Contacts of the strand formed by residues 188 - 197 (chain E) in PDB entry 1OGA
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 TYR 188 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149E GLY 3.0 22.2 + - - -
150E PHE* 2.7 46.6 + - + +
151E TYR* 4.0 15.5 - + - -
153E ASP* 3.7 35.0 - - + -
176E PRO* 3.8 22.4 - - + -
177E LEU 3.2 12.6 - - - +
178E LYS* 3.3 44.0 + - + -
179E GLU* 4.0 2.0 - - - -
184E ASN 5.1 5.5 + - - -
186E SER 3.4 18.5 + - - -
187E ARG* 1.3 74.4 - - - +
189E SER* 1.3 61.5 + - - +
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Residues in contact with SER 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D TYR* 5.6 2.7 - - - -
176D TRP* 3.7 30.0 + - - -
147E ALA 3.2 8.3 - - - -
148E THR* 3.4 14.5 - - - +
150E PHE* 3.9 2.0 - - - -
176E PRO* 3.0 8.7 - - - +
177E LEU* 2.9 39.4 + - - +
179E GLU* 2.8 26.6 + - - +
188E TYR* 1.3 71.0 - - - +
190E LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D TRP* 5.5 1.3 - - - -
145E CYS 3.8 0.3 - - - +
146E LEU* 3.6 3.7 - - - +
147E ALA* 2.8 37.9 + - + +
150E PHE* 3.9 14.6 - - + -
155E VAL* 4.0 24.0 - - + +
157E LEU* 4.5 19.2 - - + +
172E THR* 4.2 15.5 - - + -
173E ASP* 3.4 40.6 - - + +
174E PRO 5.2 0.2 - - - -
176E PRO* 4.1 23.3 - - + -
189E SER* 1.3 75.9 - - - +
191E SER* 1.3 65.5 - - - +
212E VAL* 6.4 0.4 - - + -
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Residues in contact with SER 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D THR* 3.6 15.8 + - - +
174D VAL* 4.4 10.0 - - - +
176D TRP* 4.7 0.4 - - - -
144E VAL* 4.9 1.6 - - - -
145E CYS 3.2 6.1 - - - -
146E LEU* 3.5 23.1 - - - -
157E LEU* 5.0 0.9 - - - -
172E THR* 3.8 3.3 - - - +
173E ASP* 2.5 56.5 + - - +
190E LEU* 1.3 75.6 - - - +
192E SER* 1.3 63.4 + - - +
193E ARG* 3.2 9.6 + - - -
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Residues in contact with SER 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E VAL* 3.4 5.9 - - - +
145E CYS* 2.8 33.0 + - - +
157E LEU* 3.7 24.2 - - - -
159E TRP* 2.9 25.8 + - - -
170E VAL* 4.0 0.3 - - - +
171E SER 3.4 9.6 + - - -
172E THR* 2.7 28.0 + - - -
191E SER* 1.3 76.8 - - - +
193E ARG* 1.3 67.8 + - - +
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Residues in contact with ARG 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 4.1 2.7 - - + -
156D THR* 4.4 2.8 + - - -
157D ASP 4.7 0.2 + - - -
159D THR* 3.0 26.5 + - - +
161D LEU* 3.9 18.6 - - + -
172D SER* 3.1 36.2 + - - +
173D ALA* 4.1 7.1 - - - +
174D VAL* 4.0 16.1 - - - +
142E THR* 3.8 14.8 - - + -
143E LEU 3.3 3.8 - - - +
144E VAL* 3.7 19.7 - - + -
159E TRP* 4.0 2.7 - - - -
169E GLY 3.6 0.2 - - - +
170E VAL* 3.3 6.2 - - - +
171E SER* 2.9 46.7 + - - +
173E ASP* 2.5 32.9 + - - +
191E SER* 3.2 17.3 + - - -
192E SER* 1.3 82.1 + - - +
194E LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 4.6 0.2 - - - -
142E THR* 4.6 1.1 - - - -
143E LEU* 2.8 41.8 + - + +
159E TRP* 3.6 44.6 - - + +
161E VAL* 4.0 13.9 - - + -
166E VAL* 4.3 8.7 - - + -
168E SER 3.6 23.8 - - - +
169E GLY 3.4 1.6 - - - -
170E VAL* 3.6 12.1 - - + -
193E ARG* 1.3 73.2 - - - +
195E ARG* 1.3 62.3 + - - +
196E VAL* 4.3 14.8 - - + -
208E PHE* 3.8 29.6 - - + -
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Residues in contact with ARG 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D THR* 4.0 7.5 + - - +
138D ASP* 2.8 40.7 + - - -
161D LEU* 3.8 25.1 - - + +
163D MET* 3.4 31.6 - - - +
168D PHE* 3.3 12.3 - - - -
170D SER* 3.0 22.5 + - - -
134E GLU* 3.0 21.6 + - - +
138E THR* 3.7 16.8 + - - -
140E LYS* 3.7 14.7 - - + +
141E ALA 3.4 7.4 - - - +
142E THR* 3.0 24.2 + - - +
168E SER 5.0 0.2 - - - +
169E GLY* 2.9 17.9 + - - +
194E LEU* 1.3 77.3 - - - +
196E VAL* 1.3 69.9 + - - +
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Residues in contact with VAL 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D MET* 3.5 11.7 - - - +
140E LYS* 3.5 3.1 - - - +
141E ALA* 2.7 44.4 + - + +
143E LEU* 4.4 9.4 - - + -
161E VAL* 5.8 1.8 - - + -
194E LEU* 4.3 16.2 - - + -
195E ARG* 1.3 79.2 - - - +
197E SER* 1.3 67.2 + - - +
200E PHE* 4.1 23.6 - - + -
201E TRP* 4.0 22.0 - - + +
208E PHE* 4.3 13.5 - - + -
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Residues in contact with SER 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D MET* 3.8 6.7 - - - +
166D MET* 4.3 20.4 - - - -
139E GLN 3.9 7.9 - - - -
140E LYS* 4.4 1.1 - - - +
196E VAL* 1.3 81.4 - - - +
198E ALA* 1.3 64.2 + - - +
199E THR* 2.8 26.7 + - - -
200E PHE* 3.2 19.4 + - - +
201E TRP* 3.2 9.5 + - - +
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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