Contacts of the helix formed by residues 192 - 200 (chain A) in PDB entry 3V30
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 THR 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ILE 5.2 0.2 - - - -
184A ASN* 3.7 24.7 - - + +
185A ILE 3.4 2.9 - - - +
186A TYR* 4.6 7.4 - - + -
191A GLY* 1.3 80.7 - - - +
193A PRO* 1.3 77.0 - - - +
194A LEU* 3.6 7.5 + - - +
195A LEU* 3.1 30.3 + - + +
196A TYR* 3.0 28.4 + - - -
215A ASP 5.7 0.7 + - - -
218A THR* 4.1 26.8 + - + +
219A GLU 5.7 0.4 - - - +
226A PRO* 5.6 0.3 - - - +
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Residues in contact with PRO 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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161A LEU* 3.5 26.7 - - + -
162A SER* 3.5 16.6 - - - +
165A SER* 3.5 31.4 - - - +
183A ILE 3.4 24.2 - - - +
185A ILE* 3.3 21.5 - - + +
192A THR* 1.3 86.7 - - - +
194A LEU* 1.3 55.5 + - - +
196A TYR* 3.2 2.6 + - + -
197A ALA* 2.9 26.9 + - - +
209A LEU* 3.7 11.9 - - + -
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Residues in contact with LEU 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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183A ILE 5.0 1.6 + - - +
184A ASN* 6.1 0.2 - - - +
192A THR* 3.2 7.7 + - - +
193A PRO* 1.3 79.4 - - - +
195A LEU* 1.3 62.2 + - - +
197A ALA* 3.3 0.9 + - - +
198A VAL* 2.9 33.0 + - + +
206A VAL* 4.1 24.5 - - + -
209A LEU* 3.8 19.2 - - + +
210A LEU* 3.9 25.8 - - + -
214A ALA* 4.3 14.8 - - + -
215A ASP 3.6 26.0 - - - +
216A LEU* 3.8 16.6 - - + -
226A PRO* 3.7 23.1 - - + -
242A ILE* 5.9 0.2 - - + -
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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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191A GLY* 4.0 4.3 - - - -
192A THR* 3.1 33.8 + - + +
194A LEU* 1.3 77.0 - - - +
196A TYR* 1.3 57.9 + - - +
198A VAL* 3.4 4.8 + - - +
199A ARG* 2.9 30.0 + - - +
218A THR 4.0 7.9 - - - +
219A GLU 4.0 1.8 - - - +
220A ALA* 3.6 32.5 - - + +
224A TYR 3.7 14.1 - - - +
226A PRO* 3.6 37.9 - - + -
229A LEU* 3.9 17.3 - - + +
12B LEU* 3.7 18.0 - - + +
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Residues in contact with TYR 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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162A SER* 3.7 25.8 - - - +
165A SER 4.2 4.6 - - - +
166A THR* 3.4 30.6 - - - +
187A ASP* 2.6 34.5 + - - -
189A ASN* 3.0 28.4 + - - +
191A GLY* 3.2 13.3 + - - -
192A THR 3.0 30.6 + - - -
193A PRO* 3.2 5.1 + - + +
195A LEU* 1.3 74.4 - - - +
197A ALA* 1.3 64.3 + - - +
199A ARG* 3.3 3.6 + - - +
200A GLY* 3.1 20.1 + - - -
9B LEU* 3.9 9.1 - - + +
10B PRO* 3.5 33.9 - - + +
12B LEU* 3.9 14.6 - - + -
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Residues in contact with ALA 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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165A SER* 3.7 13.8 + - - +
193A PRO 2.9 15.7 + - - +
194A LEU 3.8 2.7 - - - +
196A TYR* 1.3 73.5 - - - +
198A VAL* 1.3 64.7 + - - +
201A ASN 3.3 2.6 + - - -
202A HIS* 2.9 31.6 + - - +
205A CYS* 4.1 12.1 - - + -
206A VAL* 3.7 25.3 - - + +
209A LEU* 3.9 16.8 - - + -
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Residues in contact with VAL 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 LEU* 2.9 24.1 + - + +
195A LEU* 3.7 5.8 - - - +
197A ALA* 1.3 77.0 - - - +
199A ARG* 1.3 63.6 + - - +
201A ASN* 2.9 12.0 + - - -
202A HIS 5.0 0.7 - - - +
206A VAL* 3.8 18.2 - - + -
226A PRO* 3.5 39.0 - - + +
229A LEU* 3.9 9.6 - - + -
230A ALA* 3.8 24.5 - - + +
233A LEU* 5.6 0.2 - - + -
235A TYR* 3.3 13.1 - - + -
238A VAL* 3.9 13.5 - - + -
242A ILE* 4.3 5.6 - - + -
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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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195A LEU 2.9 21.2 + - - +
196A TYR 3.3 4.9 + - - +
198A VAL* 1.3 75.2 - - - +
200A GLY* 1.3 56.2 + - - +
201A ASN 3.3 0.2 - - - -
229A LEU* 4.5 12.1 - - + -
233A LEU* 3.6 21.2 - - - +
235A TYR* 3.4 22.5 + - - -
10B PRO* 4.1 18.4 - - + -
11B GLY 3.3 21.3 + - - +
12B LEU* 3.8 11.7 - - + -
13B ASP 3.1 22.1 + - - -
14B LEU 4.3 1.6 + - - -
15B LYS 3.5 22.0 + - - -
17B SER* 2.7 34.2 + - - +
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Residues in contact with GLY 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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166A THR 5.0 2.0 - - - -
196A TYR 3.1 11.2 + - - -
198A VAL 3.2 0.2 - - - -
199A ARG* 1.3 75.7 - - - +
201A ASN* 1.3 70.0 + - - +
202A HIS* 3.2 36.0 + - - -
235A TYR* 5.3 0.2 - - - -
10B PRO* 5.6 1.5 - - - +
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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