Contacts of the strand formed by residues 162 - 172 (chain E) in PDB entry 1E81
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 PRO 162 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E THR* 3.8 17.9 - - + -
4E THR 3.2 13.2 - - - +
5E THR* 4.6 16.4 - - + +
6E PRO* 4.1 4.5 - - + -
156E GLY* 3.9 7.0 - - - -
159E ALA* 1.3 97.1 - - + +
163E GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 163 (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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3E THR* 3.4 10.6 - - - +
4E THR* 2.7 38.0 + - - +
154E ASP* 3.0 16.6 - - - -
156E GLY 4.0 6.0 - - - +
159E ALA 3.8 1.2 + - - -
162E PRO* 1.3 74.8 - - - +
164E THR* 1.3 66.9 + - - -
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Residues in contact with THR 164 (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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1E SER* 3.4 12.3 - - - +
2E ALA 3.6 11.0 - - - +
3E THR* 5.0 3.9 + - - +
4E THR* 3.9 1.5 - - - +
152E THR* 3.7 2.9 + - - +
153E ALA* 4.0 0.5 - - - -
154E ASP* 2.8 50.0 + - - +
155E LEU* 5.6 0.2 - - - +
163E GLY* 1.3 78.3 + - - +
165E TYR* 1.3 69.3 + - - +
166E ASN* 3.2 33.0 - - - +
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Residues in contact with TYR 165 (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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0E GLY 3.8 0.7 - - - +
1E SER* 3.4 1.6 - - - -
2E ALA* 2.9 37.9 + - + +
4E THR* 3.7 31.9 - - + -
14E TYR* 5.4 3.2 - - + +
16E THR* 3.6 12.1 - - + -
31E PHE* 3.5 52.2 + + + +
123E LEU* 5.0 5.4 - - + -
151E PHE* 4.9 11.4 - + - -
152E THR 3.5 11.7 - - - -
153E ALA* 3.9 20.0 - - + -
155E LEU* 3.8 15.6 - - + +
164E THR* 1.3 73.3 - - - +
166E ASN* 1.3 63.2 + - - +
167E PHE* 4.2 11.0 - + + -
216E THR* 3.4 32.4 + - + +
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Residues in contact with ASN 166 (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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0E GLY 3.2 1.8 - - - -
1E SER* 2.4 32.0 + - - -
151E PHE* 3.0 8.5 - - - +
152E THR* 2.8 47.3 + - - +
164E THR* 3.2 18.2 - - - +
165E TYR* 1.3 73.9 - - - +
167E PHE* 1.3 61.3 - - - +
169E PHE* 3.5 41.0 - - + +
171E ASP* 4.1 18.0 + - - +
311E PHE* 5.6 1.6 - - - -
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Residues in contact with PHE 167 (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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-1E THR* 3.1 9.7 - - - -
0E GLY* 2.7 43.3 + - - +
31E PHE* 3.9 22.9 - + - -
91E VAL* 3.9 26.0 - - + -
94E LEU* 3.7 26.7 - - + -
121E LEU* 5.3 0.2 - - + -
123E LEU* 4.1 24.9 - - + -
138E PHE* 4.2 19.1 - + - -
139E PHE* 4.2 13.2 - + - -
142E ALA* 6.0 0.2 - - + -
146E LEU* 3.9 4.7 - - + -
150E VAL 3.6 1.3 - - - -
151E PHE* 3.4 30.1 - + + -
165E TYR* 4.2 15.7 - - + -
166E ASN* 1.3 74.9 - - - +
168E GLY* 1.3 60.7 + - - +
169E PHE* 3.4 2.8 + - - -
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Residues in contact with GLY 168 (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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-2E SER 4.1 4.0 - - - -
-1E THR* 3.7 2.6 - - - +
146E LEU* 3.9 14.8 - - - +
147E ASP* 3.4 11.4 - - - +
148E SER* 3.2 44.8 + - - -
150E VAL 2.6 14.3 + - - -
167E PHE* 1.3 71.8 - - - +
169E PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 169 (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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-1E THR* 3.8 20.6 - - + -
0E GLY 3.9 11.9 - - - -
1E SER* 4.7 6.1 - - - -
147E ASP* 5.6 0.9 - - + +
148E SER* 4.8 2.9 - - - -
150E VAL* 3.9 8.9 - - - +
152E THR* 3.8 15.6 - - - +
166E ASN* 3.5 51.3 - - + +
167E PHE 3.7 10.1 - - - -
168E GLY* 1.3 80.1 + - - +
170E ILE* 1.3 66.8 + - - +
171E ASP* 4.0 22.2 + - + -
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Residues in contact with ILE 170 (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 SER* 6.2 0.9 - - - -
150E VAL* 4.4 11.0 - - + -
152E THR* 3.9 19.5 - - + -
169E PHE* 1.3 81.0 - - - +
171E ASP* 1.3 60.1 + - - +
172E THR* 2.9 20.9 + - + +
175E TYR* 3.8 29.6 - - + +
179E ILE* 4.0 9.2 - - + -
181E TYR* 3.6 23.1 - - + +
311E PHE* 4.1 4.9 - - + -
313E VAL* 3.8 16.6 - - + -
315E ASN* 6.1 1.6 - - - +
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Residues in contact with ASP 171 (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 THR* 5.4 0.2 - - - +
166E ASN* 4.1 21.4 + - - +
169E PHE* 4.0 17.1 + - + -
170E ILE* 1.3 68.4 - - - +
172E THR* 1.3 54.5 + - - +
173E THR* 2.7 52.0 + - - +
174E ALA* 2.9 27.9 + - + +
175E TYR* 3.5 11.6 - - - -
311E PHE* 4.1 7.6 - - + -
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Residues in contact with THR 172 (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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170E ILE* 2.9 23.0 + - + +
171E ASP* 1.3 69.2 + - - +
173E THR* 1.3 60.5 + - - +
174E ALA 3.5 0.4 - - - -
175E TYR* 3.4 43.5 - - - +
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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