Contacts of the helix formed by residues 162 - 167 (chain A) in PDB entry 3H1S
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 TYR 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR* 5.4 0.7 - - - -
157A VAL* 3.6 21.5 - - - -
158A TRP 3.6 12.3 - - - -
159A GLU* 3.6 22.9 + - - +
160A HIS 4.7 0.2 - - - -
161A ALA* 1.3 81.3 - - + +
163A TYR* 1.3 68.6 + + - +
164A ILE* 3.2 3.1 - - - -
165A ASP* 3.0 6.5 + - - +
166A TYR* 2.8 37.3 + - + +
167A ARG 3.3 27.4 - - - -
168A ASN* 4.6 4.2 + - - -
170A ARG* 3.0 54.6 + - + +
173A TYR* 3.4 47.1 - + + -
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 2.9 34.2 + - + +
160A HIS 4.2 1.8 + - - -
162A TYR* 1.3 80.0 - + - +
164A ILE* 1.3 60.8 + - - +
167A ARG* 2.9 75.2 + - + -
168A ASN* 3.6 4.1 + - - -
26B TYR* 3.8 13.7 - - - +
27B HIS 5.1 0.2 + - - -
31B HIS* 2.6 38.2 + + - -
160B HIS* 3.6 24.5 + - + +
163B TYR* 4.3 28.3 - + + -
164B ILE* 3.7 29.6 - - + -
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 4.3 1.8 - - - +
22A GLU* 3.7 27.1 - - + +
23A THR* 3.5 31.4 - - - +
26A TYR* 4.0 17.0 - - + -
160A HIS 5.2 4.5 - - - +
162A TYR 3.2 0.8 - - - -
163A TYR* 1.3 76.7 - - - +
165A ASP* 1.3 70.8 + - - +
167A ARG* 3.0 20.9 + - - +
163B TYR* 3.7 27.6 - - + +
167B ARG* 3.8 30.3 - - - +
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Residues in contact with ASP 165 (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 SER 6.0 0.7 - - - +
18A THR 4.4 1.3 - - - +
19A ILE* 3.7 7.0 - - - +
20A SER* 2.6 46.9 + - - -
23A THR* 2.8 23.8 + - - +
161A ALA 5.1 1.7 - - - +
162A TYR* 3.0 3.8 + - - +
164A ILE* 1.3 83.8 - - - +
166A TYR* 1.3 88.8 + - + +
167A ARG* 5.7 0.7 - - - -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 4.1 3.5 + - - -
18A THR* 2.6 33.5 + - - -
19A ILE* 5.4 0.7 - - + -
162A TYR* 2.8 16.6 + - + +
165A ASP* 1.3 95.8 - - + +
167A ARG* 1.3 75.5 + - - +
168A ASN* 4.6 0.2 - - - +
169A ALA* 2.9 35.9 + - + +
172A LYS* 3.9 19.7 - - + -
173A TYR* 3.7 49.1 - + + -
176A ALA* 3.2 20.5 - - + +
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Residues in contact with ARG 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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162A TYR* 3.3 17.0 - - - -
163A TYR* 2.9 63.1 + - + -
164A ILE* 3.0 25.1 + - - +
165A ASP 5.7 0.4 - - - -
166A TYR* 1.3 80.9 - - - +
168A ASN* 1.3 61.2 + - - +
22B GLU* 2.7 33.9 + - - -
26B TYR* 3.4 37.2 - - + +
164B ILE* 3.7 35.8 - - - +
167B ARG* 5.4 9.3 - - - +
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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