Contacts of the helix formed by residues 163 - 168 (chain A) in PDB entry 3DLX
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 THR 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 4.5 0.2 - - - +
160A GLY* 2.8 24.2 + - - +
161A TYR 3.7 11.2 - - - +
162A GLY* 1.3 82.6 - - - +
164A LEU* 1.3 62.1 + - - +
165A VAL* 3.2 13.9 + - - +
166A GLN 3.1 1.9 + - - -
167A GLU* 2.8 32.1 + - - +
427A MET* 3.5 12.7 - - + +
460A LEU* 3.3 28.5 - - + +
461A THR 3.5 24.0 - - - +
462A GLY* 4.1 1.8 - - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 1.3 72.6 - - - +
165A VAL* 1.3 60.3 + - - +
167A GLU* 4.9 2.9 - - + -
168A GLY* 2.8 48.7 + - - +
169A GLY* 4.2 18.4 - - - +
170A SER* 4.1 15.5 - - - +
184A SER* 3.7 5.6 + - - -
413A TRP* 4.2 11.7 - - + -
414A MET* 4.1 20.6 - - + -
459A PRO* 4.1 30.5 - - + -
460A LEU 4.8 2.0 + - - +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU 4.9 4.3 - - - +
137A PRO* 4.0 19.5 - - + -
159A THR 4.9 0.2 - - - +
160A GLY* 4.0 7.0 - - - -
163A THR* 3.5 13.5 - - - +
164A LEU* 1.3 80.7 - - + +
166A GLN* 1.3 60.4 + - - +
168A GLY 4.0 2.1 + - - -
170A SER* 5.6 4.5 - - - -
184A SER* 4.9 4.1 + - - -
185A LYS 4.1 5.4 - - - +
187A ARG* 3.3 29.3 + - - +
198A ILE* 4.0 17.9 - - + -
200A GLU* 4.0 12.6 - - - +
413A TRP* 5.4 1.1 - - + -
423A MET* 3.7 29.8 - - + -
427A MET* 3.9 9.6 - - + -
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Residues in contact with GLN 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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160A GLY 3.2 17.5 + - - +
161A TYR* 3.7 11.8 - - + -
162A GLY* 3.0 22.3 + - - -
163A THR 3.1 2.7 + - - +
165A VAL* 1.3 78.1 - - - +
167A GLU* 1.3 72.0 + - - +
186A PRO* 3.4 2.1 - - - +
187A ARG* 2.9 34.7 + - - +
189A VAL* 3.3 34.4 - - + +
198A ILE* 3.4 17.3 - - + -
189C VAL* 2.9 40.1 + - - +
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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
----------------------------------------------------------
162A GLY* 4.2 14.3 - - - +
163A THR 2.8 25.7 + - - +
164A LEU* 4.9 2.5 - - + -
166A GLN* 1.3 94.5 - - - +
168A GLY* 1.3 65.3 + - - +
186A PRO* 3.7 6.9 - - - +
156C TYR* 4.6 2.9 + - - -
188C GLU* 3.3 41.1 - - + +
189C VAL 3.7 16.6 - - - +
190C ARG* 3.2 44.4 + - - +
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Residues in contact with GLY 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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164A LEU* 2.8 36.5 + - - +
165A VAL 4.0 0.2 + - - -
166A GLN 3.3 3.8 + - - -
167A GLU* 1.3 84.4 - - - +
169A GLY* 1.3 58.4 + - - -
184A SER* 3.3 13.7 - - - -
185A LYS 3.6 16.4 - - - -
186A PRO* 3.8 1.1 - - - +
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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