Contacts of the helix formed by residues 189 - 203 (chain B) in PDB entry 1U31
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 ASP 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ALA* 3.6 6.3 - - - +
164B ARG* 3.9 9.9 - - + +
188B GLY* 1.3 70.7 - - - -
190B ALA* 1.3 60.1 + - - +
191B LYS* 3.0 29.9 + - - +
192B LYS* 3.3 42.3 + - + +
193B THR* 2.9 31.7 + - - -
400B NDP 2.9 31.2 + - - -
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Residues in contact with ALA 190 (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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55B GLY 3.9 9.6 - - - +
56B LEU* 4.4 0.2 - - - -
59B ALA* 3.8 10.8 - - + -
61B ALA* 3.9 12.3 - - + -
127B ILE* 4.2 19.3 - - + -
128B GLY 5.3 0.4 - - - +
162B MET* 5.2 6.5 - - - +
188B GLY 4.4 1.1 - - - -
189B ASP* 1.3 72.4 - - - +
191B LYS* 1.3 57.7 + - - +
193B THR* 3.8 4.1 - - - -
194B CYS* 2.8 35.7 + - - +
400B NDP 2.9 28.1 + - + +
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA* 3.2 29.3 - - - +
60B LYS* 4.2 20.2 - - + +
61B ALA* 3.8 8.5 - - + +
64B PRO* 4.6 6.1 - - + -
189B ASP* 3.0 9.8 + - - +
190B ALA* 1.3 75.6 - - - +
192B LYS* 1.3 57.5 + - + +
194B CYS* 4.0 1.3 - - - +
195B ASP* 2.7 71.2 + - - +
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Residues in contact with LYS 192 (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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188B GLY* 6.3 0.2 - - - -
189B ASP* 3.3 35.0 + - + +
191B LYS* 1.3 77.7 - - + +
193B THR* 1.3 60.4 + - - +
195B ASP* 3.9 7.5 - - - +
196B ALA* 3.3 22.9 + - - +
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Residues in contact with THR 193 (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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35B LEU* 4.2 7.1 - - + +
162B MET* 3.9 19.7 - - + -
186B LEU* 3.7 42.1 + - + +
187B LEU 4.4 4.5 + - - -
188B GLY* 3.9 15.8 + - - -
189B ASP 2.9 18.5 + - - -
190B ALA* 3.8 5.4 - - - -
192B LYS* 1.3 74.5 - - - +
194B CYS* 1.3 60.3 + - - +
196B ALA* 3.2 5.9 + - - +
197B LEU* 3.0 30.8 + - + +
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Residues in contact with CYS 194 (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 ALA* 4.4 5.2 - - + -
64B PRO* 3.7 26.1 - - + +
65B ILE* 3.8 30.3 - - + +
68B LEU* 5.4 3.5 - - + +
127B ILE* 4.0 25.6 - - - -
162B MET* 4.3 10.1 - - - -
190B ALA 2.8 26.7 + - - +
191B LYS 4.0 0.2 - - - +
193B THR* 1.3 70.6 - - - +
195B ASP* 1.3 60.4 + - - +
197B LEU* 3.9 8.9 - - - +
198B GLN* 3.0 29.3 + - - +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 3.2 24.8 - - - +
191B LYS* 2.7 60.9 + - - +
192B LYS* 3.9 7.6 + - - +
194B CYS* 1.3 73.2 - - - +
196B ALA* 1.3 56.3 + - - +
198B GLN* 3.4 13.8 - - - +
199B ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 196 (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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35B LEU* 3.7 32.3 - - + -
192B LYS 3.3 14.9 + - - +
193B THR 3.2 5.7 + - - +
195B ASP* 1.3 77.3 - - - +
197B LEU* 1.3 60.1 + - - +
199B ALA* 3.3 5.8 + - - +
200B LYS* 3.0 37.6 + - + +
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Residues in contact with LEU 197 (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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35B LEU* 4.4 10.5 - - + +
38B ALA* 4.1 24.0 - - + -
39B ILE* 3.8 24.9 - - + +
42B ILE* 4.1 10.8 - - + -
68B LEU* 3.7 22.2 - - + -
162B MET* 3.6 37.9 - - + -
186B LEU* 4.3 3.4 - - + -
193B THR* 3.0 28.0 + - + +
194B CYS* 3.9 8.5 - - - +
195B ASP 3.4 0.2 - - - -
196B ALA* 1.3 72.7 - - - +
198B GLN* 1.3 59.6 + - - +
200B LYS* 4.9 0.4 - - - -
201B VAL* 3.0 35.9 + - - +
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Residues in contact with GLN 198 (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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63B TYR 5.1 0.2 - - - -
64B PRO* 3.9 25.3 - - - +
67B ASP* 2.8 35.7 + - + +
68B LEU* 3.9 10.9 - - - +
71B MET* 3.6 16.5 - - + +
194B CYS 3.0 19.7 + - - +
195B ASP* 3.4 17.9 - - - +
196B ALA 3.2 0.2 - - - -
197B LEU* 1.3 77.1 - - - +
199B ALA* 1.3 53.8 + - - +
202B ARG* 2.8 39.1 + - + +
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Residues in contact with ALA 199 (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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195B ASP 3.0 17.0 + - - +
196B ALA* 3.3 7.6 + - - +
198B GLN* 1.3 78.7 - - - +
200B LYS* 1.3 64.6 + - + +
202B ARG* 3.3 8.5 - - - +
203B GLU* 3.3 30.3 + - - +
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Residues in contact with LYS 200 (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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35B LEU* 3.7 32.1 - - + +
36B ASP* 2.8 37.1 + - - +
39B ILE* 3.9 30.1 - - + +
196B ALA* 3.0 19.9 + - - +
199B ALA* 1.3 74.1 - - + +
201B VAL* 1.3 64.4 + - - +
202B ARG 3.2 1.7 + - - -
203B GLU* 3.6 12.5 + - - +
204B SER* 3.4 17.0 + - - -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.6 24.2 - - + +
42B ILE* 5.2 7.6 - - + -
68B LEU* 3.8 15.7 - - + -
71B MET* 4.1 22.1 - - + +
72B LEU* 4.0 20.2 - - + -
75B GLN* 3.8 25.8 + - - +
197B LEU 3.0 21.5 + - - +
198B GLN 4.1 1.3 - - - +
200B LYS* 1.3 74.8 - - - +
202B ARG* 1.3 63.4 + - - +
204B SER* 3.9 17.4 + - - +
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Residues in contact with ARG 202 (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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67B ASP* 6.3 1.0 - - - +
71B MET* 3.4 36.5 - - - +
74B GLU* 5.7 1.6 + - - -
198B GLN* 2.8 21.6 + - + +
199B ALA* 3.3 13.0 - - - +
200B LYS 3.2 0.2 - - - -
201B VAL* 1.3 78.3 - - - +
203B GLU* 1.3 61.3 + - + +
204B SER 3.0 13.0 + - - +
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Residues in contact with GLU 203 (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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199B ALA* 3.3 16.8 + - - +
200B LYS* 3.6 7.8 + - - +
201B VAL 3.5 0.6 - - - -
202B ARG* 1.3 78.1 - - + +
204B SER* 1.3 64.7 + - - +
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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