Contacts of the helix formed by residues 190 - 199 (chain A) in PDB entry 2G9Y
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 SER 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.6 1.8 - - - -
168A CYS 3.8 0.9 - - - -
170A GLY* 3.2 29.1 - - - -
171A PRO* 3.7 1.5 - - - +
174A THR* 3.0 30.2 + - - +
183A LEU 5.3 0.2 - - - +
189A GLY* 1.3 75.8 - - - +
191A ILE* 1.3 64.9 + - - +
192A THR* 3.5 3.6 + - - -
193A GLU* 2.9 35.3 + - - +
194A GLN* 2.9 22.6 + - - +
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Residues in contact with ILE 191 (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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120A LEU* 3.5 24.5 - - + -
151A LEU 4.9 0.9 - - - +
152A GLN* 3.8 24.5 - - - +
157A ALA* 3.6 24.7 - - + -
161A ALA* 3.9 17.9 - - + +
163A VAL* 3.8 22.4 - - + +
166A ARG 3.5 20.2 - - - +
168A CYS 3.0 25.0 + - - +
169A TYR* 3.8 6.7 - - - +
190A SER* 1.3 75.0 - - - +
192A THR* 1.3 59.2 + - - +
194A GLN* 3.4 1.7 + - - +
195A LEU* 2.9 31.4 + - + +
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Residues in contact with THR 192 (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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152A GLN* 3.2 20.9 + - - +
169A TYR 2.9 19.1 + - - -
190A SER* 4.0 0.4 - - - -
191A ILE* 1.3 75.4 - - - +
193A GLU* 1.3 63.1 + - - +
195A LEU* 3.3 8.7 + - - +
196A LEU* 3.1 23.9 + - + +
210A THR* 3.3 7.7 - - + +
211A PHE* 3.6 39.7 - - + -
225A LEU* 3.5 29.6 - - + -
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Residues in contact with GLU 193 (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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171A PRO* 3.6 21.2 - - - +
183A LEU* 3.3 31.9 + - + +
188A LYS 4.8 1.6 - - - +
189A GLY* 3.9 9.9 - - - -
190A SER* 2.9 42.2 + - - +
192A THR* 1.3 78.1 - - - +
194A GLN* 1.3 62.9 + - - +
196A LEU* 3.4 11.8 + - - +
197A ASN* 3.2 27.2 + - - +
215A ALA* 4.1 12.6 - - - +
216A THR 4.9 0.5 + - - -
225A LEU* 3.7 21.5 - - + -
228A GLN* 4.8 8.3 + - - +
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Residues in contact with GLN 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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160A VAL 3.6 13.5 - - - +
161A ALA* 3.4 4.9 - - - -
162A HIS* 2.7 57.8 + - - +
163A VAL* 3.6 7.5 - - - +
181A ASN* 5.0 1.2 - - - +
188A LYS* 3.6 37.7 - - + +
189A GLY 2.9 20.0 + - - -
190A SER 2.9 14.5 + - - +
191A ILE 3.9 2.7 - - - +
193A GLU* 1.3 73.0 - - - +
195A LEU* 1.3 61.1 + - - +
197A ASN* 2.9 12.2 + - + +
198A ALA* 2.8 30.3 + - - +
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Residues in contact with LEU 195 (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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145A ASN* 5.3 3.8 - - - +
151A LEU* 4.2 35.9 - - + +
152A GLN* 6.2 1.1 - - + +
160A VAL* 3.7 31.5 + - + +
191A ILE* 2.9 21.2 + - + +
192A THR* 3.5 10.8 - - - +
194A GLN* 1.3 76.8 - - - +
196A LEU* 1.3 76.5 + - + +
198A ALA* 3.3 3.5 + - - +
199A ARG* 3.3 15.9 + - - -
200A ALA 4.9 1.0 + - - -
203A THR* 4.4 24.5 - - + +
211A PHE* 4.8 9.2 - - + -
234A TYR* 3.7 5.2 + - + +
256A LEU* 4.7 12.3 - - + -
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Residues in contact with LEU 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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192A THR* 3.1 18.4 + - + +
193A GLU* 3.5 9.2 - - - +
195A LEU* 1.3 81.4 - - + +
197A ASN* 1.3 61.1 + - - +
199A ARG* 3.6 4.2 + - - +
211A PHE* 4.3 7.6 - - + -
225A LEU* 3.6 34.1 - - + +
228A GLN* 3.8 31.6 - - + +
229A ALA* 3.7 17.7 - - + +
232A ARG* 4.2 11.9 + - - +
234A TYR* 2.8 47.6 + - + -
256A LEU* 4.2 13.2 - - + -
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Residues in contact with ASN 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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137A LYS* 5.0 1.6 + - - -
188A LYS* 4.1 14.3 + - - +
193A GLU* 3.2 15.8 + - - +
194A GLN* 2.9 16.2 + - - +
196A LEU* 1.3 75.8 - - - +
198A ALA* 1.3 65.7 + - - +
199A ARG* 3.1 8.9 + - - +
220A TRP* 5.3 1.2 - - - -
232A ARG* 3.0 34.1 + - - +
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Residues in contact with ALA 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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133A LEU* 5.2 4.5 - - + -
134A GLU* 5.2 9.0 - - + +
137A LYS* 3.0 27.5 + - - +
159A LEU 5.4 0.2 - - - +
160A VAL* 3.5 44.4 - - + +
194A GLN 2.8 12.3 + - - +
195A LEU 3.5 6.1 - - - +
197A ASN* 1.3 72.4 - - - +
199A ARG* 1.3 66.2 + - - +
200A ALA 3.4 1.8 - - - +
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Residues in contact with ARG 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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137A LYS* 3.4 6.4 + - - +
195A LEU 3.3 6.6 + - - -
196A LEU 4.0 2.6 + - - +
197A ASN 3.1 10.1 - - - +
198A ALA* 1.3 82.1 - - - +
200A ALA* 1.3 67.2 + - - +
232A ARG* 3.0 39.2 + - - +
233A GLY* 4.5 0.4 - - - -
234A TYR* 3.1 29.3 - - - +
251A GLN* 2.7 64.0 + - - +
252A GLN* 3.7 8.3 + - - +
254A PRO* 3.3 31.1 - - + +
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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