181B PRO* 3.5 8.7 - - + +
183B VAL* 1.3 77.4 - - - +
185B ALA* 1.3 61.2 + - - +
187B ALA* 3.2 12.5 + - - +
188B LEU* 3.2 17.2 + - - +
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Residues in contact with ALA 185 (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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228A THR* 3.5 17.4 - - + +
181B PRO 2.9 17.4 + - - +
182B GLU* 3.7 8.7 - - - +
184B ALA* 1.3 75.5 - - - +
186B VAL* 1.3 54.7 + - + +
188B LEU* 3.0 7.1 + - - +
189B LYS* 2.7 39.2 + - + +
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Residues in contact with VAL 186 (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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186A VAL* 3.7 25.8 - - + -
189A LYS* 6.0 2.9 - - - -
190A GLY* 3.5 25.6 - - - +
191A GLY* 3.5 20.4 - - - +
182B GLU 3.3 13.6 + - - +
183B VAL 3.2 7.8 + - - +
185B ALA* 1.3 76.6 - - + +
187B ALA* 1.3 58.2 + - - +
188B LEU 3.0 1.0 + - - -
189B LYS* 4.3 8.1 - - + -
190B GLY* 2.6 31.5 + - - +
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Residues in contact with ALA 187 (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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190A GLY 5.2 1.3 + - - +
224A LEU* 4.7 9.9 - - + +
168B ARG* 5.5 5.6 + - - +
179B MET* 4.2 16.4 - - + -
183B VAL* 3.0 13.5 + - + +
184B ALA* 3.2 11.2 + - - +
186B VAL* 1.3 76.1 - - - +
188B LEU* 1.3 60.2 - - - +
190B GLY* 4.8 0.4 - - - -
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Residues in contact with LEU 188 (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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221A LEU* 4.2 18.2 - - + -
224A LEU* 3.6 33.2 - - + +
225A PHE* 4.2 22.2 - - + +
228A THR* 3.5 32.5 - - + +
161B GLN* 4.9 8.3 - - - +
184B ALA 3.2 7.0 + - - +
185B ALA* 3.0 7.7 + - - +
187B ALA* 1.3 80.6 - - - +
189B LYS* 1.3 67.9 + - - +
190B GLY* 3.4 1.4 + - - -
192B TYR* 5.5 1.7 - - - -
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Residues in contact with LYS 189 (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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185B ALA* 2.7 23.1 + - + +
186B VAL* 4.2 4.9 - - + +
188B LEU* 1.3 76.1 - - - +
190B GLY* 1.3 72.5 + - - +
191B GLY 4.9 1.8 + - - -
192B TYR* 3.4 44.4 + - - +
193B ASN* 5.7 1.6 - - - +
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Residues in contact with GLY 190 (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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186A VAL* 3.5 16.3 - - - +
186B VAL* 2.6 24.8 + - - +
187B ALA 5.5 0.7 - - - -
188B LEU 3.4 1.2 - - - -
189B LYS* 1.3 92.9 + - - +
191B GLY* 1.3 59.2 + - - -
192B TYR* 3.1 13.7 + - - -
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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