Contacts of the helix formed by residues 188 - 198 (chain A) in PDB entry 2N5T
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 SER 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A PHE* 5.7 0.3 - - - -
183A ALA* 4.2 22.2 - - - +
184A GLY 5.1 0.7 - - - -
185A GLY 3.1 11.5 + - - -
186A ARG 2.7 4.2 + - - +
187A THR* 1.3 81.3 + - - +
189A HIS* 1.3 65.1 + - - +
190A THR* 3.9 4.6 + - - -
191A SER* 2.3 49.7 + - - -
192A ILE* 3.4 2.3 + - - +
203A VAL* 4.5 4.9 - - - +
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Residues in contact with HIS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU 5.6 1.1 + - - +
165A PRO* 3.7 42.0 - - + +
168A THR* 5.8 0.9 - - - +
187A THR 3.8 4.6 + - - -
188A SER* 1.3 70.0 - - - +
190A THR* 1.3 66.1 + - - +
192A ILE* 3.0 31.2 + - - +
193A MET* 3.5 2.1 + - - +
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Residues in contact with THR 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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163A LEU* 3.4 34.0 + - + +
164A THR 5.2 0.5 - - - -
168A THR* 3.5 19.2 + - + +
171A LEU* 6.0 2.9 - - + -
179A PHE* 3.0 49.5 - - + -
188A SER* 3.3 4.6 + - - -
189A HIS* 1.3 78.5 - - - +
191A SER* 1.3 63.3 + - - +
193A MET* 2.9 38.7 - - + +
194A ALA* 3.3 2.9 + - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 4.4 9.8 - - - +
179A PHE* 5.6 0.2 - - - -
185A GLY 3.5 10.3 - - - -
186A ARG* 2.6 28.0 + - - +
188A SER* 2.3 39.2 + - - -
190A THR* 1.3 78.6 - - - +
192A ILE* 1.3 60.9 + - - +
194A ALA* 3.2 16.9 + - - +
195A ARG* 3.5 9.2 + - - +
203A VAL* 3.8 23.9 - - - +
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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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186A ARG 5.2 2.9 - - - +
188A SER 4.5 2.7 - - - +
189A HIS* 3.0 20.4 + - - +
191A SER* 1.3 83.3 + - - +
193A MET* 1.3 71.0 + - + +
195A ARG* 3.1 25.5 + - + +
196A SER* 3.1 19.6 + - - +
299A PHE* 5.5 13.0 - - + -
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Residues in contact with MET 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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168A THR* 4.8 18.8 - - + -
171A LEU* 5.8 9.6 - - + -
173A LEU* 5.5 3.1 - - + -
176A VAL* 6.4 1.1 - - + -
178A GLY* 5.8 1.1 - - - -
179A PHE* 4.1 25.6 - - + +
189A HIS 3.5 2.4 + - - +
190A THR* 2.9 28.9 + - + +
192A ILE* 1.3 86.1 - - + +
194A ALA* 1.3 73.4 - - + +
196A SER* 4.5 3.1 - - - +
197A LEU* 2.6 81.2 + - + +
199A LEU* 5.3 7.4 - - + -
201A ALA* 5.4 0.7 - - + -
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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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7A ALA* 4.4 7.6 - - + -
8A SER* 3.7 24.2 - - - +
179A PHE* 5.6 1.6 - - + -
190A THR 3.3 3.1 + - - +
191A SER* 3.2 11.9 + - - +
193A MET* 1.3 94.7 - - + +
195A ARG* 1.3 58.5 + - - +
197A LEU* 4.5 1.6 - - - -
198A GLU* 2.8 24.8 + - - -
199A LEU 3.4 11.9 + - - +
201A ALA* 3.8 18.6 - - + -
203A VAL* 6.1 0.4 - - + -
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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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7A ALA* 4.7 19.6 + - + +
8A SER* 5.2 1.6 - - - -
186A ARG* 3.8 36.2 - - - +
191A SER 3.5 5.1 + - - +
192A ILE* 3.1 21.4 + - + +
194A ALA* 1.3 83.4 - - - +
196A SER* 1.3 65.8 + - - +
198A GLU* 3.1 21.1 + - - +
526A SER* 5.9 2.7 - - - -
528A ILE* 5.1 15.7 - - + +
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Residues in contact with SER 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 ILE* 3.1 18.6 + - - +
193A MET* 4.0 3.4 - - - -
195A ARG* 1.3 82.5 - - - +
197A LEU* 1.3 71.4 + - - +
198A GLU* 3.3 3.1 + - - +
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Residues in contact with LEU 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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173A LEU* 3.4 44.2 - - + -
193A MET* 2.6 65.8 + - + +
194A ALA* 4.1 2.2 - - - +
196A SER* 1.3 77.7 - - - +
198A GLU* 1.3 70.8 + - - +
199A LEU* 3.1 22.3 - - + +
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Residues in contact with GLU 198 (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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8A SER* 5.0 4.5 - - - -
9A PRO* 5.2 13.0 - - - +
194A ALA 2.8 12.1 + - - -
195A ARG* 3.1 13.5 + - - +
196A SER 3.1 5.3 - - - +
197A LEU* 1.3 81.1 - - - +
199A LEU* 1.3 63.9 + - - +
200A PRO* 4.6 1.4 - - - +
250A LYS* 5.2 17.1 + - - +
528A ILE* 4.2 28.7 - - - +
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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