Contacts of the strand formed by residues 188 - 195 (chain E) in PDB entry 3E2A
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 LEU 188 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.8 22.4 - - + -
8C PHE* 3.6 29.1 - - + -
11C ASN* 2.8 35.3 + - + +
39E TRP* 4.3 0.9 - - + -
52E LEU* 4.1 8.1 - - + -
53E THR* 4.3 9.6 - - + -
96E CYS* 3.8 18.4 - - - -
179E TRP* 3.8 27.6 - - + -
180E VAL 3.8 1.1 - - - -
181E PHE* 3.8 27.6 - - + +
187E PHE* 1.3 78.8 - - - +
189E VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 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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8C PHE* 4.8 0.4 - - - -
179E TRP* 3.5 3.6 - - - -
180E VAL* 3.0 29.4 + - + +
182E ASP* 5.4 7.2 - - + -
185E ASP* 5.8 1.8 - - - +
187E PHE* 4.1 14.1 - - + +
188E LEU* 1.3 79.6 - - - +
190E ASP* 1.3 69.3 + - - +
191E GLN* 2.9 28.2 + - - +
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Residues in contact with ASP 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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8C PHE* 4.3 14.9 - - + -
177E HIS* 5.7 0.2 - - - +
178E GLY 3.2 11.1 + - - +
179E TRP* 3.5 22.5 + - + -
188E LEU 4.3 0.4 - - - -
189E VAL* 1.3 82.5 - - - +
191E GLN* 1.3 70.8 + - - +
192E GLY* 3.0 20.3 + - - -
193E VAL 4.5 3.6 + - - +
194E MET* 5.2 9.9 - - - +
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Residues in contact with GLN 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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148E LYS* 3.3 37.5 - - - +
151E VAL* 3.9 16.8 - - + -
152E ALA* 5.1 7.2 - - + +
178E GLY 3.0 17.9 + - - +
179E TRP 4.2 0.2 - - - -
180E VAL* 3.4 36.6 - - + +
189E VAL* 2.9 35.9 + - - +
190E ASP* 1.3 77.7 + - - +
192E GLY* 1.3 59.9 + - - +
193E VAL* 3.5 4.4 + - + +
208E ALA* 3.9 9.4 - - - +
211E ARG* 3.5 14.3 + - - -
212E LEU* 4.2 16.0 - - + +
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Residues in contact with GLY 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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190E ASP* 3.0 20.9 + - - -
191E GLN* 1.3 78.1 - - - +
193E VAL* 1.3 63.0 + - - +
194E MET* 3.6 5.9 + - - +
204E SER* 3.7 12.5 - - - +
208E ALA* 4.2 0.4 - - - -
211E ARG* 3.5 28.3 + - - -
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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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152E ALA* 3.6 33.0 - - + +
155E VAL* 3.5 31.9 - - + +
156E TYR 4.8 0.2 - - - +
176E LEU 3.8 3.1 - - - +
177E HIS* 3.9 0.7 - - - -
178E GLY* 3.7 22.8 + - - -
190E ASP* 4.7 2.7 - - - +
191E GLN* 3.5 3.7 - - + +
192E GLY* 1.3 76.0 - - - +
194E MET* 1.3 61.8 + - - +
201E LEU* 4.3 9.6 - - + -
204E SER* 3.9 12.8 - - - +
205E TYR* 4.1 20.9 - - + -
208E ALA* 3.4 24.9 - - + -
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Residues in contact with MET 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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175E SER* 4.2 4.0 - - - -
176E LEU 3.2 13.5 - - - +
177E HIS* 3.6 28.9 - - + +
190E ASP* 5.2 9.6 - - - +
192E GLY 3.6 6.9 + - - +
193E VAL* 1.3 74.8 - - - +
195E ALA* 1.3 63.2 + - - +
196E THR* 4.1 23.8 - - + -
200E THR* 3.8 6.6 - - - +
204E SER* 3.0 21.4 + - - -
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Residues in contact with ALA 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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155E VAL* 5.2 0.2 - - + -
168E TRP* 3.9 14.1 - - + -
174E LEU 3.7 0.9 - - - +
175E SER* 3.2 5.0 - - - -
176E LEU* 2.9 39.4 + - + +
193E VAL 4.3 0.2 - - - -
194E MET* 1.3 74.6 - - - +
196E THR* 1.3 64.1 + - - +
197E SER 3.6 0.2 - - - -
200E THR* 3.8 4.3 - - - -
201E LEU* 3.5 47.6 - - + +
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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