Contacts of the helix formed by residues 165 - 172 (chain B) in PDB entry 2UUG
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 GLY 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLN* 6.0 0.2 - - - -
164B TRP* 1.3 78.2 - - - +
166B SER* 1.3 66.0 + - - -
167B HIS* 3.2 5.1 + - - -
168B ALA 3.4 0.2 + - - -
169B GLN* 3.2 23.5 + - - +
185B ALA 2.8 13.2 + - - -
186B PRO* 3.5 5.5 - - - -
187B ASP* 3.5 22.4 - - - -
28D GLU* 3.5 11.2 - - - -
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLY* 1.3 71.4 - - - -
167B HIS* 1.3 61.5 + - - +
169B GLN* 3.4 17.2 + - - +
170B LYS* 3.1 29.6 + - - +
25D LEU* 4.0 17.3 - - - -
27D GLU* 5.3 4.5 - - - +
28D GLU* 2.9 39.1 + - - +
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Residues in contact with HIS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 5.6 0.2 - - - -
63B GLN* 4.4 28.5 - - + +
124B THR* 4.2 16.5 + - + +
134B HIS* 5.9 1.3 + - - -
142B GLU* 3.6 31.6 + - - -
165B GLY* 3.2 1.3 - - - -
166B SER* 1.3 77.7 - - - +
168B ALA* 1.3 64.7 + - + +
170B LYS* 3.3 23.2 + - - +
171B LYS* 3.6 13.1 + - + +
23D LEU* 4.5 25.7 - - + +
24D MET* 6.4 0.4 - - - -
25D LEU* 4.7 17.6 - - + +
28D GLU* 4.5 2.9 + - - +
40D ASP* 5.6 0.4 + - - -
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Residues in contact with ALA 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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61B LEU* 3.9 34.3 - - + +
62B GLY 5.6 2.0 - - - +
63B GLN* 5.8 2.0 - - + +
124B THR* 6.0 1.1 - - + -
163B LEU* 3.3 20.9 - - + +
164B TRP 3.4 29.8 + - - +
165B GLY 3.4 1.4 + - - -
167B HIS* 1.3 81.6 - - + +
169B GLN* 1.3 64.5 + - - +
171B LYS* 3.3 14.1 + - - +
172B GLY 3.6 1.6 + - - -
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Residues in contact with GLN 169 (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 LEU* 3.6 24.2 - - + +
165B GLY 3.2 17.7 + - - +
166B SER* 3.6 16.5 + - - +
167B HIS 3.2 0.2 - - - -
168B ALA* 1.3 76.4 - - - +
170B LYS* 1.3 62.6 + - - +
172B GLY* 3.1 14.9 + - - -
173B ALA* 4.0 2.8 + - - +
184B LYS* 3.5 47.7 - - + +
185B ALA* 3.1 29.6 + - - +
186B PRO* 4.8 0.7 - - - +
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Residues in contact with LYS 170 (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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166B SER* 3.1 18.5 + - - +
167B HIS* 3.4 13.5 - - - +
168B ALA 3.2 0.2 - - - -
169B GLN* 1.3 74.2 - - + +
171B LYS* 1.3 58.5 + - + +
172B GLY 3.0 9.7 + - - -
173B ALA* 3.2 21.4 + - - +
174B ILE* 5.8 0.5 - - - +
25D LEU* 4.0 27.6 - - + +
27D GLU* 5.7 0.4 + - - -
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.2 9.9 - - + -
124B THR* 3.5 25.2 - - + +
142B GLU* 3.0 38.3 + - - -
145B THR* 2.9 30.3 + - - -
146B ASP* 3.0 30.6 + - - +
149B ILE* 3.8 22.8 - - + +
163B LEU* 5.5 0.2 - - - -
167B HIS* 3.6 13.8 + - + +
168B ALA* 3.3 13.0 + - - +
170B LYS* 1.3 77.8 - - + +
172B GLY* 1.3 57.4 + - - +
173B ALA 3.3 1.6 - - - -
174B ILE* 3.6 24.3 - - - +
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Residues in contact with GLY 172 (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 LEU* 3.7 20.2 - - - -
168B ALA 3.6 3.0 + - - -
169B GLN 3.1 12.5 + - - -
170B LYS 3.0 2.0 - - - -
171B LYS* 1.3 78.1 - - - +
173B ALA* 1.3 62.2 + - - +
174B ILE 3.2 2.0 - - - -
175B ILE* 3.3 28.5 + - - +
177B LYS* 3.8 14.8 - - - -
182B VAL* 5.1 1.7 - - - +
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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