Contacts of the helix formed by residues 187 - 197 (chain A) in PDB entry 3E6J
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LYS 3.7 23.3 - - - +
158A SER* 4.4 7.1 - - - -
180A TRP* 4.1 18.2 - - + -
181A ASP 3.5 13.2 + - - +
182A CYS* 4.1 22.2 - - - +
184A CYS* 3.0 23.3 + - - +
186A ASP* 1.3 76.9 - - - +
188A MET* 1.3 67.7 + - + +
189A TYR 3.2 0.4 - - - -
190A LEU* 3.1 24.4 + - + +
191A ARG* 2.9 25.3 + - + +
224A VAL* 4.2 9.9 - - + -
227A VAL* 4.4 6.1 - - + -
232A THR* 3.8 22.7 - - + -
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Residues in contact with MET 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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185A ARG* 3.1 26.2 + - + +
187A ILE* 1.3 74.0 - - - +
189A TYR* 1.3 60.3 + - - +
191A ARG* 3.6 34.5 - - - +
192A ASN* 2.8 50.8 + - - +
227A VAL* 4.2 11.4 - - - +
229A GLU* 3.8 44.2 - - + +
232A THR* 3.9 26.9 - - + +
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Residues in contact with TYR 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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159A ILE* 3.8 27.4 - - + +
160A PRO 3.4 21.8 - - - -
161A HIS* 3.9 31.4 - + + -
162A GLY* 3.3 22.9 - - - -
163A ALA 3.7 3.4 - - - -
164A PHE* 2.9 34.5 + + + +
165A ASP* 2.6 29.0 + - - -
185A ARG 4.8 0.2 + - - -
186A ASP 3.7 6.2 + - - +
187A ILE 3.2 0.6 - - - -
188A MET* 1.3 78.3 - - - +
190A LEU* 1.3 60.2 + - - +
192A ASN* 3.8 4.8 - - + +
193A TRP* 2.9 37.2 + + + +
306A GOL 4.7 11.0 - - - -
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Residues in contact with LEU 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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159A ILE* 4.0 26.0 + - + +
164A PHE* 4.3 10.5 - - + -
175A LEU* 4.0 15.5 - - + -
180A TRP* 3.5 49.8 - - + +
186A ASP 4.7 0.8 + - - -
187A ILE* 3.1 20.1 + - + +
189A TYR* 1.3 79.1 - - - +
191A ARG* 1.3 62.3 + - - +
193A TRP* 4.2 6.5 - - + -
194A VAL* 2.8 55.5 + - + +
215A ALA* 5.3 2.7 - - + -
224A VAL* 4.2 9.4 - - + -
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Residues in contact with ARG 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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187A ILE* 2.9 16.6 + - + +
188A MET* 3.6 22.8 - - + +
190A LEU* 1.3 77.8 - - - +
192A ASN* 1.3 86.3 + - - +
195A ALA* 3.0 41.7 + - - +
196A ASP* 5.7 0.6 + - - -
224A VAL* 3.3 34.0 - - + +
225A ARG* 3.3 20.3 + - - +
226A ALA* 4.9 3.2 + - - +
227A VAL* 2.8 32.8 + - + +
228A THR* 5.1 3.6 - - - +
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Residues in contact with ASN 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 MET* 2.8 34.7 + - - +
189A TYR* 3.9 4.8 - - + +
191A ARG* 1.3 112.4 + - - +
193A TRP* 1.3 57.2 + - - +
195A ALA* 3.4 3.7 + - - +
196A ASP* 3.0 41.0 + - - +
306A GOL 3.9 7.9 - - - +
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Residues in contact with TRP 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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164A PHE* 3.6 37.3 + + + +
165A ASP* 4.9 2.9 - - - -
167A LEU 5.7 1.6 - - - -
170A LEU* 4.0 15.0 - - + -
173A ALA* 3.9 15.5 - - + -
175A LEU* 4.2 19.7 - - + -
189A TYR* 2.9 42.7 + - + +
190A LEU* 3.7 8.5 - - + +
192A ASN* 1.3 75.6 - - - +
194A VAL* 1.3 77.6 + - + +
196A ASP 3.2 0.3 + - - -
197A HIS* 2.8 65.4 + + + +
200A ILE* 3.2 40.2 - - + -
201A ALA* 5.5 4.0 - - + -
304A SO4 5.4 2.4 + - - -
306A GOL 3.4 14.7 + - - +
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Residues in contact with VAL 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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175A LEU* 4.0 17.0 - - + -
190A LEU* 2.8 45.5 + - + +
191A ARG 4.0 2.5 - - - +
193A TRP* 1.3 80.7 - - + +
195A ALA* 1.3 62.2 + - - +
196A ASP 3.1 0.7 + - - -
197A HIS 3.2 10.5 + - - -
198A THR* 3.3 15.1 + - - +
201A ALA* 4.5 9.2 - - + -
212A PRO* 3.4 33.0 - - + +
215A ALA* 4.9 11.9 - - + -
224A VAL* 5.2 2.5 - - + -
225A ARG* 3.8 16.4 - - + +
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Residues in contact with ALA 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 ARG* 3.0 38.4 + - - +
192A ASN* 3.6 5.2 - - - +
194A VAL* 1.3 77.2 - - - +
196A ASP* 1.3 64.0 + - - +
198A THR* 3.4 19.4 + - - +
225A ARG* 3.9 19.9 + - + +
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Residues in contact with ASP 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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191A ARG* 5.7 0.5 + - - -
192A ASN* 3.0 21.1 + - - +
194A VAL 3.1 0.2 - - - -
195A ALA* 1.3 84.5 - - - +
197A HIS* 1.3 68.1 + - - +
198A THR 3.8 1.3 - - - -
306A GOL 2.7 54.9 + - - -
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Residues in contact with HIS 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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193A TRP* 2.8 60.5 + + + +
194A VAL 3.2 5.1 + - - +
196A ASP* 1.3 82.5 - - + +
198A THR* 1.3 63.8 + - - +
199A SER* 3.1 6.1 + - - -
200A ILE* 3.1 36.2 + - + +
201A ALA* 3.7 6.4 + - - +
304A SO4 3.0 38.7 + - - -
306A GOL 3.4 36.7 + - - -
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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