Contacts of the helix formed by residues 201 - 206 (chain A) in PDB entry 4KPD
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
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Residue Dist Surf HB Arom Phob DC
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197A VAL 3.1 9.7 + - - -
199A TYR 3.4 0.6 - - - -
200A LYS* 1.3 77.6 - - - +
202A ALA* 1.3 67.8 + - - +
203A PHE 3.3 2.8 + - - -
204A PHE* 3.6 7.9 + - - -
205A SER* 3.0 30.2 + - - +
206A PHE* 4.9 0.7 - - + -
236A GLY 4.0 18.2 - - - +
239A PHE* 4.2 12.6 - - + -
240A GLN* 2.6 33.0 + - + +
404A IPE 3.6 13.6 - - + +
405A RIS 3.0 19.8 + - - -
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Residues in contact with ALA 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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197A VAL 3.2 4.5 + - - +
198A LYS* 3.4 22.6 + - - +
201A THR* 1.3 77.0 - - - +
203A PHE* 1.4 62.6 + - - +
206A PHE* 3.3 19.6 + - - +
207A TYR 3.3 6.6 + - - -
232A LEU 4.3 0.3 - - - +
233A LEU* 3.6 40.8 - - + +
236A GLY* 3.8 20.0 - - - -
237A GLU 4.2 0.9 - - - +
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Residues in contact with PHE 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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163A SER* 5.0 4.9 - - - +
166A GLN* 3.4 54.7 - - + +
167A THR* 5.3 0.2 - - - +
198A LYS* 3.2 55.5 + - + -
199A TYR* 4.0 26.2 + + - +
201A THR 3.3 0.8 - - - -
202A ALA* 1.4 76.4 - - - +
204A PHE* 1.3 58.7 + - - +
207A TYR* 3.2 17.6 + + + +
208A LEU* 2.9 27.9 + - - +
229A LYS* 4.0 26.0 - - + -
233A LEU* 3.7 22.0 - - + -
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Residues in contact with PHE 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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60A ARG* 3.5 14.6 - - - -
92A VAL* 4.1 6.0 - - + +
95A LEU* 4.3 13.7 - - + -
96A GLN* 3.2 40.2 - - - -
99A PHE* 4.4 15.0 - + + -
163A SER* 4.3 7.8 - - - +
167A THR* 3.5 30.7 + - + +
199A TYR 5.5 0.2 + - - -
200A LYS 3.4 22.7 - - - -
201A THR* 3.6 7.2 + - - -
203A PHE* 1.3 79.0 - - - +
205A SER* 1.4 75.8 + - - +
206A PHE 3.5 0.2 - - - -
208A LEU* 3.3 34.8 - - + +
209A PRO* 3.5 5.4 - - - +
404A IPE 3.7 14.6 - - + -
405A RIS 3.9 11.7 - + - -
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Residues in contact with SER 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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60A ARG* 2.7 50.7 + - - +
201A THR* 3.0 21.8 + - - -
204A PHE* 1.4 87.2 - - - +
206A PHE* 1.3 82.9 + - - +
209A PRO* 3.6 14.4 - - - +
344A LEU* 5.1 2.8 - - - +
404A IPE 3.6 3.1 - - - +
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Residues in contact with PHE 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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201A THR* 4.7 0.9 - - + -
202A ALA* 3.3 7.1 + - - +
204A PHE 3.5 0.2 - - - -
205A SER* 1.3 93.0 - - - +
207A TYR* 1.3 67.6 + - - +
208A LEU 3.5 0.7 - - - -
209A PRO* 3.5 11.7 - - - +
210A ILE* 3.9 5.4 - - - +
232A LEU* 3.3 41.7 - - + +
235A MET* 4.0 15.5 - - + -
236A GLY* 3.5 14.8 - - - -
239A PHE* 3.4 57.4 - + + -
344A LEU* 3.7 39.2 - - + +
348A ILE* 4.0 16.8 - - + -
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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