Contacts of the helix formed by residues 201 - 214 (chain A) in PDB entry 2OK5
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 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASN* 6.0 4.5 - - + +
199A TYR 5.2 2.0 - - - +
200A ASP* 1.3 74.6 - - - +
202A PRO* 1.3 65.1 - - - +
203A GLN* 3.4 17.9 + - - +
204A GLU* 3.0 39.8 + - - +
205A VAL* 2.9 25.5 + - - +
458A GLU* 5.1 1.2 + - - -
1354A GOL 3.3 22.9 - - - +
1355A GOL 6.2 0.2 - - - +
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Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASP 3.8 0.6 - - - +
201A THR* 1.3 87.8 - - - +
203A GLN* 1.3 71.9 + - - +
205A VAL* 3.7 1.3 - - + +
206A ALA* 2.8 31.5 + - - +
430A VAL* 5.0 0.7 - - + -
435A ASN* 3.4 42.2 - - + +
438A ASP* 3.7 21.8 - - + +
439A VAL* 3.6 22.4 - - + +
442A GLN* 5.1 0.9 - - - -
684A SER* 4.0 0.7 - - - +
1354A GOL 3.1 19.5 - - - +
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Residues in contact with GLN 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR* 3.4 21.0 + - - +
202A PRO* 1.3 85.7 - - - +
204A GLU* 1.3 64.0 + - - +
206A ALA* 3.6 2.3 + - - +
207A GLU* 3.2 17.5 + - - +
438A ASP* 5.6 0.2 + - - -
442A GLN* 3.6 33.1 + - - +
456A VAL 4.5 5.4 - - - +
457A TRP* 5.5 0.5 - - - -
458A GLU* 3.4 29.8 + - + +
681A HIS* 4.1 21.6 + - - +
684A SER* 2.7 37.9 + - - +
686A PHE* 6.3 2.5 - - + -
1354A GOL 5.3 1.6 + - - -
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 4.0 19.5 + - - -
125A ARG* 5.7 1.2 + - - -
199A TYR 4.6 1.9 - - - +
200A ASP* 3.7 13.1 - - + +
201A THR* 3.0 45.9 + - - +
203A GLN* 1.3 74.7 - - - +
205A VAL* 1.3 60.5 + - + +
207A GLU* 3.5 3.0 + - - +
208A ALA* 2.9 31.6 + - - +
458A GLU* 3.7 30.3 - - + +
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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
----------------------------------------------------------
200A ASP* 3.5 24.7 - - + -
201A THR 2.9 19.3 + - - +
204A GLU* 1.3 78.1 - - - +
206A ALA* 1.3 56.7 + - - +
208A ALA* 3.8 0.3 - - - +
209A PHE* 2.9 30.8 + - + +
403A PHE* 3.7 14.1 - - + -
428A PHE* 3.7 38.5 - - + -
430A VAL* 4.0 17.3 - - + -
439A VAL* 3.7 29.8 - - + -
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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
----------------------------------------------------------
202A PRO 2.8 18.7 + - - +
203A GLN 3.9 2.5 - - - +
205A VAL* 1.3 76.8 - - - +
207A GLU* 1.3 59.0 + - - +
209A PHE* 4.4 0.2 - - - +
210A LEU* 3.3 31.4 + - - +
439A VAL* 3.5 24.6 - - - +
442A GLN* 3.6 22.0 - - + -
443A MET* 3.8 15.4 - - + +
457A TRP* 3.8 7.1 - - + -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLN 3.2 16.0 + - - +
204A GLU 4.1 3.1 - - - +
205A VAL 3.3 0.2 - - - -
206A ALA* 1.3 73.4 - - - +
208A ALA* 1.3 61.6 + - + +
210A LEU* 4.2 0.2 - - - +
211A SER* 3.0 40.8 + - - -
234A ARG* 3.3 17.5 + - - -
457A TRP* 3.3 30.3 + - + +
458A GLU* 3.4 29.6 - - + +
459A HIS* 5.7 0.4 - - - -
460A ARG* 4.6 20.5 - - + +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU 2.9 19.3 + - - +
207A GLU* 1.3 78.4 - - + +
209A PHE* 1.3 60.9 + - - +
211A SER* 3.9 6.2 + - - -
212A SER* 3.3 22.9 + - - -
425A GLN* 4.1 25.4 + - + +
428A PHE* 3.7 23.6 - - + -
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Residues in contact with PHE 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 VAL* 2.9 23.5 + - + +
206A ALA* 4.4 2.5 - - - +
208A ALA* 1.3 69.4 - - - +
210A LEU* 1.3 62.6 + - - +
212A SER* 3.1 5.7 + - - -
213A LEU* 2.8 50.7 + - + +
271A LEU* 3.8 31.0 - - + -
360A ILE* 4.5 14.6 - - + -
401A TYR* 3.5 48.0 - + + -
403A PHE* 3.7 24.7 - + + -
428A PHE* 4.1 11.8 - + + -
439A VAL* 5.7 0.2 - - + -
440A PHE* 4.7 2.9 - + - -
443A MET* 3.8 26.9 - - + -
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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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206A ALA 3.3 16.2 + - - +
207A GLU 4.2 0.9 - - - +
209A PHE* 1.3 79.8 - - + +
211A SER* 1.3 55.3 + - - +
213A LEU* 4.5 6.7 - - + +
214A THR* 2.5 48.8 + - + -
234A ARG* 3.6 20.6 - - - +
274A LYS* 3.9 14.6 - - + -
278A TYR* 3.8 17.3 - - + +
443A MET* 3.8 31.9 - - + -
446A GLU* 3.3 26.0 - - + +
457A TRP* 3.7 18.6 - - + -
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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
----------------------------------------------------------
207A GLU* 3.0 34.9 + - - -
208A ALA* 3.9 6.8 + - - -
210A LEU* 1.3 75.8 - - - +
212A SER* 1.3 61.3 + - - +
214A THR* 3.5 12.8 - - - +
234A ARG* 3.7 17.5 - - - +
423A ASN 5.8 0.5 + - - -
424A GLU* 5.3 3.1 - - - +
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Residues in contact with SER 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.3 18.9 + - - -
209A PHE 3.1 4.8 + - - -
211A SER* 1.3 79.7 - - - +
213A LEU* 1.3 64.1 + - - +
214A THR 3.5 2.6 + - - +
356A ARG* 5.0 2.1 + - - -
399A ASP* 5.5 1.0 - - - +
401A TYR* 2.7 32.7 + - - -
424A GLU* 2.6 40.6 + - - +
425A GLN 4.0 6.5 + - - -
426A HIS* 3.6 5.4 - - - -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 2.8 44.3 + - + +
210A LEU* 4.1 9.4 - - + +
212A SER* 1.3 75.7 - - - +
214A THR* 1.3 67.3 + - + +
236A ILE* 4.2 26.7 - - + +
244A MET* 5.4 3.8 - - - -
246A ILE* 6.0 3.6 - - + -
271A LEU* 5.3 1.1 - - + -
275A VAL* 4.4 16.8 - - + -
278A TYR* 5.5 2.0 - - + -
356A ARG* 3.4 38.1 + - - +
358A VAL* 4.4 26.0 - - + -
360A ILE* 6.1 0.4 - - + -
401A TYR* 3.5 13.7 + - + +
443A MET* 5.8 0.4 - - + -
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 2.5 26.1 + - + +
211A SER* 3.5 17.8 - - - +
212A SER 4.0 2.6 - - - +
213A LEU* 1.3 90.2 - - + +
215A GLU* 1.3 66.0 + - - +
234A ARG* 3.2 23.5 + - - +
235A LYS 3.3 12.3 - - - +
236A ILE* 3.9 19.5 - - + +
278A TYR* 4.0 26.5 - - + +
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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