Contacts of the helix formed by residues 202 - 215 (chain A) in PDB entry 5UAK
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 TRP 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A MET* 5.4 12.3 - - + +
85A GLY 5.1 2.7 - - - -
86A ILE* 5.3 9.6 - - + -
89A TYR* 3.7 28.5 - + + -
199A HIS* 3.4 49.0 + + - -
201A VAL* 1.3 81.1 - - + +
203A ILE* 1.3 83.7 + - + +
204A ALA 3.6 0.4 - - - -
205A PRO* 3.8 7.1 - - - +
206A LEU* 3.4 43.4 + - + +
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Residues in contact with ILE 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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88A LEU* 5.2 0.9 - - + -
89A TYR* 3.6 28.7 - - + +
92A GLU* 3.9 35.7 - - + -
199A HIS* 3.5 29.4 - - + +
200A PHE* 3.4 23.0 + - + -
202A TRP* 1.3 113.8 - - + +
204A ALA* 1.3 55.6 + - - +
206A LEU* 3.2 5.2 + - - +
207A GLN* 2.8 35.6 + - + +
353A GLN* 5.2 1.8 - - - +
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Residues in contact with ALA 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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200A PHE* 3.3 14.0 + - + +
203A ILE* 1.3 79.6 - - - +
205A PRO* 1.4 64.7 - - + +
207A GLN* 3.4 8.5 - - - +
208A VAL* 2.8 33.2 + - - +
349A ALA* 4.6 16.5 - - + +
350A VAL* 6.0 0.2 - - - -
353A GLN* 5.8 4.5 - - + +
354A PHE* 3.8 27.4 - - + +
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Residues in contact with PRO 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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201A VAL 3.1 26.7 - - - +
202A TRP* 3.8 8.5 - - - +
203A ILE 3.7 2.0 - - - -
204A ALA* 1.4 94.1 - - + +
206A LEU* 1.3 60.8 + - + +
208A VAL* 3.2 11.8 - - + +
209A ALA* 3.0 28.7 + - - +
354A PHE* 4.3 10.8 - - + -
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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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89A TYR* 3.5 31.3 + - + +
93A VAL* 6.0 0.7 - - - -
202A TRP* 3.4 45.0 + - + +
203A ILE 3.2 7.8 + - - +
205A PRO* 1.3 76.6 - - + +
207A GLN* 1.3 60.5 + - - +
209A ALA* 3.7 8.5 - - + +
210A LEU* 2.9 31.2 + - - +
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Residues in contact with GLN 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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89A TYR* 5.3 0.9 - - - -
92A GLU* 2.8 47.5 + - - +
93A VAL* 3.6 13.5 + - - +
95A LYS* 4.7 0.4 - - - +
96A ALA* 3.7 22.2 - - - +
203A ILE* 2.8 18.1 + - + +
204A ALA* 3.2 14.6 + - - +
206A LEU* 1.3 76.0 - - - +
208A VAL* 1.3 56.6 + - - +
210A LEU* 3.2 6.8 + - - +
211A LEU* 2.8 43.5 + - + +
345A VAL* 3.7 17.9 - - + +
349A ALA* 4.4 14.8 - - + -
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Residues in contact with VAL 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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204A ALA 2.8 19.2 + - - +
205A PRO* 3.2 18.4 - - + +
207A GLN* 1.3 74.5 - - - +
209A ALA* 1.3 55.5 + - - +
211A LEU* 4.1 8.3 - - + +
212A MET* 2.8 44.4 + - + +
227A LEU* 4.1 25.4 - - + -
346A LEU* 3.5 26.7 - - + -
349A ALA* 5.7 2.6 - - + +
350A VAL* 6.1 2.7 - - + -
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Residues in contact with ALA 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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205A PRO 3.0 20.7 + - - +
206A LEU* 3.7 13.7 - - + +
208A VAL* 1.3 76.9 - - + +
210A LEU* 1.3 62.2 + - - +
212A MET* 3.6 23.3 - - - +
213A GLY* 3.8 3.6 + - - -
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Residues in contact with LEU 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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89A TYR* 5.5 3.4 - - - +
93A VAL* 4.2 33.4 - - + +
96A ALA* 4.3 9.6 - - + -
97A VAL* 5.1 11.4 - - + -
206A LEU 2.9 17.4 + - - +
207A GLN* 3.6 6.1 - - - +
209A ALA* 1.3 74.8 - - - +
211A LEU* 1.3 60.1 + - + +
213A GLY* 3.0 18.7 + - - -
214A LEU* 3.1 46.6 + - + +
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Residues in contact with LEU 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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96A ALA* 3.9 15.3 - - + -
207A GLN* 2.8 45.3 + - + +
208A VAL* 3.3 5.8 + - - +
210A LEU* 1.3 70.0 - - - +
212A MET* 1.3 62.7 + - - +
213A GLY 3.3 0.2 - - - -
214A LEU* 3.9 23.1 - - + +
215A ILE* 3.3 29.3 + - + +
223A ALA* 5.2 0.2 - - - +
342A PHE* 3.7 30.3 - - + +
345A VAL* 4.2 7.6 - - + -
346A LEU* 3.7 41.5 - - + +
349A ALA* 5.4 0.9 - - + -
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Residues in contact with MET 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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208A VAL* 2.8 32.1 + - + +
209A ALA* 3.6 15.0 - - - +
210A LEU 3.2 0.2 - - - -
211A LEU* 1.3 74.1 - - - +
213A GLY* 1.3 56.8 + - - +
215A ILE* 3.0 26.3 + - - +
223A ALA* 4.5 20.2 - - + +
224A PHE* 3.6 39.5 - - + -
227A LEU* 4.6 19.5 - - + -
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Residues in contact with GLY 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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209A ALA 3.8 3.8 + - - -
210A LEU* 3.0 8.4 + - - -
212A MET* 1.3 78.0 - - - +
214A LEU* 1.3 65.7 + - - +
215A ILE 3.5 6.1 + - - +
216A TRP* 4.3 18.5 + - - -
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Residues in contact with LEU 214 (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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96A ALA* 3.3 31.6 - - + +
97A VAL* 5.5 1.3 - - + -
100A LEU* 3.7 31.2 - - + -
210A LEU* 3.1 35.9 + - + +
211A LEU* 3.9 15.5 - - + +
212A MET 3.4 0.2 - - - -
213A GLY* 1.3 76.3 - - - +
215A ILE* 1.3 58.2 + - - +
216A TRP* 3.2 23.8 + - - +
342A PHE* 3.7 34.5 - - + -
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Residues in contact with ILE 215 (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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211A LEU* 3.3 18.4 + - + +
212A MET 3.0 17.3 - - - +
213A GLY 3.3 3.7 - - - +
214A LEU* 1.3 74.1 - - - +
216A TRP* 1.3 63.1 + - - +
217A GLU* 3.7 4.3 + - - +
222A SER* 3.4 26.9 - - - +
223A ALA* 3.8 25.1 - - + +
339A THR* 4.7 22.7 - - + +
342A PHE* 4.2 24.7 - - + -
343A CYS* 5.4 5.6 - - + +
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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