Contacts of the helix formed by residues 186 - 200 (chain A) in PDB entry 4OGB
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 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL 5.2 0.2 - - - +
185A PHE* 1.3 75.6 - - - +
187A ASP* 1.3 59.0 + - - +
188A LEU* 3.6 9.7 + - - +
189A GLU* 2.8 42.0 + - - +
190A ILE* 2.8 28.7 + - - +
306A ARG* 4.3 7.9 - - - +
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Residues in contact with ASP 187 (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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129A ARG 5.2 3.6 - - - +
131A LEU* 4.5 8.2 - - + +
134A THR* 3.9 21.0 + - + +
135A PHE* 3.5 23.4 - - + -
185A PHE 4.1 0.2 + - - -
186A THR* 1.3 73.4 - - - +
188A LEU* 1.3 57.2 + - - +
190A ILE* 3.5 16.6 - - - +
191A LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 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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135A PHE* 3.5 25.2 - - + -
186A THR* 3.2 9.6 + - - +
187A ASP* 1.3 79.8 - - - +
189A GLU* 1.3 57.3 + - - +
191A LEU* 3.6 3.8 - - + +
192A ALA* 2.9 27.7 + - - +
252A LEU* 4.3 11.0 - - + -
256A GLN* 3.7 22.9 - - + +
259A SER* 3.5 28.5 - - - +
260A LEU* 3.9 22.8 - - + +
263A MET* 3.9 8.3 - - + -
505A EDO 3.8 20.9 - - - +
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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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185A PHE* 3.4 15.4 - - + -
186A THR* 2.8 30.1 + - - +
188A LEU* 1.3 73.1 - - - +
190A ILE* 1.3 60.0 + - - +
192A ALA* 3.3 3.9 + - - +
193A ALA* 3.0 29.5 + - - +
263A MET* 3.5 30.2 - - + +
303A TYR* 5.6 3.3 - - - -
306A ARG* 2.7 53.0 + - - +
310A LEU* 4.1 18.1 - - + +
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Residues in contact with ILE 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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129A ARG* 3.8 42.8 - - + +
131A LEU* 4.6 9.9 - - + -
176A LEU* 4.1 19.5 - - + -
185A PHE* 3.9 25.6 - - + +
186A THR 2.8 21.5 + - - +
187A ASP* 3.5 16.2 - - - +
189A GLU* 1.3 75.2 - - - +
191A LEU* 1.3 62.5 + - - +
193A ALA* 3.3 3.2 + - - +
194A ILE* 3.1 31.7 + - + +
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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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126A PHE* 3.6 35.9 - - + -
131A LEU* 4.3 10.7 - - + +
135A PHE* 3.9 39.5 - - + -
137A ILE* 5.1 2.2 - - + -
187A ASP 2.8 19.9 + - - +
188A LEU* 3.6 6.3 - - + +
190A ILE* 1.3 74.2 - - - +
192A ALA* 1.3 54.0 + - - +
194A ILE* 3.4 2.6 + - - -
195A PHE* 2.8 40.9 + - + +
249A PHE* 3.9 19.7 - - + -
252A LEU* 4.5 0.9 - - + -
260A LEU* 3.9 29.2 - - + -
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Residues in contact with ALA 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 LEU 2.9 20.8 + - - +
189A GLU* 3.3 6.3 + - - +
191A LEU* 1.3 73.7 - - - +
193A ALA* 1.3 56.4 + - - +
196A ALA* 2.8 34.0 + - - +
260A LEU* 3.6 18.8 - - + +
263A MET* 3.8 33.2 - - + -
264A VAL* 3.8 9.5 - - + +
267A ILE* 4.2 5.6 - - + -
310A LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 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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172A THR* 3.9 18.1 - - + +
176A LEU* 4.3 9.6 - - + -
189A GLU 3.0 16.2 + - - +
190A ILE 3.8 3.6 - - - +
192A ALA* 1.3 75.6 - - - +
194A ILE* 1.3 59.4 + - - +
196A ALA* 3.9 1.6 - - - +
197A SER* 2.8 33.0 + - - -
267A ILE* 4.0 12.7 - - + +
310A LEU* 4.2 19.7 - - + -
313A MET* 5.1 0.7 - - - -
314A VAL* 4.0 9.9 - - + +
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Residues in contact with ILE 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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122A MET* 3.6 24.0 - - - -
125A ILE* 3.8 16.2 - - + -
126A PHE* 3.9 14.6 - - + -
129A ARG* 3.6 35.4 - - - +
131A LEU* 4.4 6.7 - - + -
169A VAL* 4.1 11.5 - - + +
172A THR* 4.7 5.8 - - + -
173A HIS* 4.8 5.6 - - - +
176A LEU* 3.9 13.5 - - + -
190A ILE* 3.1 22.6 + - + +
191A LEU* 4.0 3.4 - - - +
193A ALA* 1.3 75.1 - - - +
195A PHE* 1.3 67.9 + - - +
197A SER* 3.1 8.8 + - - -
198A ALA* 3.0 20.6 + - - +
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Residues in contact with PHE 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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122A MET* 4.7 10.5 - - + -
126A PHE* 5.6 2.5 - + + -
145A TYR* 3.4 42.4 - + - -
191A LEU* 2.8 28.7 + - + +
192A ALA 4.1 1.6 - - - +
194A ILE* 1.3 73.6 - - - +
196A ALA* 1.3 62.9 + - - +
198A ALA* 3.1 15.6 + - + +
199A ILE* 3.1 37.6 + - + +
237A GLY 4.1 7.6 - - - -
238A PHE* 4.1 15.7 - + - -
241A LEU* 4.8 4.0 - - + -
248A ILE* 4.0 7.9 - - + -
249A PHE* 3.7 42.0 - + + -
260A LEU* 5.3 0.9 - - + -
264A VAL* 3.8 21.1 - - + -
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Residues in contact with ALA 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 ALA 2.8 20.7 + - - +
193A ALA 3.9 2.5 - - - +
195A PHE* 1.3 75.7 - - - +
197A SER* 1.3 64.2 + - - +
199A ILE* 3.3 5.9 + - - +
200A HIS* 3.0 28.9 + - - +
264A VAL* 4.2 11.7 - - + +
267A ILE* 3.6 32.8 - - + -
268A VAL* 3.7 16.2 - - + +
314A VAL* 5.3 0.9 - - - -
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Residues in contact with SER 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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153A TYR* 4.4 0.2 + - - -
165A ALA* 4.2 4.0 - - - +
168A VAL* 3.9 8.3 - - - -
169A VAL* 3.7 26.9 - - - +
172A THR* 2.8 25.3 + - - -
193A ALA 2.8 18.6 + - - -
194A ILE* 3.4 9.6 - - - -
196A ALA* 1.3 77.4 - - - +
198A ALA* 1.3 59.4 + - - +
200A HIS* 2.6 33.5 + - - -
314A VAL* 3.8 10.7 - - - +
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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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118A LEU* 3.8 9.0 - - + +
122A MET* 3.6 37.0 - - + -
149A LEU* 3.6 18.8 - - + +
153A TYR* 2.6 31.5 + - - -
165A ALA* 3.9 1.4 - - - +
169A VAL* 3.4 9.6 - - + -
194A ILE 3.0 7.4 + - - +
195A PHE* 3.1 9.4 + - + +
197A SER* 1.3 76.8 - - - +
199A ILE* 1.3 55.5 + - + +
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Residues in contact with ILE 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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145A TYR* 3.6 24.2 - - - +
149A LEU* 3.8 18.6 - - + -
153A TYR* 3.4 3.4 - - - -
195A PHE* 3.1 43.0 + - + +
196A ALA* 3.6 7.2 - - - +
198A ALA* 1.3 77.7 - - + +
200A HIS* 1.3 67.4 + - - +
201A ASP 3.0 4.9 + - - -
202A VAL* 3.0 18.3 + - + +
233A HIS* 3.6 5.6 - - - +
234A LEU* 4.0 22.9 - - + +
237A GLY* 4.1 20.9 - - - -
238A PHE* 4.6 1.8 - - + -
264A VAL* 3.8 17.5 - - + -
268A VAL* 4.3 2.0 - - + -
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Residues in contact with HIS 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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153A TYR* 4.6 0.2 + - - -
164A HIS* 3.3 6.9 + + - -
165A ALA* 4.4 6.1 - - - -
168A VAL* 3.6 31.9 - - + +
196A ALA 3.0 16.6 + - - +
197A SER* 2.6 25.2 + - - -
198A ALA 3.4 2.6 - - - -
199A ILE* 1.3 76.1 - - - +
201A ASP* 1.3 70.6 + - + +
202A VAL 3.7 0.2 - - - -
233A HIS* 2.8 23.1 - - - +
268A VAL* 4.0 26.0 - - + +
271A THR* 4.5 17.6 + - + -
314A VAL* 5.4 1.6 - - + -
318A ASP* 3.3 8.9 + - - -
509A ZN 2.3 36.9 - - - -
510A ZN 4.2 5.5 - - - -
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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