Contacts of the helix formed by residues 187 - 197 (chain A) in PDB entry 2R8K
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 LEU 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.4 32.5 - - + +
183A LEU* 2.9 48.9 + - + +
184A LYS 4.6 0.2 - - - -
186A ALA* 1.3 78.6 - - - +
188A SER* 1.3 62.9 + - - +
189A ASN 3.3 2.5 - - - +
190A ILE* 3.4 9.2 + - + +
191A ARG* 2.9 32.8 + - - +
209A PRO* 3.8 16.6 - - + -
212A ILE* 4.1 15.3 - - + -
233A TRP* 3.6 36.3 - - + -
236A VAL* 5.2 0.7 - - + -
240A LEU* 5.7 0.4 - - + -
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Residues in contact with SER 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 LYS 2.8 23.4 + - - -
185A ASP* 3.0 20.5 + - - -
186A ALA 3.5 2.2 - - - -
187A LEU* 1.3 76.5 - - - +
189A ASN* 1.3 55.5 + - - +
191A ARG* 4.5 4.0 - - - -
192A GLU* 2.7 57.0 + - - +
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Residues in contact with ASN 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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186A ALA 5.3 0.2 + - - -
187A LEU* 3.3 0.6 - - - -
188A SER* 1.3 78.7 - - - +
190A ILE* 1.3 62.1 + - - +
192A GLU* 4.0 5.3 - - - +
193A ALA* 3.0 26.2 + - - +
206A PRO* 4.2 20.6 - - + +
209A PRO* 5.6 11.9 - - + -
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Residues in contact with ILE 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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6A TRP* 3.3 30.0 - - + -
9A LEU* 4.4 9.0 - - + -
169A LEU* 4.5 4.5 - - + +
170A MET* 3.7 21.3 - - + -
187A LEU* 3.4 22.6 + - + +
188A SER 3.4 0.2 - - - -
189A ASN* 1.3 82.1 + - - +
191A ARG* 1.3 70.2 + - + +
193A ALA* 3.6 2.6 + - - -
194A PHE* 3.1 22.5 + - - +
205A LEU* 4.5 4.9 - - + -
206A PRO* 4.0 11.2 - - + +
209A PRO* 5.7 1.7 - - + +
233A TRP* 3.4 42.4 - - + -
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Residues in contact with ARG 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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168A MET 2.8 28.7 + - - -
169A LEU 3.0 20.4 + - - +
170A MET* 3.0 37.7 + - - +
171A PHE 4.5 0.2 - - - -
172A ASP 3.0 30.1 + - - +
173A ASN* 3.6 7.7 + - - -
183A LEU* 4.0 20.2 - - - +
184A LYS* 3.3 28.0 - - - +
187A LEU* 2.9 24.7 + - - +
188A SER* 3.9 3.4 - - - +
190A ILE* 1.3 80.0 - - + +
192A GLU* 1.3 65.5 + - + +
193A ALA 3.1 1.6 - - - -
194A PHE* 3.0 13.0 + - - +
195A ILE* 3.3 22.6 + - + +
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Residues in contact with GLU 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 SER* 2.7 39.9 + - - +
189A ASN* 4.0 4.5 - - - +
191A ARG* 1.3 74.1 - - + +
193A ALA* 1.3 61.0 + - - +
195A ILE* 3.8 3.9 + - - +
196A GLY* 3.2 19.6 + - - -
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Residues in contact with ALA 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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6A TRP* 3.9 19.3 - - + -
189A ASN* 3.0 23.3 + - - +
190A ILE* 3.7 6.3 - - - +
191A ARG 3.1 0.2 - - - -
192A GLU* 1.3 77.8 - - - +
194A PHE* 1.3 63.2 + - - +
196A GLY* 3.4 3.1 + - - -
197A GLY 3.3 14.6 + - - -
198A ASN* 4.3 5.5 + - - +
199A TYR* 3.6 10.7 - - + -
206A PRO* 5.9 2.2 - - + -
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Residues in contact with PHE 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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6A TRP* 3.7 18.1 - + + -
10A ILE* 3.3 25.8 - - + -
166A PHE* 3.4 25.1 - + - -
170A MET* 3.8 26.0 - - + -
171A PHE* 3.8 25.8 - + - -
190A ILE 3.1 13.3 + - - +
191A ARG 3.0 9.9 + - - +
193A ALA* 1.3 76.4 - - - +
195A ILE* 1.3 70.1 + - + +
197A GLY 3.1 4.3 + - - -
199A TYR* 3.6 15.1 - - - -
140B LYS* 2.7 58.4 + - + -
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Residues in contact with ILE 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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170A MET 5.8 3.4 - - - +
171A PHE* 4.7 12.3 - - + -
191A ARG* 3.3 21.4 + - + +
192A GLU* 4.5 3.4 - - - +
194A PHE* 1.3 86.9 - - + +
196A GLY* 1.3 67.8 + - - +
197A GLY* 2.9 5.0 + - - -
137B LYS* 3.1 51.2 - - + +
140B LYS* 4.5 9.6 + - + -
141B ILE* 5.1 9.9 - - + -
255B ILE* 4.5 19.1 - - + -
256B LEU* 4.0 13.0 - - + -
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Residues in contact with GLY 196 (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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192A GLU 3.2 16.6 + - - -
193A ALA* 3.7 5.4 - - - -
194A PHE 3.2 0.8 - - - -
195A ILE* 1.3 77.6 - - - +
197A GLY* 1.3 53.6 + - - +
198A ASN* 2.7 39.4 + - - -
133B ARG* 3.1 16.0 + - - -
137B LYS* 4.2 7.4 - - - -
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Residues in contact with GLY 197 (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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193A ALA 3.3 3.6 + - - -
194A PHE 3.1 4.8 + - - -
195A ILE 2.9 5.7 + - - -
196A GLY* 1.3 74.5 - - - +
198A ASN* 1.3 53.4 + - - +
199A TYR* 2.6 34.5 + - - +
133B ARG* 4.6 6.5 - - - -
140B LYS* 3.7 22.0 - - - -
432B GLN* 4.1 7.6 - - - +
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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