Contacts of the helix formed by residues 194 - 206 (chain A) in PDB entry 5A0Q
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.0 17.3 - - + +
44A GLY* 3.6 29.4 - - - -
45A LYS 5.2 0.4 - - - +
47A CYS* 3.1 28.8 - - - -
49A VAL* 3.2 16.4 - - - +
193A GLN* 1.3 76.1 - - + +
195A VAL* 1.4 70.4 + - - +
197A THR* 3.1 18.5 + - - -
198A ALA* 3.1 14.4 + - - +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A CYS* 5.7 1.3 - - - -
49A VAL* 3.6 25.6 - - + -
193A GLN 5.3 3.1 - - - +
194A THR* 1.4 78.0 + - - +
196A GLU* 1.3 57.0 + - - +
198A ALA* 3.4 1.7 + - - +
199A ILE* 2.9 50.7 + - + +
217A VAL* 4.9 3.4 - - + -
219A VAL* 4.3 13.9 - - + -
230A LEU* 3.8 25.1 - - + -
235A ILE 6.2 0.7 - - - +
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 6.0 1.9 - - - +
193A GLN* 3.4 45.1 + - - +
195A VAL* 1.3 77.3 - - - +
197A THR* 1.4 63.4 + - - +
199A ILE* 4.6 4.3 - - - +
200A THR* 2.8 56.1 + - + +
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.1 20.0 - - + +
178A PHE* 4.7 3.6 - - + +
179A LEU* 5.0 9.9 - - + -
182A LYS* 4.1 32.4 - - + +
193A GLN 2.7 22.2 + - - -
194A THR* 3.1 12.9 + - - -
196A GLU* 1.4 84.8 + - - +
198A ALA* 1.4 57.3 + - - +
200A THR* 3.5 3.3 + - - -
201A CYS* 3.0 30.6 + - + +
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.5 5.6 - - + +
42A VAL* 3.9 18.1 - - + +
49A VAL* 4.1 13.9 - - + -
51A VAL* 3.6 23.1 - - + -
194A THR 3.1 9.8 + - - +
195A VAL 3.7 7.2 - - - +
197A THR* 1.4 80.1 - - - +
199A ILE* 1.4 56.4 + - + +
201A CYS* 3.2 6.0 + - - +
202A LEU* 2.9 36.1 + - - +
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.8 7.9 - - + -
195A VAL* 2.9 40.2 + - + +
196A GLU* 4.4 3.4 - - - +
198A ALA* 1.4 72.1 - - + +
200A THR* 1.4 62.2 + - + +
202A LEU* 3.3 6.7 + - - +
203A SER* 2.9 28.2 + - - -
210A PHE* 4.2 5.8 - - + -
215A ILE* 4.3 27.4 - - + -
217A VAL* 4.4 24.5 - - + -
235A ILE* 4.7 19.7 - - + -
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Residues in contact with THR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PHE* 3.9 15.1 - - - -
196A GLU* 2.8 48.3 + - + +
197A THR* 3.5 4.3 + - - -
199A ILE* 1.4 72.8 - - + +
201A CYS* 1.4 61.7 + - - +
203A SER* 4.2 7.2 - - - -
204A THR* 2.9 39.1 + - - -
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Residues in contact with CYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.3 11.2 - - + -
175A SER* 3.4 41.5 - - - -
178A PHE* 3.6 19.7 - - + -
179A LEU* 4.2 15.3 - - + -
197A THR* 3.0 22.4 + - + +
198A ALA* 3.2 8.5 + - - +
200A THR* 1.4 76.5 + - - +
202A LEU* 1.3 62.2 + - - +
205A VAL* 2.9 35.0 + - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 3.6 22.7 - - + +
40A VAL* 3.4 29.4 - - + +
51A VAL* 3.4 36.6 - - + -
52A THR 4.3 11.2 - - - +
198A ALA 2.9 30.6 + - - +
199A ILE* 3.9 3.4 - - - +
201A CYS* 1.3 75.6 - - - +
203A SER* 1.4 58.1 + - - +
205A VAL* 4.7 2.7 - - - -
206A LEU* 3.1 42.9 + - + +
210A PHE* 3.4 20.6 - - + -
215A ILE* 4.1 12.6 - - + -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ILE* 2.9 19.1 + - - -
200A THR* 3.8 8.7 - - - -
201A CYS 3.2 0.2 - - - -
202A LEU* 1.4 77.0 - - - +
204A THR* 1.3 58.6 + - - +
207A SER* 3.1 6.8 + - - -
208A ILE 3.1 45.6 + - - +
209A ASP* 4.3 12.6 + - - -
210A PHE* 3.7 10.0 - - - -
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PHE* 4.5 23.2 - - + -
200A THR* 2.9 22.7 + - - -
201A CYS 4.2 1.3 - - - -
203A SER* 1.3 77.8 - - - +
205A VAL* 1.3 65.8 + - + +
207A SER* 3.6 13.3 + - - +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 5.4 2.5 - - + -
171A LYS* 3.3 39.5 - - + +
174A GLU* 3.7 15.5 - - + +
175A SER* 3.3 44.4 - - - +
178A PHE* 4.3 10.1 - - + -
201A CYS* 2.9 27.0 + - - +
202A LEU* 4.5 1.8 - - - +
204A THR* 1.3 80.7 - - + +
206A LEU* 1.4 61.3 + - + +
207A SER* 3.1 7.2 + - - -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 6.0 0.9 - - - +
38A THR* 3.7 32.5 - - + +
170A VAL* 5.6 1.6 - - + -
171A LYS* 3.5 31.4 - - + +
202A LEU* 3.1 33.8 + - + +
205A VAL* 1.4 75.1 - - + +
207A SER* 1.4 67.8 + - - +
208A ILE* 3.5 17.7 + - + +
210A PHE* 4.0 18.8 - - + -
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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