Contacts of the helix formed by residues 163 - 168 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLY* 2.7 25.2 + - - +
161B TYR 3.1 14.5 - - - +
162B GLY* 1.3 81.8 - - - +
164B LEU* 1.3 61.1 + - - +
165B VAL* 3.1 14.3 + - - +
166B GLN* 3.2 5.9 + - - +
167B GLU* 3.1 24.6 + - - +
427B MET* 3.8 6.3 - - + +
460B LEU* 3.5 25.6 - - - +
461B THR 3.4 27.8 - - - +
462B GLY* 4.1 4.3 - - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 1.3 73.1 - - - +
165B VAL* 1.3 60.2 + - + +
167B GLU* 3.7 11.4 - - + -
168B GLY* 2.8 39.0 + - - +
169B GLY 6.1 0.4 - - - -
170B SER* 4.1 22.7 + - - +
184B SER* 4.8 1.2 + - - -
413B TRP* 4.5 14.1 - - + -
414B MET* 4.4 13.5 - - + -
427B MET* 5.4 0.4 - - - +
459B PRO* 3.8 33.9 - - + -
460B LEU 4.9 1.8 + - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU 5.4 2.9 - - - +
136B THR* 5.8 0.9 - - - +
137B PRO* 3.9 17.9 - - + -
159B THR 4.8 0.4 - - - +
160B GLY* 4.0 6.7 - - - -
163B THR* 3.1 12.9 - - - +
164B LEU* 1.3 79.8 - - + +
166B GLN* 1.3 62.7 + - - +
168B GLY* 3.9 2.9 + - - -
185B LYS 4.4 3.8 - - - +
187B ARG* 3.3 23.4 + - + +
198B ILE* 4.1 10.5 - - + -
200B GLU* 3.7 22.7 - - - +
413B TRP* 5.9 0.4 - - + -
423B MET* 3.8 19.7 - - + -
427B MET* 3.7 22.2 - - + -
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Residues in contact with GLN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLY 3.4 15.2 + - - +
161B TYR* 3.5 15.1 - - - -
162B GLY* 3.0 26.2 + - - -
163B THR 3.2 4.9 + - - +
165B VAL* 1.3 79.4 - - - +
167B GLU* 1.3 63.4 + - - +
186B PRO* 3.2 5.2 - - - +
187B ARG* 2.9 45.1 + - - +
189B VAL* 3.9 23.1 - - + +
198B ILE* 3.9 16.1 - - + +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR 3.1 13.8 + - - +
164B LEU* 4.0 15.3 - - + -
165B VAL 3.4 0.2 - - - -
166B GLN* 1.3 83.5 - - - +
168B GLY* 1.3 66.7 + - - +
186B PRO* 3.6 15.2 - - - +
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LEU* 2.8 25.0 + - - +
165B VAL 3.9 1.1 + - - -
166B GLN 3.3 3.6 - - - -
167B GLU* 1.3 87.5 - - - +
169B GLY* 1.3 60.9 + - - -
170B SER* 3.5 6.0 + - - -
184B SER* 3.3 18.4 - - - -
185B LYS 3.8 15.0 - - - -
186B PRO* 3.9 0.9 - - - -
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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