Contacts of the helix formed by residues 187 - 195 (chain A) in PDB entry 6BQG
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 VAL 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ILE* 2.9 18.3 + - + +
184A GLY* 3.3 13.9 - - - +
186A SER* 1.3 77.2 - - - +
188A PRO* 1.3 73.8 - - + +
190A PRO* 3.0 26.8 - - + +
191A VAL* 3.2 22.8 + - + +
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Residues in contact with PRO 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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184A GLY 3.0 18.4 - - - +
185A VAL* 3.1 18.6 - - - +
186A SER 3.3 0.7 - - - -
187A VAL* 1.3 94.3 - - + +
189A ILE* 1.3 52.8 + - - +
191A VAL* 4.2 7.4 - - + -
192A ILE* 2.7 50.4 + - + +
214A PHE* 3.7 26.0 - - + -
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Residues in contact with ILE 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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128A PRO* 3.6 29.3 - - + +
131A ILE* 3.9 14.6 - - + -
132A SER* 3.6 15.3 - - - +
135A VAL* 4.0 14.8 - - + -
186A SER 3.0 10.6 + - - +
188A PRO* 1.3 75.2 - - - +
190A PRO* 1.3 65.9 - - + +
192A ILE* 4.1 2.2 - - + +
193A GLY* 2.7 30.3 + - - -
200A VAL* 5.2 4.4 - - + +
209A LEU* 3.8 18.2 - - + -
214A PHE* 3.6 40.6 - - + -
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Residues in contact with PRO 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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128A PRO* 5.7 4.9 - - + +
132A SER* 4.1 10.5 - - - -
186A SER 3.1 13.5 - - - +
187A VAL* 3.0 34.3 - - + +
189A ILE* 1.3 86.7 - - + +
191A VAL* 1.3 52.0 + - + +
193A GLY* 4.5 0.9 - - - +
194A LEU* 2.7 51.0 + - + +
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Residues in contact with VAL 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 VAL* 3.2 33.3 + - + +
188A PRO* 3.7 6.3 - - + +
190A PRO* 1.3 77.3 - - + +
192A ILE* 1.3 70.5 + - + +
194A LEU* 3.8 2.3 - - - +
195A ARG* 3.0 45.5 + - - +
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Residues in contact with ILE 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 PRO* 2.7 34.9 + - + +
189A ILE* 4.1 3.1 - - + +
191A VAL* 1.3 80.0 - - + +
193A GLY* 1.3 63.3 + - - +
195A ARG* 3.5 4.1 + - - +
196A ASP* 3.2 23.2 + - - +
199A LYS* 3.4 35.1 - - + +
200A VAL* 6.1 0.4 - - + -
211A ASP* 3.7 24.7 - - + +
214A PHE* 4.2 21.5 - - + -
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Residues in contact with GLY 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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128A PRO* 5.3 4.7 - - - -
189A ILE 2.7 22.1 + - - -
190A PRO* 5.0 0.4 - - - -
192A ILE* 1.3 74.7 - - - +
194A LEU* 1.3 62.2 + - - +
196A ASP 2.9 22.3 - - - +
197A GLU* 3.8 10.4 + - - +
200A VAL* 3.7 28.6 - - - +
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Residues in contact with LEU 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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128A PRO* 5.8 8.7 - - + -
190A PRO* 2.7 35.9 + - + +
191A VAL* 3.9 3.4 - - - +
193A GLY* 1.3 75.1 - - - +
195A ARG* 1.3 63.3 + - + +
196A ASP* 3.2 1.8 + - - -
197A GLU 5.1 0.3 + - - -
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Residues in contact with ARG 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 VAL* 3.0 33.8 + - - +
192A ILE* 3.8 3.8 - - - +
194A LEU* 1.3 79.2 - - + +
196A ASP* 1.3 62.6 + - - +
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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