Contacts of the helix formed by residues 204 - 221 (chain A) in PDB entry 5DSG
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 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 5.5 1.1 - - - -
200A ALA 2.7 15.3 + - - +
203A ALA* 1.3 74.2 - - - +
205A TYR* 1.3 84.6 + + - +
207A PRO* 3.2 4.6 - - - +
208A VAL* 3.1 52.4 + - + +
409A PHE* 3.9 22.6 - + - -
410A ILE* 4.7 2.9 - - + -
413A TRP* 3.5 26.9 - + + -
414A THR* 3.9 30.5 - - + -
417A ASN* 3.4 36.8 - - + +
1201A 0HK 3.3 20.2 - - - +
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.2 14.6 - + - -
200A ALA* 3.1 42.5 + - + -
201A ILE* 3.8 20.6 - - + +
204A PHE* 1.3 92.7 - + - +
206A LEU* 1.3 59.8 + - + +
208A VAL* 3.2 7.1 + - + +
209A VAL* 2.9 36.9 + - + +
414A THR* 6.6 0.4 - - + -
417A ASN* 2.8 42.1 + - + +
418A VAL* 3.7 8.4 + - + +
421A LEU* 3.9 16.3 - - + +
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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
----------------------------------------------------------
201A ILE* 3.1 33.3 + - + +
202A ALA* 4.4 10.3 - - - +
205A TYR* 1.3 80.0 - - + +
207A PRO* 1.4 70.1 - - + +
209A VAL* 3.2 11.8 + - + +
210A ILE* 2.9 36.3 + - + +
1207A OLC 5.3 14.1 - - + -
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Residues in contact with PRO 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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120A VAL* 3.8 21.5 - - + -
124A LEU* 3.9 28.3 - - + -
202A ALA 4.0 8.5 - - - +
203A ALA 3.2 24.0 - - - +
204A PHE 3.2 15.0 - - - +
206A LEU* 1.4 94.5 - - + +
208A VAL* 1.3 56.2 + - + +
210A ILE* 3.4 4.3 + - + +
211A MET* 2.9 41.5 + - + +
1208A OLC 5.0 4.0 - - + -
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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
----------------------------------------------------------
204A PHE* 3.1 53.8 + - + +
205A TYR* 3.2 7.2 + - + +
207A PRO* 1.3 75.0 - - - +
209A VAL* 1.3 58.4 + - + +
211A MET* 3.8 7.7 - - + +
212A THR* 2.5 44.1 + - - +
406A LEU* 5.8 0.6 - - - +
409A PHE* 3.8 17.9 - - + -
410A ILE* 4.4 24.0 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 2.9 23.0 + - + +
206A LEU* 3.6 15.5 - - + +
208A VAL* 1.3 79.5 - - + +
210A ILE* 1.3 59.8 + - + +
212A THR* 3.1 8.3 + - - -
213A VAL* 2.9 39.0 + - + +
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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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124A LEU* 4.4 8.7 - - + -
128A PHE* 3.6 34.3 - - + -
206A LEU* 2.9 29.3 + - + +
207A PRO* 3.8 7.2 - - + +
209A VAL* 1.3 78.9 - - + +
211A MET* 1.3 57.6 + - - +
213A VAL* 3.3 7.8 + - - +
214A LEU* 2.9 34.4 + - + +
1207A OLC 3.6 44.6 - - + -
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Residues in contact with MET 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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120A VAL* 5.1 2.0 - - + +
123A LEU* 3.6 33.4 - - + -
124A LEU* 3.7 17.5 - - + -
127A SER* 3.5 26.0 + - - +
207A PRO* 2.9 36.1 + - + +
208A VAL* 3.9 9.4 - - - +
210A ILE* 1.3 76.5 - - - +
212A THR* 1.3 57.6 + - - +
214A LEU* 3.7 9.1 - - + +
215A TYR* 2.9 29.3 + - - +
406A LEU* 3.7 34.2 - - + +
409A PHE* 4.1 19.5 - - + -
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 2.5 28.6 + - - +
209A VAL* 3.1 13.0 + - - -
211A MET* 1.3 75.1 - - - +
213A VAL* 1.3 62.3 + - + +
215A TYR* 3.2 10.3 + - + +
216A ILE* 2.9 47.7 + - + +
406A LEU* 5.2 2.6 - - - +
410A ILE* 4.8 8.0 - - - +
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Residues in contact with VAL 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 VAL* 2.9 28.9 + - + +
210A ILE* 3.6 9.6 - - + +
212A THR* 1.3 76.2 - - + +
214A LEU* 1.3 66.9 + - + +
216A ILE* 3.0 14.3 + - + +
217A HIS* 2.9 53.6 + - + +
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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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127A SER* 3.9 14.4 - - - +
128A PHE* 3.7 61.7 - - + +
131A TYR* 3.5 43.6 - - + -
210A ILE* 2.9 25.4 + - + +
211A MET* 3.7 5.8 - - + +
213A VAL* 1.3 80.4 - - + +
215A TYR* 1.3 56.0 + - - +
217A HIS* 3.3 3.8 + - + +
218A ILE* 2.9 36.3 + - + +
1207A OLC 5.6 3.1 - - + -
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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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211A MET 2.9 19.3 + - - +
212A THR* 3.5 10.5 - - + +
214A LEU* 1.3 75.8 - - - +
216A ILE* 1.3 66.8 + - + +
218A ILE* 3.7 13.6 - - + +
219A SER* 2.9 47.6 + - - -
399A THR* 5.9 6.3 - - + -
403A PHE* 3.4 57.4 - + + -
406A LEU* 4.6 11.9 - - + -
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Residues in contact with ILE 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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212A THR* 2.9 37.0 + - + +
213A VAL* 3.0 14.1 + - + +
215A TYR* 1.3 84.0 - - + +
217A HIS* 1.3 65.9 + - + +
219A SER* 2.7 21.0 + - - +
220A LEU* 2.9 35.3 + - + +
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Residues in contact with HIS 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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131A TYR* 3.6 35.7 - + + -
135A THR* 5.3 2.6 - - + +
213A VAL* 2.9 46.4 + - + +
214A LEU* 3.8 4.0 - - - +
216A ILE* 1.3 85.1 - - + +
218A ILE* 1.3 57.7 + - - +
220A LEU* 3.4 9.2 + - + +
221A ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 218 (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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127A SER* 3.9 9.2 - - - +
130A ARG* 3.7 17.0 - - + +
131A TYR* 3.6 39.3 - - + +
134A VAL* 4.5 16.9 - - + +
135A THR* 6.1 0.7 - - + -
214A LEU* 2.9 26.2 + - + +
215A TYR* 3.7 14.1 - - + +
217A HIS* 1.3 77.7 - - - +
219A SER* 1.3 58.1 + - - +
221A ALA* 3.0 30.2 + - - +
399A THR* 4.1 25.8 - - + +
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Residues in contact with SER 219 (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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215A TYR* 2.9 37.1 + - - -
216A ILE* 2.7 25.1 + - - +
218A ILE* 1.3 79.2 - - - +
220A LEU* 1.3 63.9 + - - +
221A ALA 3.6 3.5 + - - +
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Residues in contact with LEU 220 (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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216A ILE* 2.9 39.0 + - + +
217A HIS* 3.7 9.6 - - + +
218A ILE 3.2 0.2 - - - -
219A SER* 1.3 79.5 + - - +
221A ALA* 1.3 61.7 + - - +
222A SER* 3.4 4.5 + - - -
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Residues in contact with ALA 221 (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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134A VAL* 3.6 31.6 - - + +
135A THR* 5.1 7.0 - - + -
217A HIS 3.0 16.4 + - - +
218A ILE* 3.0 17.3 + - - +
219A SER 4.3 3.4 - - - +
220A LEU* 1.3 76.9 - - - +
222A SER* 1.3 64.6 + - - +
223A ARG* 3.7 2.8 + - - +
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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