Contacts of the helix formed by residues 179 - 184 (chain A) in PDB entry 2QVH
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLU* 2.9 22.9 - - + +
157A GLN* 2.9 8.8 - - - +
177A ALA 4.1 0.8 + - - -
178A ALA* 1.3 73.4 - - - +
180A GLU* 1.3 64.2 + - - +
181A SER 3.1 0.7 - - - -
182A ILE* 2.7 25.7 + - - +
183A ARG* 2.7 46.7 + - - +
201A VAL* 3.9 14.3 - - + +
203A LYS* 3.4 9.3 - - - +
401A MG 2.1 27.6 - - - -
5550A OSB 3.1 11.3 + - - +
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Residues in contact with GLU 180 (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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132A ASN* 2.9 41.5 + - - +
157A GLN* 3.3 32.0 - - + +
160A ALA* 5.4 3.6 - - - +
179A ASP* 1.3 82.9 - - - +
181A SER* 1.3 57.4 + - - +
182A ILE 3.1 0.7 + - - -
183A ARG* 3.3 33.9 + - - +
184A ARG* 2.8 45.1 + - + +
401A MG 4.2 1.2 - - - -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLN* 2.9 27.2 + - - +
160A ALA 4.0 5.6 + - - -
162A VAL* 3.6 35.4 + - - +
165A LEU* 3.7 9.7 - - - +
178A ALA* 4.4 1.6 - - - -
179A ASP 3.1 0.8 - - - -
180A GLU* 1.3 76.7 - - - +
182A ILE* 1.3 58.5 + - - +
184A ARG 4.9 0.4 - - - -
185A ALA* 3.1 23.7 - - - +
187A ASP 4.8 0.3 - - - +
188A PRO* 4.0 6.1 - - - +
191A VAL* 3.9 18.6 - - - +
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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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49A ARG* 5.1 1.0 + - - -
178A ALA* 3.5 25.6 - - + +
179A ASP 2.7 8.7 + - - +
181A SER* 1.3 80.1 - - - +
183A ARG* 1.3 62.6 + - + +
184A ARG 3.5 0.4 - - - -
185A ALA 4.4 1.6 + - - -
188A PRO* 3.3 42.3 - - + +
191A VAL* 3.6 26.9 - - + -
200A VAL* 3.8 25.1 - - + -
201A VAL 3.6 18.4 - - - +
202A LEU* 4.7 0.4 - - + -
207A LEU* 4.0 14.3 - - + +
216A LEU* 3.9 20.2 - - + -
220A CYS* 4.6 6.1 - - - -
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Residues in contact with ARG 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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42A TYR* 4.7 7.3 + - - -
49A ARG* 3.5 21.3 + - - -
50A TRP* 6.3 0.6 - - - -
132A ASN* 4.4 0.2 - - - +
179A ASP* 2.7 50.3 + - - +
180A GLU* 3.3 29.6 + - - +
182A ILE* 1.3 79.7 - - + +
184A ARG* 1.3 86.5 + - + +
185A ALA 3.7 0.9 - - - -
201A VAL 5.9 0.7 - - - +
203A LYS* 3.4 26.8 - - + +
206A PRO* 3.9 32.2 - - + +
207A LEU* 3.8 17.3 - - + -
5550A OSB 3.8 20.5 - - - -
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Residues in contact with ARG 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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17A ARG* 5.9 0.2 - - - +
41A GLU* 5.7 2.0 + - - +
42A TYR* 3.7 34.7 + - - -
46A GLU* 3.2 26.1 + - - -
49A ARG* 5.3 0.9 - - - +
180A GLU* 2.8 31.8 + - + +
181A SER* 4.9 0.5 - - - -
183A ARG* 1.3 103.2 - - + +
185A ALA* 1.3 56.7 + - - +
206A PRO* 6.1 1.6 - - + -
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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