Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 4B94
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A VAL* 4.0 35.4 - - + +
174A ALA 4.0 10.6 + - - +
175A VAL* 4.1 3.0 - - + +
176A PRO* 1.3 71.3 - - - +
178A GLU* 1.3 62.1 + - - +
180A LEU* 3.0 20.1 + - + +
181A GLU* 3.1 40.2 + - + +
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Residues in contact with GLU 178 (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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176A PRO* 3.3 7.3 - - + +
177A LEU* 1.3 77.6 - - - +
179A MET* 1.3 56.3 + - - +
181A GLU* 3.2 14.4 + - - +
182A ILE* 3.0 49.4 + - + +
185A ARG* 3.2 27.2 + - - -
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Residues in contact with MET 179 (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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143A ALA* 4.4 2.5 - - + -
144A PHE* 3.9 32.5 - - + -
147A ILE* 3.6 25.8 - - + +
176A PRO* 3.4 37.8 + - + +
177A LEU 3.3 0.4 - - - -
178A GLU* 1.3 77.1 - - - +
180A LEU* 1.4 57.6 + - - +
182A ILE* 3.5 12.1 + - + +
183A ALA* 3.1 27.5 + - - +
195A LEU* 3.8 22.4 - - + +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ALA* 3.8 17.7 - - + +
146A HIS* 4.6 0.7 - - + -
147A ILE* 3.9 25.1 - - + -
166A LEU* 4.3 12.6 - - + +
169A ALA* 3.7 24.7 - - + +
170A VAL* 3.8 40.4 - - + +
174A ALA* 3.5 27.8 - - + +
176A PRO 4.2 2.2 - - - +
177A LEU* 3.0 13.7 + - + +
179A MET* 1.4 73.2 - - - +
181A GLU* 1.4 60.0 + - - +
183A ALA* 3.4 3.3 + - - +
184A LEU* 2.9 34.5 + - - +
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Residues in contact with GLU 181 (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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170A VAL* 5.6 4.0 - - + +
177A LEU* 3.1 43.7 + - + +
178A GLU* 3.2 18.1 + - - +
180A LEU* 1.4 71.7 - - + +
182A ILE* 1.4 60.6 + - - +
184A LEU* 3.4 10.1 + - + +
185A ARG* 3.0 47.8 + - - +
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Residues in contact with ILE 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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178A GLU* 3.0 42.1 + - + +
179A MET* 3.7 9.6 - - + +
181A GLU* 1.4 75.3 - - - +
183A ALA* 1.4 56.9 + - - +
185A ARG* 3.2 26.4 + - - +
186A ASN* 3.0 46.3 + - - +
195A LEU* 4.1 14.4 - - + -
198A GLU* 5.8 11.7 - - + +
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Residues in contact with ALA 183 (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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147A ILE* 4.1 11.2 - - + -
166A LEU* 3.9 26.5 - - + -
179A MET 3.1 18.3 + - - +
180A LEU 3.6 5.2 - - - +
181A GLU 3.4 0.2 - - - -
182A ILE* 1.4 76.1 - - - +
184A LEU* 1.4 55.5 + - - +
186A ASN* 3.4 1.0 + - - -
187A LEU* 3.0 23.9 + - - +
194A LEU* 3.5 36.5 - - + +
195A LEU* 4.2 2.2 - - + +
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Residues in contact with LEU 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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163A LYS* 4.3 19.3 - - + -
166A LEU* 3.8 33.4 - - + +
167A GLN* 4.2 21.8 - - + +
170A VAL* 3.9 25.6 - - + -
180A LEU 2.9 21.3 + - - +
181A GLU* 3.8 8.5 - - + +
183A ALA* 1.4 71.3 - - - +
185A ARG* 1.4 59.6 + - - +
187A LEU* 3.4 4.1 + - + +
188A ASN* 3.0 38.8 + - - +
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Residues in contact with ARG 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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178A GLU* 3.2 24.7 + - - -
181A GLU* 3.0 32.5 + - - +
182A ILE* 3.2 31.6 + - - +
184A LEU* 1.4 74.6 - - - +
186A ASN* 1.4 59.9 + - - +
188A ASN* 3.3 7.6 + - - +
189A LEU* 2.9 41.8 + - + +
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Residues in contact with ASN 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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182A ILE* 3.0 27.5 + - - +
183A ALA 3.8 1.8 - - - +
185A ARG* 1.4 74.5 - - - +
187A LEU* 1.4 62.2 + - - +
189A LEU* 3.4 5.6 + - - +
190A GLN 3.2 4.3 + - - -
191A LYS* 2.9 66.4 + - + +
193A GLN 3.9 13.8 + - - +
194A LEU* 2.7 34.3 + - - +
195A LEU* 4.4 3.2 - - - +
196A SER* 5.0 4.0 - - - +
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Residues in contact with LEU 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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154A LEU* 3.7 31.0 - - + -
159A VAL* 4.2 18.8 - - + +
162A SER* 3.8 13.2 - - - +
163A LYS* 3.5 48.2 - - + +
166A LEU* 3.9 12.6 - - + -
183A ALA 3.0 17.2 + - - +
184A LEU* 3.7 7.2 - - + +
185A ARG 3.3 0.2 - - - -
186A ASN* 1.4 74.6 - - - +
188A ASN* 1.3 58.1 + - - +
190A GLN* 3.0 23.3 + - - +
191A LYS 4.9 2.9 - - - +
194A LEU* 3.8 11.6 - - + +
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Residues in contact with ASN 188 (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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163A LYS* 4.0 30.9 + - - +
184A LEU* 3.0 27.8 + - - +
185A ARG* 3.3 7.4 + - - +
187A LEU* 1.3 73.1 - - - +
189A LEU* 1.4 57.3 + - + +
190A GLN* 3.1 16.3 + - - +
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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