Contacts of the helix formed by residues 185 - 190 (chain H) in PDB entry 1W4R
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 CYS 185 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 3.4 30.7 - - - +
144E GLU* 6.5 0.4 - - - -
153H CYS* 3.5 6.1 - - + +
156H CYS* 3.8 1.1 - - - -
158H ARG* 5.1 0.4 - - + -
159H GLU 3.5 23.3 - - - +
160H ALA* 4.1 1.1 - - - +
161H ALA 4.6 0.2 - - - +
162H TYR* 3.8 5.8 - - - -
184H VAL* 1.3 75.5 - - - +
186H ARG* 1.3 62.3 + - - +
187H LEU 3.7 2.0 - - - -
188H CYS* 3.4 16.0 + - - -
189H TYR* 2.9 28.2 + - - +
400H ZN 2.3 35.7 - - - -
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Residues in contact with ARG 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 6.2 0.2 - - - +
19E GLY* 3.7 18.0 + - - +
21E ILE* 3.5 16.6 - - - +
110E GLU* 2.9 23.4 + - - -
113E ALA* 3.5 22.1 - - - +
114E ASN* 2.9 32.4 + - - +
142E LEU 2.9 27.3 + - - -
144E GLU* 2.9 38.6 + - - +
130H ARG* 3.6 6.9 - - - +
162H TYR* 3.3 17.2 + - + -
185H CYS* 1.3 74.7 - - - +
187H LEU* 1.3 71.5 + - + +
189H TYR* 3.2 6.6 + - - +
190H PHE* 3.2 31.9 + - + -
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Residues in contact with LEU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 3.5 63.2 - - + +
19E GLY 6.1 1.1 - - - +
185H CYS* 3.3 2.3 - - - -
186H ARG* 1.3 88.9 - - + +
188H CYS* 1.3 63.8 + - - +
190H PHE* 3.3 13.5 + - + +
191H LYS 3.4 11.1 + - - +
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Residues in contact with CYS 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG* 5.1 1.1 - - - -
153H CYS* 3.7 10.1 - - - -
155H GLU* 3.8 23.3 - - - +
156H CYS* 3.8 14.4 - - - -
164H LYS* 2.7 28.3 + - - -
184H VAL* 4.1 5.2 - - + -
185H CYS* 3.4 6.2 + - - +
186H ARG 3.3 0.2 - - - -
187H LEU* 1.3 76.5 - - - +
189H TYR* 1.3 62.8 + - - +
191H LYS* 3.1 14.6 + - - +
400H ZN 2.4 34.1 - - - -
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Residues in contact with TYR 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG 5.5 1.6 - - - -
83B ASP* 5.6 1.0 + - - -
86B GLN* 3.1 41.9 + - - +
128H PHE 2.7 28.6 + - - -
129H GLN* 3.2 18.8 + - - -
130H ARG* 3.4 36.1 - - + -
162H TYR* 4.2 6.7 - - + -
163H THR 3.8 10.5 - - - -
164H LYS* 4.2 18.8 - - + +
184H VAL* 3.8 22.3 - - + +
185H CYS 2.9 18.9 + - - +
186H ARG* 3.2 10.3 + - - +
188H CYS* 1.3 79.0 - - - +
190H PHE* 1.3 79.7 + + - +
191H LYS* 3.2 2.8 + - - -
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Residues in contact with PHE 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG* 4.0 29.6 - - + -
85B ALA* 4.1 17.9 - - + -
86B GLN* 3.7 14.8 - - - -
89B LEU* 3.3 20.7 - - + +
110E GLU* 3.6 11.9 - - - -
114E ASN* 3.6 30.7 - - - -
1193E DTU 5.3 8.3 - - - -
130H ARG* 3.5 26.5 - - - -
186H ARG* 3.2 25.5 + - + +
187H LEU* 3.7 7.9 - - + +
188H CYS 3.1 0.4 - - - -
189H TYR* 1.3 92.8 - + - +
191H LYS* 1.3 71.9 - - - +
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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