Contacts of the helix formed by residues 187 - 194 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127J THR* 5.1 1.2 + - - -
184J SER 5.3 0.7 - - - -
185J GLN* 3.1 54.6 + - - -
186J SER* 1.3 77.9 - - - +
188J LEU* 1.3 75.7 + - + +
189J VAL 3.4 1.1 - - - -
190J GLU* 3.8 5.6 - - - +
191J ASP* 2.9 30.5 + - - +
139N LYS 4.6 14.1 - - - -
140N VAL* 3.8 31.4 + - + +
142N THR* 5.9 3.0 - - + +
145N GLN* 4.7 9.2 + - - -
168N ALA* 3.5 25.8 - - + +
169N TRP* 4.4 16.7 + + - -
170N ASN* 4.6 17.4 + - - +
173N CYS* 5.7 4.0 - - - -
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Residues in contact with LEU 188 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ALA 5.4 0.4 - - - +
122J LEU* 4.3 11.2 - - + -
125J ARG* 3.3 69.8 - - + +
126J VAL* 3.7 26.2 - - + -
181J LEU* 5.4 2.0 - - + -
185J GLN* 3.8 31.2 - - + +
187J TYR* 1.3 83.6 - - + +
189J VAL* 1.3 66.1 + - + +
191J ASP* 3.5 2.8 + - + -
192J LEU* 3.1 36.5 + - + +
168N ALA 4.4 4.5 - - - +
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Residues in contact with VAL 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J PHE* 3.7 27.1 - - + -
122J LEU* 6.1 0.7 - - + -
178J LEU* 4.2 3.8 - - + -
181J LEU* 3.8 43.3 - - + +
182J ARG* 3.7 29.6 - - + +
185J GLN* 4.9 0.2 - - - +
186J SER* 5.1 5.8 - - - +
187J TYR 3.4 1.0 - - - +
188J LEU* 1.3 79.2 - - + +
190J GLU* 1.3 58.0 + - - +
192J LEU 3.4 0.9 + - - -
193J GLU* 3.0 48.4 + - - +
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Residues in contact with GLU 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J SER 3.9 19.0 + - - +
187J TYR* 3.5 6.7 + - - +
188J LEU 3.3 0.2 - - - -
189J VAL* 1.3 80.9 - - - +
191J ASP* 1.3 57.0 + - - +
193J GLU* 3.7 18.4 - - - +
194J ARG* 3.0 41.0 + - + +
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Residues in contact with ASP 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J ARG* 3.7 24.5 + - - +
187J TYR 2.9 18.8 + - - +
188J LEU* 4.0 6.1 - - - +
189J VAL 3.3 0.2 - - - -
190J GLU* 1.3 77.2 - - - +
192J LEU* 1.3 61.5 + - + +
194J ARG* 3.8 16.9 + - - +
170N ASN* 3.4 37.5 + - + +
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Residues in contact with LEU 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J PHE* 3.6 22.2 - - + -
118J HIS* 3.3 57.2 + - + +
121J ALA* 4.2 14.1 - - + -
122J LEU* 3.9 21.8 - - + -
125J ARG* 3.3 29.2 - - - +
188J LEU* 3.1 29.7 + - + +
191J ASP* 1.3 80.1 - - - +
193J GLU* 1.3 64.2 + - - +
194J ARG 4.0 4.0 - - - +
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Residues in contact with GLU 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J PHE* 3.6 21.1 - - + -
118J HIS* 5.2 0.7 - - - -
182J ARG* 3.3 26.7 + - - -
189J VAL* 3.0 29.3 + - - +
190J GLU* 3.7 22.7 - - - +
191J ASP 3.4 0.2 - - - -
192J LEU* 1.3 78.6 - - - +
194J ARG* 1.3 62.9 + - - +
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Residues in contact with ARG 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J GLU* 3.0 30.0 + - - +
191J ASP* 3.8 14.7 + - - +
192J LEU 3.4 4.9 - - - +
193J GLU* 1.3 82.5 - - - +
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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