Contacts of the helix formed by residues 187 - 194 (chain B) in PDB entry 6N1H
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 TYR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B SER 5.3 0.2 - - - -
185B GLN* 3.1 39.8 + - - -
186B SER* 1.3 77.5 - - - +
188B LEU* 1.3 62.1 + - - +
189B VAL 3.4 1.1 - - - -
190B GLU* 3.8 1.8 - - - -
191B ASP* 2.9 22.3 + - - +
139F LYS 5.3 1.8 - - - -
140F VAL* 3.3 23.6 - - + +
145F GLN* 5.0 2.8 + - - -
165F PHE* 3.1 10.0 + - - +
168F ALA 2.0 30.3 - - - -
169F TRP* 1.6 83.3 + + - -
170F ASN* 2.8 41.4 + - - +
173F CYS* 3.6 11.9 - - + -
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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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121B ALA 5.4 0.4 - - - +
122B LEU* 4.3 12.1 - - + -
125B ARG* 3.3 55.4 - - + +
126B VAL* 3.7 24.5 - - + -
181B LEU* 5.4 1.6 - - + -
185B GLN* 3.8 15.8 - - + +
187B TYR* 1.3 75.1 - - - +
189B VAL* 1.3 66.3 + - + +
191B ASP* 3.5 3.2 + - + -
192B LEU* 3.1 36.2 + - + +
167F PRO 3.4 16.8 - - - +
168F ALA* 2.7 27.7 + - + +
169F TRP 5.0 0.2 - - - -
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Residues in contact with VAL 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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114B PHE* 3.7 27.5 - - + -
122B LEU* 6.1 0.7 - - + -
178B LEU* 4.2 3.8 - - + -
181B LEU* 3.8 43.1 - - + +
182B ARG* 3.7 29.4 - - + +
185B GLN* 4.9 0.2 - - - +
186B SER* 5.1 5.6 - - - +
187B TYR 3.4 1.2 - - - +
188B LEU* 1.3 79.7 - - + +
190B GLU* 1.3 57.9 + - - +
192B LEU 3.4 0.7 + - - -
193B GLU* 3.0 48.4 + - - +
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Residues in contact with GLU 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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186B SER 3.9 16.3 + - - +
187B TYR* 3.5 2.0 + - - +
188B LEU 3.3 0.6 - - - -
189B VAL* 1.3 80.1 - - - +
191B ASP* 1.3 57.6 + - - +
193B GLU* 3.7 18.1 - - - +
194B ARG* 3.0 41.2 + - + +
170F ASN* 3.9 18.4 - - - +
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Residues in contact with ASP 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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125B ARG* 3.7 23.9 + - - +
187B TYR 2.9 9.8 + - - +
188B LEU* 4.0 6.1 - - - +
189B VAL 3.3 0.2 - - - -
190B GLU* 1.3 77.2 - - - +
192B LEU* 1.3 61.2 + - + +
194B ARG* 3.8 17.6 + - - +
170F ASN* 3.1 38.6 - - + +
171F TRP* 4.0 7.3 + - - +
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Residues in contact with LEU 192 (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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114B PHE* 3.6 22.4 - - + -
118B HIS* 3.3 57.6 - - + +
121B ALA* 4.2 13.9 - - + -
122B LEU* 3.9 21.8 - - + -
125B ARG* 3.3 28.7 - - - +
188B LEU* 3.1 29.7 + - + +
191B ASP* 1.3 80.1 - - - +
193B GLU* 1.3 63.9 + - - +
194B ARG 4.0 4.0 - - - +
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Residues in contact with GLU 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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114B PHE* 3.6 20.4 - - + -
118B HIS* 5.2 0.9 - - - -
182B ARG* 3.3 26.5 + - - -
189B VAL* 3.0 28.9 + - - +
190B GLU* 3.7 23.2 - - - +
191B ASP 3.4 0.2 - - - -
192B LEU* 1.3 77.8 - - - +
194B ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 194 (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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190B GLU* 3.0 30.2 + - - +
191B ASP* 3.8 14.7 + - - +
192B LEU 3.4 4.7 - - - +
193B GLU* 1.3 81.4 - - - +
172F THR* 6.0 3.6 - - - -
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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