Contacts of the strand formed by residues 176 - 184 (chain E) in PDB entry 5HMG
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 LYS 176 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E GLU* 2.6 27.9 + - - -
168E MET* 4.4 0.2 - - - +
169E PRO 3.2 19.3 + - - -
170E ASN* 3.3 33.2 - - + +
171E ASN 5.4 0.2 - - - +
172E ASP* 4.5 9.6 - - - -
174E PHE* 4.1 4.9 - - + -
175E ASP* 1.3 76.6 - - - +
177E LEU* 1.3 58.3 + - - +
178E TYR* 3.0 27.9 + - + +
235E THR 3.8 0.5 - - - +
236E ILE* 3.3 4.3 - - - +
237E VAL* 2.8 35.5 + - + +
257E TYR* 3.5 44.0 - - + -
258E PHE 3.8 4.7 - - - -
260E MET* 4.8 0.7 - - - -
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Residues in contact with LEU 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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70E LEU* 4.7 7.4 - - + -
111E LEU* 4.1 9.6 - - + -
112E VAL* 4.8 9.0 - - + -
176E LYS* 1.3 72.6 - - - +
178E TYR* 1.3 62.3 + - - +
179E ILE* 3.9 15.0 - - + -
234E TRP* 3.9 30.7 - - + -
235E THR 3.7 2.7 - - - +
236E ILE* 3.9 19.3 - - + +
257E TYR* 3.6 2.5 - - - -
258E PHE* 2.9 61.6 + - + +
260E MET* 3.7 33.6 - - + +
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Residues in contact with TYR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E GLU* 2.8 30.6 + - - -
125E PHE* 3.9 8.5 - + - -
168E MET* 3.5 12.2 + - + +
169E PRO 5.3 0.2 - - - -
176E LYS* 3.0 36.4 + - + +
177E LEU* 1.3 73.7 - - - +
179E ILE* 1.3 60.6 + - - +
180E TRP* 3.8 9.6 - - + -
234E TRP* 3.3 4.3 - - - -
235E THR* 2.8 37.8 + - - +
237E VAL* 3.5 34.9 - - + +
243E LEU* 3.7 31.0 - - + -
254E PRO* 4.2 15.7 - - + -
256E GLY 3.2 28.7 - - - -
257E TYR* 4.0 2.2 - - + -
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Residues in contact with ILE 179 (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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70E LEU* 3.9 10.8 - - + -
71E LEU* 3.6 29.4 - - + -
108E LEU* 3.7 23.3 - - + -
150E ARG* 5.0 2.2 - - + +
151E LEU* 3.5 15.0 - - + +
177E LEU* 3.9 11.6 + - + -
178E TYR* 1.3 71.1 - - - +
180E TRP* 1.3 63.9 + - - +
232E ILE* 3.7 15.9 - - + -
233E TYR 3.4 2.5 - - - +
234E TRP* 3.7 25.8 - - + -
254E PRO* 3.5 17.8 - - - +
256E GLY 5.1 1.2 + - - -
258E PHE* 3.8 30.9 - - + -
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Residues in contact with TRP 180 (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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151E LEU* 4.1 9.0 - - - -
178E TYR* 3.8 20.9 - - + -
179E ILE* 1.3 76.2 - - - +
181E GLY* 1.3 82.8 + - - +
182E ILE* 5.3 0.4 - - + -
202E VAL* 3.8 22.7 - - + -
204E VAL* 3.4 39.0 - - + +
211E GLN* 3.7 19.1 - - + -
213E ILE* 3.3 29.2 - - + -
232E ILE* 3.6 8.9 - - - +
233E TYR* 2.8 54.8 + + + +
234E TRP 4.1 0.8 - - - -
235E THR* 2.9 23.9 + - - +
243E LEU* 6.3 0.2 - - + -
245E ILE* 6.1 1.3 - - + -
251E LEU* 4.9 2.7 - - + -
252E ILE 3.8 12.1 - - - +
254E PRO* 3.9 17.5 - - + -
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Residues in contact with GLY 181 (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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180E TRP* 1.3 91.1 - - - +
182E ILE* 1.3 62.0 + - - +
202E VAL* 4.6 0.7 - - - +
230E ILE* 5.9 0.4 - - - -
231E SER 3.2 14.4 - - - -
232E ILE* 4.4 3.4 - - - -
233E TYR* 4.3 1.3 - - - -
251E LEU* 3.7 9.4 - - - +
252E ILE* 3.0 37.8 + - - +
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Residues in contact with ILE 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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180E TRP* 5.3 0.4 - - + -
181E GLY* 1.3 75.1 - - - +
183E HIS* 1.3 63.6 + - - +
184E HIS* 4.0 19.0 + - + +
201E ARG 4.9 0.2 - - - -
202E VAL* 3.7 19.5 - - + +
213E ILE* 3.5 49.1 - - + +
215E PRO* 3.5 27.6 - - + -
230E ILE* 3.3 4.7 - - - +
231E SER 3.1 26.8 + - - +
233E TYR* 4.1 13.0 - - + -
250E ASN* 3.2 20.6 - - + +
252E ILE* 4.1 4.7 - - - +
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Residues in contact with HIS 183 (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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98E TYR* 2.9 28.8 + + - -
153E TRP* 3.8 10.7 - + - -
182E ILE* 1.3 72.2 - - - +
184E HIS* 1.3 59.8 + - - +
185E PRO* 3.6 13.2 - - + +
190E GLU* 3.3 22.5 + - - -
194E LEU* 3.8 13.9 - - + -
195E TYR* 2.8 37.3 + - + +
215E PRO* 3.4 7.6 - - - +
228E SER* 4.0 1.8 - - - -
229E ARG 4.0 5.2 - - - -
230E ILE* 3.7 23.1 - - + -
250E ASN* 2.8 38.9 + - - +
252E ILE* 4.1 8.3 - - + +
329E SIA 3.7 4.0 + - - -
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Residues in contact with HIS 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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210A GLN* 3.8 18.7 + - - -
182E ILE* 4.1 14.2 - - + +
183E HIS* 1.3 73.9 - - - +
185E PRO* 1.3 65.7 - - - +
213E ILE* 5.2 2.2 - - + -
214E ILE 4.3 3.1 - - - -
215E PRO* 3.3 11.7 - - + +
216E ASN* 2.7 54.8 + - - +
220E ARG* 3.3 13.8 + - - +
228E SER* 3.3 20.3 - - - -
229E ARG 2.9 23.2 + - - +
231E SER* 2.8 34.5 + - - -
233E TYR* 5.9 0.4 - - - -
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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