Contacts of the strand formed by residues 179 - 184 (chain E) in PDB entry 5IJ7
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 ILE 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134E TYR* 3.6 18.0 - - - +
135E THR* 4.1 3.4 - - + +
152E ALA* 3.9 16.2 - - + -
153E GLY* 2.9 16.3 + - - +
156E GLY* 3.5 32.8 - - - +
158E ILE* 3.7 26.0 - - + -
175E HIS* 3.6 27.8 - - + +
178E ALA* 1.4 73.4 - - - +
180E ASN* 1.3 60.9 + - - +
181E GLU 3.4 25.8 - - - +
182E LEU* 3.6 17.9 - - + -
194E SER* 4.1 0.4 - - - -
195E VAL 3.4 10.8 - - - +
196E SER* 4.6 0.2 - - - -
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Residues in contact with ASN 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E TYR* 3.9 18.9 - - - -
135E THR* 3.7 9.4 - - - -
178E ALA* 4.7 4.2 - - - +
179E ILE* 1.3 75.2 - - - +
181E GLU* 1.3 60.4 + - - +
195E VAL 2.8 6.5 + - - -
197E LYS 3.9 8.3 - - - +
224E GLU* 2.8 34.0 + - - +
225E VAL 2.8 25.0 + - - +
226E LEU* 3.6 21.1 - - - +
350E TRP* 5.5 2.3 - - - -
351E TYR* 2.8 39.3 + - + -
353E ARG* 3.0 9.5 + - - -
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Residues in contact with GLU 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E GLN* 5.4 0.9 - - - +
135E THR* 3.7 15.8 + - - -
179E ILE* 3.4 6.5 - - - +
180E ASN* 1.3 78.4 - - - +
182E LEU* 1.3 69.1 + - - +
183E LYS* 3.7 22.0 - - + -
193E LEU 4.4 0.4 - - - -
194E SER* 3.4 1.0 - - - -
195E VAL* 2.9 45.4 + - + +
226E LEU 4.1 6.5 - - - +
227E SER* 2.7 31.5 + - - -
228E ALA 3.8 4.9 + - - +
299E ARG* 3.2 24.4 + - - -
353E ARG* 3.9 18.5 + - - -
401E GLN* 4.2 8.1 + - - -
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Residues in contact with LEU 182 (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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135E THR* 3.4 17.1 + - + +
136E CYS 4.2 3.3 - - - +
137E ALA* 3.7 18.3 - - + +
150E ALA* 3.6 25.1 - - + +
151E VAL* 3.6 32.5 - - - +
152E ALA* 3.9 8.5 - - + +
158E ILE* 4.2 12.6 - - + -
179E ILE* 3.6 28.3 - - + -
181E GLU* 1.3 74.6 - - - +
183E LYS* 1.3 71.0 + - - +
192E LEU* 3.8 15.3 - - + -
193E LEU 3.2 3.6 - - - +
194E SER* 3.8 16.4 - - - -
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Residues in contact with LYS 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E GLN* 5.1 14.5 + - - +
137E ALA* 4.4 2.9 - - - -
181E GLU* 3.7 21.5 + - + -
182E LEU* 1.3 77.0 - - - +
184E PHE* 1.3 58.3 + - - +
192E LEU* 3.6 7.2 - - - +
193E LEU* 2.8 47.5 + - + +
228E ALA* 3.5 19.3 - - + +
229E ASP* 4.0 14.7 + - - +
230E TYR* 3.6 19.1 - - + +
299E ARG* 3.4 40.4 - - - +
401E GLN* 5.9 0.2 - - - +
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Residues in contact with PHE 184 (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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90E HIS* 6.0 0.9 - - + -
137E ALA* 3.5 36.1 - - + +
138E TRP 3.6 21.8 - - - +
139E THR* 3.4 27.8 - - + +
150E ALA* 3.6 19.5 - - + -
160E ILE* 4.5 7.2 - - + -
183E LYS* 1.3 72.6 - - - +
185E HIS* 1.3 68.0 + - - +
186E PRO* 3.4 4.2 - - - +
189E PRO* 3.4 26.9 - - + +
190E ASN 4.9 0.2 - - - -
191E LEU 3.6 12.3 - - - -
192E LEU* 3.7 32.1 - - + -
206E ILE* 4.8 9.4 - - + -
230E TYR* 3.5 9.6 - - - -
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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