Contacts of the helix formed by residues 163 - 168 (chain D) in PDB entry 2UZ1
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 TRP 163 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C PHE* 4.1 17.6 - + - -
28D ALA* 3.5 40.2 + - + -
29D HIS* 3.4 59.2 + + + -
32D THR* 5.9 1.2 - - + +
101D SER 3.0 18.4 + - - +
102D GLY 4.0 1.6 + - - -
103D ALA* 4.2 15.5 - - + +
112D LEU* 6.2 1.8 - - + -
161D LEU 3.6 1.0 + - - -
162D PRO* 1.3 70.0 - - - +
164D ASP* 1.3 57.8 + - - +
166D LEU* 3.1 3.9 + - + -
167D MET* 2.9 61.2 + - + +
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Residues in contact with ASP 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ALA* 3.3 10.1 - - + +
104D LEU* 2.8 30.6 + - - +
105D ARG* 2.9 67.3 + - - +
162D PRO* 3.6 7.3 - - - +
163D TRP* 1.3 76.3 - - - +
165D ILE* 1.3 65.1 + - - +
167D MET* 4.4 3.1 - - - +
168D ASN* 2.9 39.7 + - - +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLY* 3.7 2.3 - - - -
104D LEU* 3.9 11.4 - - + -
132D VAL* 3.8 35.7 - - + +
133D MET 3.6 24.7 - - - +
134D ALA* 3.8 7.6 - - - -
135D THR* 2.7 38.6 + - - +
138D ILE* 3.9 18.6 - - + -
161D LEU* 5.0 3.4 - - + -
162D PRO* 2.9 30.8 + - + +
164D ASP* 1.3 80.6 + - - +
166D LEU* 1.3 59.6 + - - +
168D ASN* 3.7 8.0 - - - +
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D THR* 3.5 5.5 - - - -
6D GLY 2.9 22.6 + - - -
7D GLY* 3.1 25.3 + - - +
10D VAL* 3.9 21.5 - - + -
29D HIS 3.6 22.4 - - - +
30D ILE* 4.3 8.1 - - + -
32D THR* 3.5 15.9 + - + +
33D ILE* 4.1 17.0 - - + -
138D ILE* 4.4 2.9 - - + -
161D LEU* 3.7 41.3 - - + +
162D PRO 3.0 10.0 + - - +
163D TRP* 3.6 6.7 - - + +
165D ILE* 1.3 78.7 - - + +
167D MET* 1.3 59.5 + - - +
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Residues in contact with MET 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C PHE* 5.5 5.8 - - - -
5D THR* 4.0 6.1 - - - +
32D THR* 4.2 17.5 - - + -
105D ARG* 3.5 27.4 - - - +
163D TRP* 2.9 59.6 + - + +
164D ASP* 4.1 4.9 - - + +
166D LEU* 1.3 74.3 - - - +
168D ASN* 1.3 68.6 + - - +
169D GLN* 3.4 13.9 + - - +
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Residues in contact with ASN 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D THR* 3.3 1.2 - - - -
6D GLY 3.0 26.0 + - - -
105D ARG* 4.1 18.0 - - - +
135D THR* 3.0 35.5 + - + +
164D ASP* 2.9 27.5 + - - +
165D ILE* 3.7 9.1 - - - +
166D LEU 3.4 0.4 - - - -
167D MET* 1.3 76.7 - - - +
169D GLN* 1.3 61.1 + - - +
170D ILE* 5.1 2.0 - - + -
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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