Contacts of the helix formed by residues 206 - 217 (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 PHE 206 (chain A).
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Specific contacts
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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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Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.8 17.5 - - + +
163A SER* 5.3 2.9 - - - -
166A GLN* 5.7 0.9 - - - -
202A ALA 3.3 6.2 + - - +
203A PHE* 3.2 23.6 + + + +
206A PHE* 1.3 79.9 - - - +
208A LEU* 1.4 55.7 + - - +
210A ILE* 3.9 1.2 - - - +
211A ALA* 2.8 56.0 + - + +
215A TYR* 4.6 3.6 + - - -
225A HIS* 2.8 52.4 - + - +
228A ALA* 4.9 3.6 - - + -
229A LYS* 3.7 48.1 + - + -
232A LEU* 3.9 16.7 - - + +
233A LEU* 4.5 8.5 - - + -
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Residues in contact with LEU 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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92A VAL* 3.8 18.2 - - + -
95A LEU* 3.5 32.8 - - + -
159A LEU* 3.6 30.3 - - + +
160A PHE* 4.2 26.7 - - + -
163A SER* 3.8 17.3 - - - +
203A PHE 2.9 13.3 + - - +
204A PHE* 3.3 23.8 - - - +
207A TYR* 1.4 75.3 - - - +
209A PRO* 1.4 65.2 - - + +
211A ALA* 3.8 4.0 - - - +
212A ALA* 3.0 21.9 + - + +
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Residues in contact with PRO 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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60A ARG* 3.4 32.5 - - + +
63A THR* 3.6 21.1 - - + -
64A VAL* 3.6 22.7 - - + +
92A VAL* 4.6 5.2 - - + -
204A PHE 3.5 13.0 - - - +
205A SER 3.6 15.9 - - - +
206A PHE* 3.5 13.7 - - - +
208A LEU* 1.4 94.3 - - + +
210A ILE* 1.4 61.2 + - - +
212A ALA 3.5 0.3 + - - -
213A ALA* 3.2 20.4 + - - +
344A LEU* 5.5 0.2 - - + -
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Residues in contact with ILE 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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63A THR* 3.4 27.6 - - + -
67A ALA* 3.9 11.0 - - + -
71A LEU* 5.6 0.9 - - + -
206A PHE 3.9 5.6 - - - +
207A TYR* 3.4 1.2 + - + -
208A LEU 3.4 0.2 - - - -
209A PRO* 1.4 73.4 - - - +
211A ALA* 1.4 60.4 + - - +
213A ALA* 3.2 7.0 + - - +
214A MET* 2.9 46.9 + - + +
232A LEU* 3.6 40.4 - - + -
336A LEU* 5.1 1.1 - - + -
340A VAL* 3.7 43.1 - - + +
341A PHE* 4.5 7.6 - - + -
344A LEU* 4.6 2.9 - - + -
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Residues in contact with ALA 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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159A LEU* 3.7 20.0 - - + -
207A TYR* 2.8 55.7 + - + +
208A LEU 3.8 0.9 - - - +
210A ILE* 1.4 71.8 - - - +
212A ALA* 1.4 56.5 + - - +
214A MET* 3.3 6.8 + - - +
215A TYR* 3.0 33.3 + - - -
225A HIS* 3.6 12.7 + - + -
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Residues in contact with ALA 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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64A VAL* 4.7 2.7 - - + -
88A VAL* 3.9 26.5 - - + -
92A VAL* 5.3 0.4 - - + -
156A LEU* 3.8 12.9 - - + +
159A LEU* 3.5 12.7 - - + +
160A PHE* 4.8 6.7 - - + -
208A LEU* 3.0 19.2 + - + +
209A PRO* 3.7 6.5 - - + +
210A ILE 3.3 0.2 - - - -
211A ALA* 1.4 72.4 - - - +
213A ALA* 1.3 59.6 + - - +
215A TYR* 3.3 3.3 + - - +
216A MET* 3.0 35.8 + - - +
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Residues in contact with ALA 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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64A VAL* 3.8 14.2 - - - +
67A ALA* 3.7 29.6 - - + -
68A PHE* 3.7 19.6 - - + +
71A LEU* 4.1 4.4 - - + +
209A PRO 3.2 8.5 + - - +
210A ILE 3.2 8.4 + - - +
212A ALA* 1.3 76.5 - - - +
214A MET* 1.4 56.6 + - - +
216A MET* 3.3 9.0 + - - +
217A ALA* 2.9 30.5 + - - +
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Residues in contact with MET 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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71A LEU* 4.0 19.3 - - + +
210A ILE* 2.9 34.7 + - + +
211A ALA* 3.3 12.3 + - - +
213A ALA* 1.4 75.7 - - - +
215A TYR* 1.4 55.5 + - - +
217A ALA* 3.2 8.4 + - - -
219A ILE* 2.8 59.4 + - + +
224A GLU* 3.8 24.9 - - + +
225A HIS* 3.8 29.8 - - + +
228A ALA* 3.9 12.6 - - - -
336A LEU* 4.0 18.4 - - + -
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Residues in contact with TYR 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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152A TYR* 3.5 23.5 - - + +
155A ASN* 3.8 41.1 + - + -
156A LEU* 4.2 11.9 - - + -
159A LEU* 3.8 36.0 - - + +
207A TYR* 4.6 2.6 + - - -
211A ALA 3.0 19.8 + - - -
212A ALA 3.7 5.2 - - - +
214A MET* 1.4 72.1 - - - +
216A MET* 1.3 61.1 + - - +
218A GLY* 3.1 17.7 + - - -
219A ILE 3.9 2.5 - - - +
220A ASP* 3.8 26.7 + - + +
225A HIS* 3.5 36.7 + + - +
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Residues in contact with MET 216 (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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64A VAL* 4.7 5.6 - - - -
68A PHE* 3.8 28.8 - - + -
72A VAL* 4.9 0.7 - - - +
81A SER 4.8 0.2 - - - +
84A ARG* 3.6 35.2 - - + +
85A ALA* 3.6 11.2 - - - +
88A VAL* 3.7 33.0 - - + -
152A TYR* 3.4 55.0 - - + +
156A LEU* 4.1 4.5 - - + -
212A ALA 3.0 20.9 + - - +
213A ALA* 3.3 5.4 + - - +
215A TYR* 1.3 75.0 - - - +
217A ALA* 1.4 58.5 + - - +
218A GLY 3.2 0.7 + - - -
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Residues in contact with ALA 217 (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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71A LEU* 3.9 15.7 - - + +
72A VAL* 3.7 27.1 - - + -
213A ALA 2.9 15.8 + - - +
214A MET 3.2 5.5 + - - +
216A MET* 1.4 75.0 - - - +
218A GLY* 1.3 60.0 + - - +
219A ILE* 3.3 22.6 + - + +
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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