Contacts of the helix formed by residues 163 - 167 (chain A) in PDB entry 5L0T
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 ALA 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.7 3.0 - - - -
150A PHE* 3.9 25.8 - - + +
161A TYR* 3.3 6.2 + - - -
162A PRO* 1.3 76.9 - - - +
164A TRP* 1.3 67.5 + - + +
165A THR* 3.1 7.3 + - + -
166A PHE* 3.2 26.1 + - + +
278A PHE* 3.5 37.2 - - + -
299A GLU* 4.4 6.3 + - - +
300A PHE* 5.2 0.2 - - - -
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Residues in contact with TRP 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 3.3 64.7 - - + +
110A GLY* 3.9 14.8 - - - +
111A VAL* 4.2 4.3 - - + +
114A PHE* 4.4 1.2 - - - -
130A ASN 4.6 0.2 - - - -
131A VAL* 3.5 23.6 - - + -
132A ARG 4.1 5.4 - - - -
133A ASP* 4.6 0.2 - - - -
150A PHE* 3.7 31.9 - + + -
161A TYR* 3.3 30.9 - + - -
162A PRO 3.6 0.8 + - - -
163A ALA* 1.3 71.2 - - + +
165A THR* 1.3 70.2 + - - +
167A TRP* 2.9 24.1 + - - +
168A GLU 2.9 20.9 + - - +
169A GLY 3.3 29.4 + - - -
170A GLY* 4.1 0.6 - - - -
278A PHE* 3.8 27.1 - + - -
408A GOL 4.1 8.0 + - - -
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Residues in contact with THR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 3.9 6.7 - - + +
164A TRP* 1.3 78.5 - - - +
166A PHE* 1.3 70.1 + - + +
167A TRP 2.9 2.9 + - - -
168A GLU 3.3 11.9 - - - -
170A GLY* 3.7 4.9 - - - -
181A LEU* 2.8 29.4 + - - +
182A GLY* 3.1 18.9 - - - -
184A TRP* 4.5 1.2 + - - +
278A PHE* 3.5 52.4 - - + -
281A LYS* 4.1 13.3 + - - +
282A HIS* 6.0 0.2 - - - -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.8 18.8 - - + -
162A PRO* 4.0 7.6 - - + -
163A ALA* 3.2 42.5 + - + +
164A TRP 3.0 1.0 + - - -
165A THR* 1.3 79.9 - - + +
167A TRP* 1.3 56.6 + - - +
184A TRP* 3.0 56.4 + + + +
281A LYS* 3.6 34.5 - - + +
299A GLU* 4.7 3.8 - - - -
300A PHE* 4.1 11.2 - + - -
301A PHE* 4.1 18.8 - + - -
350A LEU* 4.2 4.5 - - + -
352A MET* 3.3 13.4 - - - +
355A ILE* 3.6 29.6 - - + -
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Residues in contact with TRP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY* 4.3 3.1 - - - +
113A HIS* 3.3 53.1 + + + +
114A PHE* 3.7 18.1 - - + -
164A TRP 2.9 6.8 + - - +
165A THR 3.7 0.4 - - - -
166A PHE* 1.3 79.8 - - - +
168A GLU* 1.3 89.3 + - + +
182A GLY* 3.7 0.3 - - - -
183A ARG* 2.9 77.0 + - - +
185A ASP* 4.3 2.0 - - - -
352A MET* 3.4 24.2 - - + -
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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