Contacts of the helix formed by residues 187 - 193 (chain A) in PDB entry 3G33
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 ALA 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TYR 3.7 1.8 + - - -
186A ARG* 1.3 74.5 - - - +
188A PRO* 1.3 73.7 - - + +
189A GLU* 3.2 25.8 - - - +
190A VAL* 3.0 18.5 + - + +
191A LEU* 3.2 12.5 + - - +
200A VAL* 3.7 34.3 + - + +
203A TRP* 3.7 10.1 - - + -
204A SER* 5.1 0.2 + - - -
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Residues in contact with PRO 188 (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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186A ARG 3.9 0.6 - - - +
187A ALA* 1.3 87.6 - - + +
189A GLU* 1.3 64.8 + - - +
191A LEU* 3.3 5.9 + - + +
192A LEU* 2.9 35.1 + - - +
203A TRP* 3.4 48.9 - - + -
228A LEU* 4.3 17.7 - - + +
231A ILE* 4.5 6.9 - - + -
232A PHE* 5.8 0.4 - - + -
283A PHE* 3.8 32.8 - - + -
288A ARG* 3.9 2.7 - - - +
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Residues in contact with GLU 189 (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 ALA* 3.3 12.9 - - - +
188A PRO* 1.3 77.5 - - - +
190A VAL* 1.3 54.8 + - + +
192A LEU* 3.1 7.2 + - - +
193A GLN* 2.4 32.7 + - - -
194A SER* 3.2 28.4 + - - +
195A THR 3.9 17.4 + - - +
197A ALA* 5.9 0.7 - - + -
200A VAL* 3.5 22.9 + - + +
244A PRO* 6.2 0.9 - - + -
283A PHE* 3.9 3.0 - - - +
285A PRO* 3.7 26.6 - - + +
288A ARG* 3.0 39.1 + - - -
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Residues in contact with VAL 190 (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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144A ARG* 5.7 3.1 - - - +
186A ARG* 3.8 29.2 - - - +
187A ALA* 3.0 11.8 + - + +
189A GLU* 1.3 75.2 - - + +
191A LEU* 1.3 66.4 + - + +
193A GLN* 3.1 21.4 + - - +
195A THR 5.8 0.9 - - - +
196A TYR* 4.7 28.0 + - + +
200A VAL* 3.7 38.6 - - + -
224A GLU* 6.0 0.2 - - - -
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Residues in contact with LEU 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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183A LEU* 4.4 12.3 - - + -
186A ARG* 3.8 29.8 - - + +
187A ALA 3.2 12.7 + - - +
188A PRO* 3.3 6.7 + - + +
190A VAL* 1.3 77.4 - - + +
192A LEU* 1.3 62.9 + - - +
193A GLN* 4.2 5.2 - - - +
224A GLU* 3.7 39.4 - - + +
227A GLN* 3.4 29.2 - - + -
228A LEU* 3.4 38.1 - - + -
231A ILE* 4.5 7.0 - - + -
248A SER* 5.3 2.1 + - - -
249A LEU* 4.9 6.8 - - - +
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Residues in contact with LEU 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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188A PRO* 2.9 21.0 + - + +
189A GLU* 3.6 7.2 - - - +
191A LEU* 1.3 79.0 - - - +
193A GLN* 1.3 70.2 + - - +
194A SER* 3.2 4.6 + - - +
228A LEU* 4.7 14.8 - - + -
243A TRP* 4.3 20.0 - - + +
244A PRO* 5.0 7.9 - - + -
247A VAL* 4.0 24.4 - - + +
248A SER* 4.4 11.0 + - - -
249A LEU* 3.8 45.8 - - + +
254A PHE* 5.9 1.3 - - + -
283A PHE* 4.0 30.7 - - + -
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Residues in contact with GLN 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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189A GLU 2.4 15.8 + - - -
190A VAL* 3.1 16.9 + - - +
191A LEU 4.2 3.6 + - - +
192A LEU* 1.3 77.9 - - - +
194A SER* 1.3 64.1 + - - +
195A THR* 3.8 1.1 - - - -
196A TYR* 5.1 20.5 - - + +
224A GLU* 4.6 16.6 + - - -
246A ASP 5.2 2.8 - - - +
247A VAL* 5.0 1.0 - - - +
248A SER* 5.1 8.6 + - - -
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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