Contacts of the helix formed by residues 183 - 189 (chain B) in PDB entry 4M6W
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 SER 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2026A ILE 3.8 8.7 - - - -
2027A HIS 4.2 3.8 - - - -
2028A TYR 3.3 21.1 - - - -
2029A VAL* 4.1 9.6 - - - +
2030A PHE* 5.8 0.9 - - - -
178B LEU* 6.1 1.3 - - - -
181B PHE 2.8 10.9 + - - +
182B PRO* 1.3 75.0 - - - +
184B ILE* 1.3 59.9 + - - +
185B GLN* 3.4 9.2 + - - +
186B GLN* 3.0 31.4 + - - +
187B LEU* 2.9 29.6 + - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975A PHE* 4.0 21.8 - - + -
2000A MET* 5.7 0.7 - - + -
2001A ALA* 4.8 3.6 - - + -
2025A TYR* 4.1 11.7 - - + +
2026A ILE* 3.3 32.2 + - + +
2028A TYR 4.9 0.2 + - - -
159B LEU* 3.7 30.7 - - + -
162B THR* 4.1 24.0 - - + -
163B VAL* 4.4 19.1 - - + -
166B ILE* 6.0 0.9 - - + -
178B LEU* 6.4 0.7 - - + -
183B SER* 1.3 71.4 - - - +
185B GLN* 1.3 60.9 + - - +
187B LEU* 3.4 8.1 + - + +
188B SER* 2.9 28.4 + - - -
211B PHE* 4.5 12.1 - - + -
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Residues in contact with GLN 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001A ALA* 4.1 14.3 + - - +
2002A ASN* 3.5 26.0 + - - +
2026A ILE* 3.2 14.4 + - - +
2027A HIS* 3.2 40.1 + - + +
183B SER* 3.5 9.0 + - - +
184B ILE* 1.3 74.5 - - - +
186B GLN* 1.3 63.2 + - + +
188B SER* 2.4 32.0 + - - -
189B ASN* 3.0 13.9 - - - +
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2029A VAL* 3.8 22.4 - - - +
180B LYS 4.8 0.5 - - - +
181B PHE* 4.0 19.9 - - + -
182B PRO* 3.2 31.5 - - - +
183B SER* 3.0 25.6 + - - +
185B GLN* 1.3 81.2 + - + +
187B LEU* 1.3 61.5 + - - +
188B SER 3.4 0.2 + - - -
189B ASN* 3.5 16.1 - - - +
190B ALA* 3.5 16.8 + - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 4.3 28.0 - - + -
166B ILE* 5.6 4.5 - - + -
177B LEU* 4.0 34.1 - - + +
178B LEU* 4.3 14.4 - - + -
181B PHE* 3.8 28.9 - - + +
183B SER 2.9 25.7 + - - +
184B ILE* 3.6 9.6 - - + +
185B GLN 3.2 0.2 - - - -
186B GLN* 1.3 77.8 - - - +
188B SER* 1.3 61.2 + - - +
190B ALA* 3.4 15.7 - - - +
195B LEU* 4.9 5.9 - - + +
207B ILE* 5.0 11.2 - - + +
211B PHE* 3.5 20.7 - - + -
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998A LYS* 4.0 17.8 + - - +
2001A ALA* 3.6 15.6 - - - +
2002A ASN* 3.4 16.9 + - - -
184B ILE 2.9 13.2 + - - -
185B GLN 2.4 25.0 + - - -
187B LEU* 1.3 78.6 - - - +
189B ASN* 1.3 60.7 + - - +
190B ALA 3.3 5.7 + - - +
208B HIS* 5.4 4.5 - - - -
211B PHE* 3.7 43.3 - - - +
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1998A LYS* 3.6 22.9 - - - +
2002A ASN* 2.9 35.0 + - - +
185B GLN* 3.0 19.5 + - - +
186B GLN* 3.5 14.3 - - - +
188B SER* 1.3 76.9 + - - +
190B ALA* 1.3 57.7 + - - +
191B SER 4.2 1.1 + - - -
194B GLU* 5.0 1.0 - - - +
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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