Contacts of the strand formed by residues 185 - 194 (chain E) in PDB entry 2P5W
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 185 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145E THR 3.5 0.7 - - - -
146E GLY 2.8 29.3 + - - -
147E PHE* 2.6 46.7 + - + -
148E TYR* 3.7 19.8 - + - -
150E ASP* 3.8 31.8 - - + +
173E PRO* 3.8 24.9 - - + -
174E LEU 3.4 15.5 - - - +
175E LYS* 3.6 28.4 - - + +
176E GLU* 3.1 2.9 - - - +
183E SER 3.4 18.1 + - - -
184E ARG* 1.3 74.3 - - - +
186E ALA* 1.3 58.6 + - - +
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Residues in contact with ALA 186 (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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179D TRP* 3.7 29.2 - - + -
144E ALA 3.0 10.8 - - - +
145E THR* 3.9 6.5 - - + -
147E PHE* 4.0 1.3 - - - -
170E ASP* 5.2 0.3 - - - +
173E PRO* 3.1 6.7 - - - +
174E LEU* 3.0 43.1 + - + +
176E GLU* 3.7 13.7 - - + +
185E TYR* 1.3 75.5 - - - +
187E LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 187 (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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179D TRP* 5.7 0.7 - - - -
142E CYS 4.0 0.7 - - - +
143E LEU* 3.5 5.3 - - - +
144E ALA* 2.7 41.0 + - + +
147E PHE* 4.2 13.2 - - + -
152E VAL* 4.2 22.7 - - + -
154E LEU* 4.1 21.6 - - + +
169E THR* 3.9 16.2 - - + -
170E ASP* 3.6 41.7 - - + +
172E GLN* 4.1 0.4 - - - -
173E PRO* 4.0 21.1 - - + -
186E ALA* 1.3 75.1 - - - +
188E SER* 1.3 65.0 + - - +
209E VAL* 6.1 0.7 - - + -
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Residues in contact with SER 188 (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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159D THR* 3.2 16.1 - - - +
177D VAL* 4.1 14.7 - - - +
179D TRP* 5.6 0.2 - - - -
141E VAL* 4.6 2.5 - - - -
142E CYS 3.2 11.0 - - - -
143E LEU* 3.7 16.2 - - - -
154E LEU* 4.8 0.7 - - - -
169E THR* 3.6 5.5 - - - +
170E ASP* 2.6 56.2 + - - -
187E LEU* 1.3 75.3 - - - +
189E SER* 1.3 62.6 + - - +
190E ARG* 3.6 7.9 + - - -
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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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141E VAL* 3.3 9.5 - - - +
142E CYS* 2.9 29.5 + - - +
154E LEU* 3.6 20.6 - - - +
156E TRP* 2.7 33.6 + - - -
167E VAL* 4.0 0.3 - - - +
168E CYS 3.6 8.1 + - - -
169E THR* 2.8 23.8 + - - -
188E SER* 1.3 77.0 - - - +
190E ARG* 1.3 65.5 + - - +
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Residues in contact with ARG 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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138D LEU* 4.5 7.9 - - + -
159D THR* 3.0 27.3 + - - -
160D ASP 3.8 4.2 + - - -
162D CYS* 3.1 19.0 - - - -
164D LEU* 4.2 12.1 - - + -
175D SER* 3.4 34.0 + - - +
176D ALA* 3.7 5.3 - - - +
177D VAL* 3.8 13.3 - - - +
139E THR* 3.9 20.0 - - + -
140E LEU 3.3 7.9 - - - +
141E VAL* 4.7 4.9 - - + -
156E TRP* 4.0 3.4 - - - -
166E GLY 4.2 0.7 - - - -
167E VAL* 3.2 11.4 - - - +
168E CYS* 3.0 41.1 + - - +
170E ASP* 2.9 22.8 + - - +
188E SER* 3.6 17.6 + - - -
189E SER* 1.3 79.0 + - - +
191E LEU* 1.3 61.1 + - - +
192E ARG 4.2 0.2 - - - -
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Residues in contact with LEU 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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139E THR* 4.4 1.3 - - - -
140E LEU* 2.8 44.2 + - + +
156E TRP* 3.5 47.3 - - + -
158E VAL* 3.8 26.7 - - + -
163E VAL* 4.2 6.3 - - + -
165E SER 3.9 10.8 - - - +
166E GLY 3.5 4.5 - - - +
167E VAL* 3.7 19.7 - - + -
190E ARG* 1.3 73.2 - - - +
192E ARG* 1.3 66.7 + - - +
193E VAL* 4.3 13.0 - - + -
205E PHE* 3.8 16.2 - - + -
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Residues in contact with ARG 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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140D THR* 4.0 7.4 + - - +
141D ASP* 2.9 41.7 + - - -
164D LEU* 3.6 30.5 - - + -
166D MET* 3.8 26.6 - - - +
171D PHE* 3.5 8.9 - - - -
173D SER* 3.1 19.8 + - - -
131E GLU* 3.1 19.5 + - - +
135E THR* 3.7 19.2 + - - +
137E LYS* 3.6 15.2 - - + +
138E ALA 3.4 7.9 - - - +
139E THR* 3.1 21.4 + - - +
165E SER 5.0 0.3 - - - +
166E GLY* 2.9 23.9 + - - -
190E ARG 4.2 0.2 - - - -
191E LEU* 1.3 74.6 - - - +
193E VAL* 1.3 69.6 + - - +
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Residues in contact with VAL 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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166D MET* 3.7 9.0 - - - -
137E LYS* 3.5 5.0 - - - +
138E ALA* 2.7 42.6 + - + +
140E LEU* 4.5 5.8 - - + -
158E VAL* 5.7 1.6 - - + -
191E LEU* 4.3 17.3 - - + -
192E ARG* 1.3 79.0 - - - +
194E SER* 1.3 66.1 + - - +
197E PHE* 4.0 25.1 - - + -
198E TRP* 3.9 24.0 - - + +
205E PHE* 4.1 17.5 - - + -
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Residues in contact with SER 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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166D MET* 3.9 7.0 - - - +
169D MET* 4.8 16.4 - - - -
136E GLN 3.9 8.1 - - - -
137E LYS* 4.3 2.2 - - - +
138E ALA 4.4 0.2 - - - -
193E VAL* 1.3 80.2 - - - +
195E ALA* 1.3 65.7 + - - +
196E THR* 3.2 21.8 + - - -
197E PHE* 3.1 19.3 + - - +
198E TRP 3.1 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