Contacts of the helix formed by residues 162 - 169 (chain A) in PDB entry 3SXW
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
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.4 30.3 + - - -
35A TYR* 4.2 5.9 + - - +
54A TYR* 4.9 2.4 + - - -
88A LYS* 4.3 26.2 - - + -
89A GLY 3.7 16.6 - - - +
90A HIS* 3.9 18.1 + - + -
160A HIS* 3.5 45.0 + + + -
161A ASP* 1.3 72.6 - - - +
163A GLY* 1.3 59.4 + - - +
164A THR 3.5 0.9 - - - -
165A ILE* 3.3 6.7 + - - +
166A ALA* 2.9 28.3 + - + +
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Residues in contact with GLY 163 (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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161A ASP* 3.2 6.8 + - - -
162A TYR* 1.3 75.7 - - - +
164A THR* 1.3 66.5 + - - +
166A ALA* 3.2 8.6 + - - +
167A GLU* 3.1 28.8 + - - +
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Residues in contact with THR 164 (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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91A PHE* 4.1 24.2 - - + -
113A GLN* 6.3 0.2 - - - +
115A PRO* 5.9 2.2 - - + +
161A ASP* 3.0 26.4 + - - -
162A TYR 3.5 0.2 - - - -
163A GLY* 1.3 74.5 - - - +
165A ILE* 1.3 58.9 + - + +
167A GLU* 3.1 14.3 - - - +
168A LYS* 3.0 52.7 + - + +
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Residues in contact with ILE 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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35A TYR* 4.1 7.0 - - + -
88A LYS 3.3 25.8 - - - +
89A GLY 3.8 21.3 - - - +
90A HIS* 4.1 8.5 - - - -
91A PHE* 3.7 29.2 - - + +
113A GLN* 3.8 15.7 - - - +
137A ALA* 4.3 1.1 - - + -
139A ARG* 3.8 13.2 - - - +
161A ASP 4.9 0.7 - - - +
162A TYR 3.3 7.0 + - - +
163A GLY 3.3 0.4 - - - -
164A THR* 1.3 75.6 - - + +
166A ALA* 1.3 63.2 + - - +
169A GLY* 2.8 31.4 + - - +
170A PHE* 3.7 24.7 - - + -
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Residues in contact with ALA 166 (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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33A GLU 5.6 0.7 - - - +
34A GLY* 4.6 12.6 - - - +
35A TYR* 3.5 29.8 + - + +
162A TYR* 2.9 15.9 + - + +
163A GLY* 3.2 13.4 + - - +
165A ILE* 1.3 76.8 - - - +
167A GLU* 1.3 59.9 + - - +
169A GLY 5.0 0.2 + - - -
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Residues in contact with GLU 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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163A GLY 3.1 14.2 + - - +
164A THR* 3.1 20.4 - - - +
166A ALA* 1.3 80.4 - - + +
168A LYS* 1.3 78.2 + - + +
169A GLY 3.8 0.2 - - - -
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Residues in contact with LYS 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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115A PRO 5.2 7.7 + - - -
164A THR* 3.0 37.9 + - + +
167A GLU* 1.3 95.3 - - + +
169A GLY* 1.3 63.7 + - - +
186A ASN* 4.8 1.7 + - - -
189A TRP* 2.8 46.0 + - + -
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Residues in contact with GLY 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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34A GLY 6.2 0.4 - - - -
35A TYR* 5.9 3.8 - - - -
113A GLN* 3.2 15.4 + - - -
139A ARG* 5.0 4.5 - - - -
165A ILE* 2.8 35.1 + - - +
166A ALA 5.0 0.2 + - - -
167A GLU 3.8 0.4 - - - -
168A LYS* 1.3 80.5 - - - +
170A PHE* 1.3 65.5 + - - -
186A ASN* 5.1 3.8 - - - -
189A TRP* 3.7 4.2 - - - -
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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