Contacts of the helix formed by residues 195 - 203 (chain A) in PDB entry 2VSH
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 ASP 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG* 4.9 7.1 + - - +
86A ASN* 4.1 1.3 - - - -
137A ASP* 5.1 0.9 - - - +
171A GLN* 3.0 19.1 + - - +
193A LEU 3.3 0.5 - - - +
194A THR* 1.3 82.4 + - - +
196A ALA* 1.3 65.7 + - - +
197A CYS* 2.8 33.1 + - - +
198A LYS* 2.9 33.8 + - + +
199A ILE* 3.5 12.0 + - - +
145B THR* 3.9 31.3 + - + +
158B ILE* 3.8 5.8 - - + +
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Residues in contact with ALA 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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85A ARG* 5.4 2.0 - - - +
86A ASN* 3.6 20.5 + - - +
89A ILE* 3.8 12.8 - - + -
171A GLN* 3.6 18.4 - - - +
173A PHE* 3.7 23.3 - - + -
178A PHE* 4.0 6.9 - - + -
195A ASP* 1.3 74.9 + - - +
197A CYS* 1.3 64.2 + - - +
199A ILE* 3.2 19.1 + - - +
200A PHE* 3.4 18.5 - - - -
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Residues in contact with CYS 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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135A ALA* 5.0 5.2 - - - -
136A VAL 3.7 14.6 - - - -
137A ASP* 3.5 40.4 - - - +
171A GLN* 3.7 19.5 - - - -
172A THR 5.3 0.2 - - - -
173A PHE* 5.3 2.0 - - - -
195A ASP* 2.8 11.0 + - - +
196A ALA* 1.3 81.1 - - - +
198A LYS* 1.3 54.2 + - - +
200A PHE* 3.1 11.9 + - - +
201A VAL* 2.8 29.6 + - - +
207A VAL* 4.1 15.2 - - + +
155B ILE* 4.6 0.2 - - + -
158B ILE* 4.0 7.0 - - + -
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Residues in contact with LYS 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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192A ILE* 5.4 6.4 + - - +
193A LEU* 3.6 37.9 - - + +
194A THR 5.4 0.2 - - - +
195A ASP* 2.9 30.9 + - + +
197A CYS* 1.3 76.3 - - - +
199A ILE* 1.3 56.4 + - - +
201A VAL* 4.3 6.1 - - + -
202A ILE* 2.9 45.1 + - + +
157B ASP* 4.9 5.1 + - - -
158B ILE* 2.8 49.8 + - + +
159B PRO* 4.5 1.0 + - - +
160B ASN* 4.5 14.3 - - - +
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Residues in contact with ILE 199 (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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86A ASN* 3.6 30.1 - - - +
178A PHE* 4.4 8.7 - - + -
181A LEU* 3.8 31.0 - - + +
182A TYR* 3.9 14.8 - - + +
185A LEU* 3.9 32.8 - - + -
193A LEU* 3.9 13.7 - - + +
195A ASP 3.6 10.3 - - - +
196A ALA 3.4 7.9 - - - +
197A CYS 3.2 0.8 - - - -
198A LYS* 1.3 76.0 - - - +
200A PHE* 1.3 64.7 + - + +
202A ILE* 3.5 6.9 - - - +
203A LYS* 3.2 34.4 + - + +
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Residues in contact with PHE 200 (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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134A ASP* 3.8 18.4 - - + -
135A ALA* 3.9 15.5 - - + -
173A PHE* 3.6 33.2 - + + -
177A ASP* 3.8 20.6 - - + -
178A PHE* 3.7 37.5 - + - -
181A LEU* 3.8 21.8 - - + -
196A ALA 3.4 17.5 - - - -
197A CYS* 3.1 8.1 + - - +
199A ILE* 1.3 81.9 - - + +
201A VAL* 1.3 59.6 + - - +
203A LYS 3.3 6.2 + - - -
205A LYS* 2.9 42.5 + - + +
207A VAL* 3.7 16.4 - - + -
1236A 1PE 6.0 0.4 - - - -
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Residues in contact with VAL 201 (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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197A CYS 2.8 21.4 + - - +
198A LYS* 3.3 11.2 + - + +
200A PHE* 1.3 76.3 - - - +
202A ILE* 1.3 57.8 + - - +
204A GLY* 3.0 20.1 + - - -
205A LYS 4.0 5.4 + - - +
207A VAL* 3.6 19.7 - - + -
155B ILE* 3.5 46.7 - - + +
156B THR 4.6 3.4 - - - +
157B ASP* 4.3 18.6 - - - +
158B ILE* 4.4 7.0 - - + +
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Residues in contact with ILE 202 (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 LEU* 4.0 39.7 - - + -
198A LYS* 2.9 33.4 + - - +
199A ILE* 3.5 8.5 - - + +
201A VAL* 1.3 78.2 - - - +
203A LYS* 1.3 70.0 + - + +
204A GLY 3.1 3.1 + - - -
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Residues in contact with LYS 203 (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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181A LEU* 3.8 33.0 - - + +
184A SER* 3.1 33.4 + - - -
185A LEU* 4.1 20.5 - - - +
199A ILE* 3.2 20.7 + - + +
200A PHE 3.8 3.6 - - - +
201A VAL 3.2 0.8 - - - -
202A ILE* 1.3 83.3 - - + +
204A GLY* 1.3 60.6 + - - +
205A LYS* 3.3 10.7 + - + -
1236A 1PE 3.6 21.9 + - - -
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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