Contacts of the helix formed by residues 202 - 211 (chain A) in PDB entry 5HKZ
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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200A VAL 3.6 0.8 + - - -
201A PRO* 1.3 71.7 - - - +
203A LYS* 1.3 71.0 + - + +
205A PHE* 3.1 24.5 + + - +
206A ARG* 2.8 64.9 + - + +
215A ILE* 5.4 0.7 - - + -
221A ALA* 3.7 12.9 + - + +
224A LEU* 4.1 17.9 - - + -
225A LYS* 3.7 69.8 - - + +
228A ILE* 3.9 10.8 - - + -
234A ASP 3.0 24.6 + - - +
236A ILE* 3.8 23.3 - - + -
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Residues in contact with LYS 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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201A PRO* 3.2 4.9 - - + +
202A TRP* 1.3 88.9 - - + +
204A SER* 1.3 62.8 + - - +
206A ARG* 3.4 6.4 + - - +
207A GLN* 3.1 24.6 + - - +
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Residues in contact with SER 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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194A PHE* 3.9 15.5 - - - -
200A VAL* 4.7 0.9 - - - -
201A PRO* 3.1 30.5 + - - +
203A LYS* 1.3 74.7 - - - +
205A PHE* 1.3 66.2 + - - +
207A GLN* 3.4 7.2 + - - +
208A ALA* 3.1 23.9 + - - +
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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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189A PHE* 4.1 9.0 - + - -
190A TRP* 4.0 9.9 - + - -
194A PHE* 3.9 21.5 - + - -
200A VAL* 3.7 14.5 - - + +
201A PRO 3.0 8.6 + - - +
202A TRP* 3.1 28.2 + + - +
204A SER* 1.3 77.0 - - - +
206A ARG* 1.3 58.5 + - - +
208A ALA* 3.3 3.1 + - - +
209A LEU* 2.9 58.0 + - + +
224A LEU* 5.9 1.1 - - + -
228A ILE* 3.8 21.8 - - + -
236A ILE* 3.8 23.3 - - + -
241A PHE* 3.6 36.6 - + - -
244A PHE* 6.1 0.2 - + - -
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Residues in contact with ARG 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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202A TRP* 2.8 53.3 + - + +
203A LYS* 3.7 7.4 - - - +
205A PHE* 1.3 79.9 - - - +
207A GLN* 1.3 57.8 + - - +
209A LEU 3.3 0.7 + - - -
210A HIS* 2.9 35.7 + - + +
215A ILE* 3.8 28.6 + - + +
216A SER 4.8 0.8 - - - -
217A SER* 3.6 38.4 + - - +
218A GLY 5.8 0.2 - - - +
221A ALA* 3.9 19.1 - - - +
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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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203A LYS 3.1 16.6 + - - +
204A SER* 3.8 7.5 - - - +
206A ARG* 1.3 79.8 - - - +
208A ALA* 1.3 63.9 + - - +
210A HIS* 3.5 14.1 + - + +
211A GLU* 3.5 19.6 + - + +
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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
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189A PHE* 3.4 21.8 - - + -
193A ALA* 4.0 11.4 - - + -
194A PHE* 3.6 23.8 - - + -
204A SER 3.1 16.4 + - - +
205A PHE 3.7 2.0 - - - +
207A GLN* 1.3 78.6 - - - +
209A LEU* 1.3 62.2 + - - +
211A GLU* 3.3 21.2 + - - +
212A VAL* 4.0 0.9 + - - +
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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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189A PHE* 3.6 14.8 - - + -
205A PHE* 2.9 44.2 + - + +
206A ARG 3.9 2.5 - - - +
208A ALA* 1.3 77.8 - - - +
210A HIS* 1.3 59.8 + - - +
212A VAL* 3.0 3.9 + - + -
213A HIS* 2.8 47.0 + - + +
215A ILE* 4.3 16.4 - - + -
224A LEU* 4.4 8.1 - - + -
241A PHE* 5.5 0.2 - - + -
244A PHE* 5.5 2.7 - - + -
251A TRP* 3.8 30.3 - - + -
254A LEU* 4.3 8.3 - - + -
255A LEU* 4.3 20.4 - - + -
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Residues in contact with HIS 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 ARG* 2.9 22.1 + - + +
207A GLN* 3.6 9.0 - - - +
209A LEU* 1.3 77.5 - - - +
211A GLU* 1.3 67.0 + - - +
212A VAL 3.3 1.0 + - - -
213A HIS 3.4 8.5 + - - -
214A PRO* 3.5 31.6 - - + +
215A ILE* 3.0 47.2 + - + +
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Residues in contact with GLU 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 GLN* 3.5 18.0 + - + +
208A ALA* 3.3 13.0 + - - +
209A LEU 3.1 1.0 - - - -
210A HIS* 1.3 85.1 - - - +
212A VAL* 1.3 63.7 + - + +
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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