Contacts of the strand formed by residues 191 - 200 (chain U) in PDB entry 2AK4
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 191 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152U GLY 3.0 23.4 + - - -
153U PHE* 2.6 48.2 + - + +
154U TYR* 3.9 17.2 - + - -
155U PRO* 5.7 0.2 - - + -
156U ASP* 3.8 39.1 + - + -
179U PRO* 3.8 19.3 - - + -
180U LEU 3.3 17.5 - - - -
181U LYS* 3.7 26.3 - - + +
182U GLU* 4.0 2.5 - - - -
187U ASN 5.7 0.7 + - - -
189U SER 3.4 17.5 - - - -
190U ARG* 1.3 74.9 - - - +
192U ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159T TYR* 5.9 0.2 - - + -
181T TRP* 3.7 31.0 - - + -
150U ALA 3.2 9.0 - - - +
151U THR* 4.0 2.7 - - + -
153U PHE* 3.9 2.0 - - - -
176U ASP* 5.3 0.3 - - - +
179U PRO* 3.4 2.8 - - - +
180U LEU* 2.6 46.7 + - + +
182U GLU* 3.7 22.0 - - + +
191U TYR* 1.3 74.3 - - - +
193U LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181T TRP* 5.4 2.0 - - - -
148U CYS 3.9 0.3 - - - +
149U LEU* 3.7 4.5 - - - +
150U ALA* 2.8 40.2 + - + +
153U PHE* 4.0 13.2 - - + -
158U VAL* 3.9 24.9 - - + +
160U LEU* 4.0 31.9 - - + +
175U THR* 4.1 11.4 - - + -
176U ASP* 3.7 39.7 - - + +
179U PRO* 3.9 24.5 - - + -
192U ALA* 1.3 74.5 - - - +
194U SER* 1.3 61.4 - - - +
215U VAL* 6.0 0.4 - - + -
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Residues in contact with SER 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T THR* 3.3 14.3 - - - +
179T VAL* 4.1 10.5 - - - +
181T TRP* 4.6 0.9 - - - -
147U VAL* 5.0 0.2 - - - -
148U CYS 3.3 4.7 - - - -
149U LEU* 3.8 20.9 - - - -
160U LEU* 4.8 0.7 - - - -
175U THR* 3.7 3.1 - - - +
176U ASP* 2.8 53.1 + - - -
193U LEU* 1.3 77.4 - - - +
195U SER* 1.3 61.7 + - - +
196U ARG* 3.3 15.5 + - - -
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Residues in contact with SER 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U VAL* 3.3 8.0 - - - +
148U CYS* 2.7 39.4 + - - +
160U LEU* 3.4 30.1 - - - +
162U TRP* 2.9 24.3 + - - -
174U CYS 3.0 11.2 + - - -
175U THR* 2.9 22.0 + - - -
194U SER* 1.3 75.0 - - - +
196U ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 196 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140T LEU* 4.5 4.9 - - + -
161T THR* 3.2 21.4 + - - -
162T ASP 4.2 0.6 + - - -
164T CYS* 3.6 20.7 - - - +
166T LEU* 4.3 9.6 - - + -
177T SER* 2.9 33.7 + - - -
179T VAL* 3.6 24.5 - - + +
145U THR* 4.0 11.9 - - + -
146U LEU 3.2 7.4 - - - +
147U VAL* 4.4 8.3 - - + -
162U TRP* 3.7 7.6 + - - -
172U GLY 4.3 0.9 - - - -
173U VAL* 3.3 4.5 - - - -
174U CYS* 2.7 59.6 + - - +
176U ASP* 3.2 27.1 + - - -
194U SER* 3.3 19.9 + - - -
195U SER* 1.3 78.8 + - - +
197U LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 197 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144U ALA 3.7 1.7 - - - +
145U THR* 3.5 2.0 - - - -
146U LEU* 2.7 44.4 + - + +
162U TRP* 3.6 44.1 - - + +
164U VAL* 3.9 13.7 - - + -
169U VAL* 4.1 7.9 - - + -
171U SER 3.8 11.7 - - - +
172U GLY 3.3 11.7 - - - +
173U VAL* 3.7 17.5 - - + -
196U ARG* 1.3 73.9 - - - +
198U ARG* 1.3 59.5 + - - +
199U VAL* 4.3 15.5 - - + -
211U PHE* 3.9 28.5 - - + -
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Residues in contact with ARG 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142T THR* 3.9 9.4 + - - +
143T ASP* 2.7 41.6 + - - -
166T LEU* 3.8 29.1 - - + +
168T MET* 3.8 34.8 - - - +
173T PHE* 3.8 9.6 - - - -
175T SER* 3.4 15.0 + - - -
137U GLU* 3.0 22.0 + - - +
141U THR* 3.6 17.8 + - - -
143U LYS* 3.5 16.3 - - + +
144U ALA 3.3 6.5 - - - +
145U THR* 3.1 23.3 + - + +
171U SER 5.0 0.3 - - - +
172U GLY* 2.8 18.0 + - - +
196U ARG 4.2 0.2 - - - -
197U LEU* 1.3 74.2 - - - +
199U VAL* 1.3 68.5 + - - +
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Residues in contact with VAL 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168T MET* 4.4 6.7 - - - -
143U LYS* 3.6 3.6 - - - +
144U ALA* 2.6 47.3 + - + +
146U LEU* 4.2 11.2 - - + -
164U VAL* 5.6 1.6 - - + -
197U LEU* 4.3 17.7 - - + -
198U ARG* 1.3 79.3 - - - +
200U SER* 1.3 64.8 + - - +
203U PHE* 4.1 26.2 - - + -
204U TRP* 4.0 22.9 - - + +
211U PHE* 4.3 12.6 - - + -
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Residues in contact with SER 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168T MET* 4.4 6.8 - - - +
142U GLN 3.9 8.7 - - - -
143U LYS* 4.3 11.4 - - - +
144U ALA 4.2 0.2 - - - -
199U VAL* 1.3 80.7 - - - +
201U ALA* 1.3 65.6 + - - +
202U THR* 3.6 17.6 + - - -
203U PHE* 3.3 13.9 + - - +
204U TRP* 3.2 17.0 + - - +
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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