Contacts of the helix formed by residues 193 - 198 (chain A) in PDB entry 2G5W
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 ILE 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A HIS 4.8 0.6 + - - +
168A TYR* 3.9 21.5 - - + +
185A ILE* 3.3 33.7 - - + -
186A HIS 3.5 15.2 + - - +
187A GLY* 3.7 15.9 - - - -
191A TYR 3.0 2.0 + - - -
192A LEU* 1.3 73.1 - - - +
194A ASP* 1.3 57.5 + - - +
196A PHE* 2.9 22.2 + - - +
197A LEU* 3.0 19.0 + - + +
218A PHE* 3.5 25.6 - - + -
219A LEU* 3.8 36.6 - - + -
222A VAL* 4.6 5.6 - - + -
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Residues in contact with ASP 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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187A GLY 4.0 11.5 + - - +
188A ALA* 3.9 8.5 - - - +
189A HIS* 3.6 4.2 + - - -
190A GLY* 2.8 34.1 + - - +
191A TYR 2.8 13.4 + - - +
193A ILE* 1.3 74.5 - - - +
195A GLN* 1.3 56.6 + - - +
196A PHE 3.1 0.4 - - - -
197A LEU* 4.0 17.9 - - - +
198A LYS* 2.9 78.5 + - - +
201A ILE* 4.8 1.1 - - - -
240A SER 4.2 3.1 - - - +
243A ILE 4.7 0.2 - - - +
248A ALA* 3.4 2.9 - - - +
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL 2.9 19.2 - - - +
111A GLY* 3.6 2.0 - - - -
112A ARG* 3.3 27.7 + - - +
113A ALA 4.1 0.2 + - - -
127A SER* 2.7 38.6 + - - +
128A SER* 2.5 24.7 + - - +
190A GLY 2.8 27.2 - - - +
191A TYR 3.0 12.8 + - - +
192A LEU* 3.0 17.5 + - - +
194A ASP* 1.3 75.8 - - - +
196A PHE* 1.3 54.8 + - - +
198A LYS 4.6 0.2 - - - -
201A ILE* 3.7 26.9 - - + +
202A ASN* 3.4 18.1 + - - +
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Residues in contact with PHE 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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127A SER 4.6 0.4 - - - -
128A SER* 3.6 30.7 - - - -
156A LEU* 4.4 11.0 - - + -
161A ILE* 4.4 13.7 - - + -
192A LEU* 3.5 28.2 + - + -
193A ILE 2.9 8.7 + - - +
195A GLN* 1.3 79.0 - - - +
197A LEU* 1.3 62.9 + - + +
198A LYS 3.5 0.4 - - - -
202A ASN* 2.7 25.8 + - - +
204A ARG* 3.7 20.9 - - - -
208A TYR* 3.8 36.6 - + + -
215A ARG* 3.2 20.2 - - - +
218A PHE* 3.5 40.4 - + + -
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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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187A GLY 3.8 23.1 - - - +
193A ILE* 3.0 24.8 + - + +
194A ASP* 3.2 16.4 + - - +
196A PHE* 1.3 78.5 - - + +
198A LYS* 1.3 55.2 + - - +
215A ARG* 2.8 44.2 + - - +
216A CYS* 3.9 19.3 - - - -
219A LEU* 4.3 19.7 - - + -
239A VAL* 4.5 9.4 - - + -
250A ASP* 3.7 0.2 - - - +
256A LEU* 3.4 25.0 - - + +
260A VAL* 4.0 22.7 - - + -
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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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194A ASP* 2.9 56.2 + - - +
197A LEU* 1.3 73.3 - - - +
199A ASP* 1.3 58.0 + - - +
200A GLY 3.1 2.5 - - - +
201A ILE* 3.2 6.4 + - + +
202A ASN* 2.8 28.9 + - - +
215A ARG* 4.0 0.9 - - - -
240A SER 2.8 23.9 + - - -
241A PRO* 3.3 21.8 + - - -
243A ILE 3.4 7.9 + - - -
248A ALA* 3.1 35.3 + - + +
249A THR 3.3 22.2 - - - +
250A ASP* 3.5 10.5 - - + +
256A LEU* 3.7 13.2 - - + -
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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