Contacts of the strand formed by residues 181 - 187 (chain A) in PDB entry 6O81
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 MET 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 6.3 0.7 - - + -
150A LEU* 4.8 8.5 - - + -
168A HIS* 4.5 0.7 - - - -
179A SER* 4.4 1.2 + - - -
180A VAL* 1.3 84.8 - - + +
182A THR* 1.3 64.7 + - - +
183A MET* 4.1 17.3 - - + +
250A SER* 3.8 19.1 - - - +
251A ILE 3.7 9.9 - - - +
252A CYS* 3.8 14.1 - - + +
256A VAL* 3.8 18.4 - - + -
260A PHE* 6.1 0.9 - - + -
269A ARG* 5.0 7.0 - - + -
272A PHE* 3.7 31.4 - - + -
273A VAL* 4.4 12.3 - - - -
286A GLN 4.6 0.6 + - - -
287A ILE* 3.3 23.7 - - + +
288A HIS* 2.9 26.0 + - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA* 4.7 6.7 - - + +
167A GLU* 6.1 0.2 - - - +
168A HIS* 2.8 32.0 + - - -
171A ARG* 3.1 25.2 + - - +
181A MET* 1.3 70.8 + - - +
183A MET* 1.3 70.1 + - - +
184A ILE* 3.8 2.7 + - + +
250A SER* 3.5 0.3 - - - -
251A ILE* 2.7 55.0 + - + +
288A HIS* 3.3 10.3 - - - +
289A MET 4.5 0.2 - - - -
290A HIS* 4.4 16.8 - - + +
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A MET* 4.1 6.5 - - + -
182A THR* 1.3 74.6 - - - +
184A ILE* 1.3 60.6 + - - +
185A PHE* 3.7 33.7 - - + -
212A VAL* 4.5 12.8 - - + -
215A PHE* 3.8 25.1 - - + -
246A ASP* 5.9 0.2 - - - +
250A SER* 3.7 12.6 - - - -
269A ARG* 3.4 29.6 - - - +
273A VAL* 4.3 20.0 - - + -
287A ILE* 3.7 25.8 - - + -
288A HIS 2.9 10.1 + - - +
289A MET* 3.3 5.7 - - + -
290A HIS 2.9 26.0 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 4.7 4.7 - - + -
161A ILE* 3.7 35.4 - - + -
164A ALA* 4.9 3.6 - - + -
182A THR* 3.9 7.6 - - + +
183A MET* 1.3 78.5 - - - +
185A PHE* 1.3 70.4 + - - +
246A ASP* 3.7 10.4 - - - +
247A CYS* 3.3 32.1 + - - -
248A HIS 4.6 1.0 + - - -
249A ILE* 3.3 29.6 + - + +
250A SER* 4.3 4.8 - - - +
251A ILE* 4.6 9.6 - - + -
290A HIS* 3.5 16.6 - - + +
292A THR* 3.9 25.6 - - + -
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Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 6.2 0.2 - - - -
183A MET* 3.7 41.3 - - + -
184A ILE* 1.3 78.9 - - - +
186A LYS* 1.3 60.6 + - - +
201A VAL* 3.9 24.5 - - + -
203A VAL* 4.2 9.2 - - + -
212A VAL* 5.8 0.7 - - + -
215A PHE* 4.3 0.7 - + - -
244A LEU* 3.6 35.9 - - + -
245A LEU 3.5 17.0 - - - -
246A ASP* 3.5 31.2 - - + -
247A CYS* 4.6 3.1 - - - -
289A MET* 3.6 28.9 - - + -
290A HIS 2.9 9.2 + - - +
291A VAL* 3.4 4.4 - - + -
292A THR* 2.9 29.1 + - - +
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 5.8 0.9 - - + -
185A PHE* 1.3 75.0 - - - +
187A GLU* 1.3 71.6 + - - +
188A SER 3.3 0.3 + - - -
243A ASP 3.4 2.9 - - - +
244A LEU* 3.4 4.7 - - - -
245A LEU* 2.9 45.3 + - + +
247A CYS* 5.8 0.9 - - + -
292A THR* 3.4 17.2 + - - +
293A ALA 4.6 5.1 + - - -
295A GLU 2.4 32.0 + - - +
296A TYR* 3.7 16.2 - - + -
297A GLY* 3.6 29.4 - - - +
292D GLU* 2.7 21.6 + - - -
297D PHE* 3.6 36.8 - - + +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LYS* 1.3 75.4 + - - +
188A SER* 1.3 60.8 + - - +
241A ARG* 3.5 25.8 + - - +
243A ASP* 3.5 11.2 - - - +
244A LEU* 4.6 1.3 - - + +
291A VAL* 4.6 15.6 - - + +
292A THR 2.9 20.3 + - - +
293A ALA* 4.1 23.4 - - + +
297D PHE* 3.7 16.1 - - - +
298D THR* 3.6 24.6 - - + +
192I ARG* 3.8 12.7 + - - -
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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