Contacts of the helix formed by residues 202 - 213 (chain A) in PDB entry 4OCA
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 ASN 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A TYR* 4.5 1.3 - - - -
200A THR* 3.3 14.0 - - - +
201A ASP* 1.3 84.6 + - - +
203A PRO* 1.3 64.6 - - - +
204A GLN* 2.8 39.7 + - - +
205A PHE* 2.8 25.6 + - + +
206A ALA* 3.1 21.7 + - - +
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Residues in contact with PRO 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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56A TYR* 3.4 39.8 - - + +
201A ASP 3.6 8.1 - - - +
202A ASN* 1.3 87.7 - - - +
204A GLN* 1.3 82.4 + - - +
206A ALA* 3.4 2.1 + - - +
207A ASP* 3.2 32.4 + - - +
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Residues in contact with GLN 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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202A ASN* 2.8 15.5 + - - +
203A PRO* 1.3 89.3 - - - +
205A PHE* 1.3 66.1 + - - +
207A ASP* 3.4 11.3 + - - +
208A LYS* 3.3 24.0 + - - +
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Residues in contact with PHE 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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70A ALA* 3.5 31.6 - - + -
73A ALA* 3.4 26.7 - - + -
74A LEU* 3.8 24.9 - - + -
158A ILE* 4.6 6.7 - - + -
179A THR* 4.2 21.8 - - + -
200A THR* 3.7 17.3 - - - -
202A ASN* 2.8 30.3 + - + +
204A GLN* 1.3 77.8 - - - +
206A ALA* 1.3 62.6 + - - +
208A LYS* 3.1 11.1 + - + +
209A LEU* 3.1 44.3 + - + +
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Residues in contact with ALA 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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56A TYR* 3.9 20.6 - - + -
58A VAL* 3.9 7.7 - - + +
200A THR* 3.9 12.8 - - + -
202A ASN 3.1 17.9 + - - +
203A PRO 3.7 4.7 - - - +
204A GLN 3.3 0.2 - - - -
205A PHE* 1.3 77.4 - - - +
207A ASP* 1.3 58.3 + - - +
209A LEU* 3.2 14.8 + - - +
210A ARG* 2.9 43.6 + - - +
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Residues in contact with ASP 207 (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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56A TYR* 6.1 1.0 - - - -
203A PRO* 3.2 19.0 + - - +
204A GLN* 3.6 11.1 - - - +
205A PHE 3.3 0.2 - - - -
206A ALA* 1.3 77.8 - - - +
208A LYS* 1.3 60.8 + - - +
210A ARG* 3.4 18.4 + - - +
211A SER* 3.1 23.7 + - - -
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Residues in contact with LYS 208 (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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73A ALA* 3.6 41.6 + - + +
204A GLN 3.3 10.8 + - - +
205A PHE* 3.1 14.2 + - - +
207A ASP* 1.3 76.0 - - - +
209A LEU* 1.3 60.3 + - - +
211A SER* 3.2 7.0 + - - -
212A LEU* 2.8 47.9 + - + +
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Residues in contact with LEU 209 (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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58A VAL* 4.1 13.5 - - + -
69A ILE* 3.4 50.0 - - + +
70A ALA* 3.6 11.7 - - + +
73A ALA* 4.0 8.1 - - + -
198A VAL* 3.5 33.9 - - + -
200A THR* 5.1 2.5 - - + -
205A PHE* 3.1 31.4 + - + +
206A ALA* 3.2 12.5 + - - +
208A LYS* 1.3 76.8 - - - +
210A ARG* 1.3 62.5 + - - +
212A LEU* 3.2 3.3 + - - -
213A LYS* 3.0 28.8 + - - +
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Residues in contact with ARG 210 (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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45A GLU* 3.3 20.5 + - - +
56A TYR* 4.4 15.6 - - - +
57A ALA 3.2 26.7 + - - +
58A VAL* 3.9 16.7 - - + +
206A ALA* 2.9 34.8 + - - +
207A ASP* 3.6 18.1 + - - +
208A LYS 3.3 0.2 - - - -
209A LEU* 1.3 75.7 - - - +
211A SER* 1.3 59.3 + - - +
213A LYS* 3.1 34.9 - - - +
214A PHE* 3.9 6.8 + - - +
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Residues in contact with SER 211 (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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207A ASP 3.1 16.5 + - - -
208A LYS* 3.5 7.0 - - - -
209A LEU 3.1 0.4 - - - -
210A ARG* 1.3 76.5 - - - +
212A LEU* 1.3 61.6 + - - +
213A LYS 3.2 0.4 - - - -
214A PHE 3.1 9.3 + - - -
216A GLY* 2.8 43.3 + - - -
217A LEU 2.9 27.0 + - - -
236A LEU* 5.7 2.9 - - - +
237A ALA 5.0 0.2 + - - -
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Residues in contact with LEU 212 (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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69A ILE* 3.8 39.1 - - + +
72A MET* 3.9 42.0 - - + -
73A ALA* 3.9 4.5 - - + +
208A LYS* 2.8 41.4 + - + +
209A LEU 4.0 1.8 - - - +
211A SER* 1.3 79.3 - - - +
213A LYS* 1.3 56.6 + - - +
214A PHE 3.2 0.2 - - - -
216A GLY* 5.4 0.4 - - - -
237A ALA* 4.9 7.6 - - + +
238A PRO 4.0 14.4 - - - +
239A GLY* 4.2 5.4 - - - -
240A TYR* 2.9 32.2 + - - +
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Residues in contact with LYS 213 (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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37A THR* 4.1 24.0 - - - +
41A ASN* 5.4 0.8 + - - -
45A GLU* 5.4 5.0 + - - -
58A VAL* 4.4 6.1 - - + -
59A ALA 3.8 22.1 + - - +
60A VAL* 4.3 2.7 - - + -
69A ILE* 4.2 13.9 - - + +
209A LEU 3.0 15.6 + - - +
210A ARG* 3.1 38.6 - - - +
212A LEU* 1.3 73.4 - - - +
214A PHE* 1.3 65.8 + - - +
240A TYR 3.1 7.2 - - - -
241A LYS* 3.5 0.7 - - - -
242A TYR* 2.7 45.7 + - + -
243A ASN* 3.4 25.4 + - + +
244A LEU 5.4 0.2 - - - +
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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