Contacts of the helix formed by residues 166 - 174 (chain A) in PDB entry 1A16
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 ARG 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP* 4.9 1.1 - - - -
130A ALA* 3.4 14.0 - - + +
131A GLN* 2.9 32.4 + - - +
132A GLY 4.7 0.8 - - - -
133A GLU* 3.0 37.7 + - - +
164A ASP* 2.9 33.4 + - - +
165A TRP* 1.3 102.0 - - + +
167A PRO* 1.3 66.1 - - + +
169A VAL 4.4 0.2 - - - +
170A HIS* 2.7 60.0 + - + +
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Residues in contact with PRO 167 (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 ASP* 3.3 31.4 - - + +
166A ARG* 1.3 90.3 - - + +
168A VAL* 1.3 61.9 + - + +
170A HIS* 4.1 4.0 - - + +
171A GLU* 3.2 23.7 + - - +
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Residues in contact with VAL 168 (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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15A LEU* 4.1 20.0 - - + -
18A GLN* 3.4 43.8 - - + +
164A ASP 5.1 1.1 + - - +
165A TRP* 3.3 9.3 + - - +
166A ARG 3.2 0.4 - - - -
167A PRO* 1.3 81.4 - - + +
169A VAL* 1.3 65.0 + - - +
171A GLU* 3.3 6.5 + - - +
172A MET* 3.0 24.1 + - - +
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Residues in contact with VAL 169 (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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15A LEU* 4.2 16.6 - - + -
48A ASP* 3.4 28.0 - - + +
51A TYR* 4.5 4.9 - - + -
52A PHE* 3.7 38.8 - - + -
165A TRP* 2.9 42.6 + - + +
166A ARG 4.0 0.7 - - - +
168A VAL* 1.3 77.6 - - - +
170A HIS* 1.3 57.3 + - + +
172A MET* 3.1 11.3 + - - +
173A ARG* 2.8 32.1 + - - +
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Residues in contact with HIS 170 (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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48A ASP* 2.7 40.8 + - - -
133A GLU* 5.9 0.2 - - - -
166A ARG* 2.7 52.6 + - + +
167A PRO* 4.2 4.2 - - + +
169A VAL* 1.3 73.0 - - + +
171A GLU* 1.3 59.6 + - - +
173A ARG* 3.7 2.1 - - - +
174A LEU* 3.0 26.2 + - - +
363A VAL* 3.4 47.2 - - + +
364A GLY* 4.1 11.8 + - - +
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Residues in contact with GLU 171 (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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167A PRO 3.2 18.9 + - - +
168A VAL* 3.6 6.5 - - - +
169A VAL 3.3 0.2 - - - -
170A HIS* 1.3 74.4 - - - +
172A MET* 1.3 66.7 + - + +
174A LEU* 3.4 9.7 + - - +
175A PHE* 3.1 37.0 - - + -
364A GLY* 5.4 0.9 - - - -
365A VAL* 5.0 5.4 + - - +
372A ARG* 2.7 45.3 + - - -
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Residues in contact with MET 172 (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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11A ARG* 3.6 28.5 - - + +
14A ALA* 3.8 16.2 - - + -
15A LEU* 4.6 7.9 - - - -
18A GLN* 3.8 26.0 - - - +
51A TYR* 3.6 31.2 + - + +
52A PHE* 4.3 7.2 - - + -
168A VAL* 3.0 20.7 + - - +
169A VAL* 3.2 15.7 - - - +
171A GLU* 1.3 77.2 - - + +
173A ARG* 1.3 61.2 + - - +
175A PHE* 3.1 27.0 + - - +
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Residues in contact with ARG 173 (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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47A SER* 3.6 15.5 - - - -
48A ASP* 2.7 47.0 + - - -
51A TYR* 3.6 41.5 - - + -
169A VAL* 2.8 18.3 + - - +
170A HIS* 3.7 0.9 + - - +
172A MET* 1.3 75.5 - - - +
174A LEU* 1.3 58.3 + - - +
175A PHE 3.3 1.1 + - - -
176A LYS* 2.9 29.7 + - - +
180A GLU* 5.1 2.6 - - - +
358A LEU* 3.7 18.7 - - + +
359A ASP* 2.9 21.8 + - - -
362A ASP* 2.8 29.8 + - - +
363A VAL* 3.5 37.8 - - + +
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Residues in contact with LEU 174 (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 HIS 3.0 13.3 + - - +
171A GLU* 3.4 19.3 - - - +
172A MET 3.1 0.6 - - - -
173A ARG* 1.3 76.0 - - - +
175A PHE* 1.3 68.5 + - + +
176A LYS* 3.9 9.2 + - - +
355A TRP* 3.5 49.8 - - + +
363A VAL 4.2 7.6 - - - +
364A GLY* 4.2 10.8 - - - -
365A VAL 4.4 2.0 - - - +
372A ARG* 3.2 40.2 - - - +
377A GLY 3.6 10.0 - - - +
378A MET* 3.6 20.3 - - + +
379A VAL 4.5 0.2 + - - -
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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