Contacts of the strand formed by residues 185 - 193 (chain E) in PDB entry 4OZH
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 PHE 185 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ILE* 5.9 4.9 - - + -
132E ASN* 5.0 15.5 - - + -
155E ASP* 3.9 18.4 - - + -
178E LEU* 5.6 0.2 - - - +
179E ASP* 3.7 1.3 + - - +
180E MET* 2.8 51.1 + - + +
183E MET* 4.1 18.6 - - + +
184E ASP* 1.3 77.7 - - - +
186E LYS* 1.3 75.3 + - - +
187E SER* 3.7 13.0 - - - -
153F LYS* 3.4 30.1 - - - +
208F ARG* 3.4 24.5 - - - -
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Residues in contact with LYS 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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15E GLU* 3.3 39.3 + - - +
96E LEU* 3.8 20.2 - - + -
128E PRO* 3.9 22.4 - - + -
129E ASN 4.9 6.3 + - - +
130E ILE* 3.4 18.7 - - + +
177E VAL* 4.6 1.3 - - + -
178E LEU 3.3 11.0 - - - +
179E ASP* 3.4 37.0 + - + +
184E ASP* 5.3 8.3 + - - -
185E PHE* 1.3 87.9 - - - +
187E SER* 1.3 60.2 + - - +
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Residues in contact with SER 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ILE* 4.2 5.8 - - - -
154E THR* 4.4 6.1 + - - -
155E ASP* 4.0 11.9 - - - +
177E VAL* 3.6 2.6 - - - -
178E LEU* 2.8 58.2 + - - +
185E PHE* 3.7 8.4 - - - -
186E LYS* 1.3 75.8 - - - +
188E ASN* 1.3 62.8 + - - +
189E SER* 5.7 0.5 + - - -
208F ARG* 3.2 30.7 + - - -
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Residues in contact with ASN 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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128E PRO* 3.7 19.6 - - - +
130E ILE* 3.7 10.1 - - - +
154E THR* 3.4 2.8 + - - -
155E ASP* 3.3 23.7 + - - +
156E PHE* 3.0 52.0 + - + +
157E ASP 3.8 0.4 - - - -
158E SER* 3.4 30.8 + - - +
175E LYS* 4.7 14.0 + - + +
176E CYS 3.8 4.2 - - - +
177E VAL* 4.1 10.4 + - - +
187E SER* 1.3 72.5 - - - +
189E SER* 1.3 60.5 + - - +
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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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152E LEU* 4.0 15.5 - - - -
153E PHE 3.3 10.3 - - - -
154E THR* 4.0 10.5 - - - -
156E PHE* 3.7 3.9 - - - -
175E LYS* 3.4 2.9 - - - -
176E CYS* 3.1 36.8 + - - +
178E LEU* 4.8 9.7 - - - +
187E SER* 5.2 1.1 - - - -
188E ASN* 1.3 76.5 - - - +
190E ALA* 1.3 59.5 + - - +
155F THR* 6.2 1.3 - - - -
184F CYS* 5.3 0.2 - - - +
206F ARG* 3.3 28.8 + - - +
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Residues in contact with ALA 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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152E LEU* 3.4 4.9 - - - +
153E PHE* 3.0 34.8 + - + +
156E PHE* 4.8 1.6 - - + -
162E VAL* 4.1 23.3 - - + -
173E THR* 3.8 19.7 - - - +
175E LYS* 4.5 2.2 - - - +
189E SER* 1.3 73.9 - - - +
191E VAL* 1.3 63.3 + - - +
205E PHE* 3.8 21.8 - - + -
206F ARG* 4.1 3.4 - - - +
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Residues in contact with VAL 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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150E VAL* 4.3 13.0 - - + -
151E CYS 3.5 8.7 - - - +
152E LEU* 3.9 9.9 - - + -
171E TYR 3.8 1.0 - - - +
172E ILE* 3.4 3.8 - - - +
173E THR* 3.0 36.5 + - - +
190E ALA* 1.3 76.2 - - - +
192E ALA* 1.4 61.8 + - - +
193E TRP* 4.1 18.5 - - + -
205E PHE* 4.2 1.8 - - - -
157F VAL* 3.9 28.7 - - + -
159F LEU* 5.1 0.7 - - + -
204F SER* 4.0 10.8 - - - +
206F ARG* 3.7 36.1 - - - +
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Residues in contact with ALA 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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150E VAL* 3.5 1.7 - - - +
151E CYS* 2.7 39.1 + - + +
170E VAL* 5.0 0.7 - - + -
171E TYR 3.2 9.9 - - - +
172E ILE* 3.8 12.6 - - + -
191E VAL* 1.4 75.0 - - - +
193E TRP* 1.4 63.2 + - - +
199E PHE* 3.6 18.4 - - + -
204E ALA* 4.4 4.7 - - + -
205E PHE* 3.6 26.9 - - + -
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Residues in contact with TRP 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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149E SER 4.3 3.1 - - - +
150E VAL* 3.7 21.1 - - + -
170E VAL* 3.8 0.2 - - - -
171E TYR* 3.1 78.1 + + + -
173E THR* 3.7 31.9 - - + -
191E VAL* 4.1 11.0 - - + -
192E ALA* 1.4 77.4 - - - +
194E SER* 1.4 65.1 + - - +
195E ASN* 6.1 2.5 - - - -
199E PHE* 3.8 10.0 - - - -
159F LEU* 3.6 40.6 - - + -
161F THR* 4.2 12.0 - - + +
190F LEU* 4.2 9.2 - - + -
192F GLU* 6.3 0.4 - - - +
202F ALA* 3.8 22.9 - - + +
204F SER* 4.5 5.2 - - - -
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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