Contacts of the strand formed by residues 170 - 177 (chain E) in PDB entry 3X0X
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 170 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 4.4 20.6 - - + +
120E ILE* 3.7 28.0 - - + -
125E TRP* 3.8 26.9 - - + -
126E TRP 3.3 2.0 + - - +
127E THR* 3.2 12.7 - - + -
128E GLY 2.9 24.9 + - - -
168E SER* 4.0 1.4 - - - -
169E ASP* 1.3 80.4 - - - +
171E LEU* 1.3 60.4 + - - +
172E PHE* 3.6 31.6 + - + -
191E ALA* 4.2 14.8 - - + +
192E ILE 3.8 20.4 - - - +
193E PRO* 4.3 3.8 - - + -
194E THR* 3.7 1.6 - - - -
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Residues in contact with LEU 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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128E GLY 3.7 17.9 - - - +
129E ASN* 3.9 12.1 - - - +
130E ALA* 4.3 2.9 - - + +
165E ALA* 4.0 21.3 - - + -
168E SER* 4.4 1.6 - - - +
170E LEU* 1.3 73.8 - - - +
172E PHE* 1.3 69.4 + - - +
173E VAL* 3.8 4.4 + - + -
190E ALA 3.5 1.6 - - - +
191E ALA* 3.4 2.0 - - - -
192E ILE* 2.7 54.7 + - + +
194E THR* 3.6 18.4 + - + +
199E VAL* 3.7 30.1 - - + -
201E PRO* 5.8 0.2 - - + -
218E THR* 4.8 4.5 - - + -
220E PHE* 4.2 17.7 - - + -
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Residues in contact with PHE 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ASN* 3.8 26.2 - - + +
101E ALA* 4.0 7.9 - - - -
103E MET* 3.8 38.1 - - + -
104E ILE* 3.8 29.8 - - + -
127E THR* 3.9 8.5 - - + -
128E GLY 2.9 21.6 + - - +
129E ASN* 3.2 4.5 - - + +
130E ALA 2.8 28.2 + - - -
131E SER* 4.2 0.9 + - - -
170E LEU* 3.6 36.8 - - + -
171E LEU* 1.3 75.2 - - - +
173E VAL* 1.3 59.2 + - - +
174E PHE* 5.1 2.5 - - + -
190E ALA 3.3 4.0 - - - -
191E ALA* 3.7 19.1 - - + -
231E LEU* 4.1 9.4 - - + -
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Residues in contact with VAL 173 (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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130E ALA* 3.4 13.0 - - + +
143E VAL* 4.7 1.6 - - + -
155E LEU* 3.7 29.6 - - + -
171E LEU* 4.7 6.1 - - + +
172E PHE* 1.3 75.6 - - - +
174E PHE* 1.3 73.2 + - - +
175E GLY 5.7 0.2 - - - +
188E ILE 3.4 3.3 - - - +
190E ALA* 2.9 54.9 + - + +
192E ILE* 4.2 15.7 - - + -
220E PHE* 3.6 33.0 - - + -
225E VAL* 5.1 0.2 - - + -
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Residues in contact with PHE 174 (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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103E MET* 3.7 27.1 - - + -
130E ALA 3.2 10.5 + - - +
131E SER* 3.5 50.1 - - - +
132E SER* 3.5 3.4 - - - -
141E TRP* 3.8 16.2 - + + -
143E VAL* 3.9 17.5 - - - +
159E LYS* 5.7 0.9 - - - +
172E PHE* 5.5 0.2 - - + -
173E VAL* 1.3 88.5 - - - +
175E GLY* 1.3 58.8 + - - +
187E ILE* 4.3 7.0 - - + -
188E ILE 3.2 4.5 - - - +
189E ALA* 4.1 13.2 - - + -
190E ALA 5.3 0.7 - - - -
237E PHE* 3.6 25.6 - + - -
250E PHE* 4.6 5.2 - + - -
415E PHE* 3.0 41.7 - + - -
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Residues in contact with GLY 175 (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 TRP* 4.8 1.8 - - - -
143E VAL* 3.3 18.8 - - - -
145E ALA* 4.7 8.5 - - - -
155E LEU* 4.7 3.9 - - - +
173E VAL 4.2 0.2 - - - -
174E PHE* 1.3 74.5 - - - +
176E VAL* 1.3 65.3 + - - -
186E ALA 3.5 0.2 - - - +
187E ILE* 3.4 5.2 - - - +
188E ILE* 2.8 40.8 + - - +
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Residues in contact with VAL 176 (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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138E VAL* 3.3 38.4 - - + +
139E LEU* 4.6 0.7 - - + -
141E TRP* 3.6 33.2 - - + +
143E VAL 3.0 9.9 + - - +
144E ARG* 3.3 9.0 - - + +
145E ALA* 2.8 25.3 + - - -
175E GLY* 1.3 73.3 - - - +
177E VAL* 1.3 64.2 + - - +
178E GLN* 3.4 13.7 + - - +
185E GLY* 3.7 27.6 - - - +
186E ALA 3.3 9.0 - - - +
187E ILE* 4.5 5.4 - - + -
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Residues in contact with VAL 177 (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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145E ALA 3.0 10.3 - - - +
147E PRO* 4.5 13.0 - - + -
153E TYR* 3.6 14.6 - - + +
175E GLY 4.0 0.8 + - - -
176E VAL* 1.3 69.9 - - - +
178E GLN* 1.3 64.2 + - - +
179E ASP 4.0 14.4 - - - +
183E GLN* 3.2 41.7 - - + +
184E GLN* 3.3 3.8 - - - +
185E GLY* 3.1 21.3 + - - -
186E ALA* 2.9 15.5 + - + +
188E ILE* 3.3 37.0 - - + -
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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