Contacts of the helix formed by residues 192 - 204 (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 ASN 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU 4.0 0.2 - - - +
191A SER* 1.3 77.6 - - - +
193A PRO* 1.3 76.4 - - - +
194A ALA* 3.5 22.6 + - - +
195A VAL* 3.1 25.7 + - + +
196A THR* 2.9 22.8 + - - -
1208A OLC 3.3 19.4 + - - +
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Residues in contact with PRO 193 (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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191A SER 3.3 9.9 - - - +
192A ASN* 1.3 92.4 - - - +
194A ALA* 1.3 55.6 + - - +
196A THR* 3.4 8.5 + - - +
197A PHE* 2.9 30.5 + - - +
420A VAL 5.0 1.4 - - - +
423A ASN* 3.3 41.5 - - + +
424A THR* 4.0 11.2 - - - +
427A GLN* 3.8 23.1 - - + +
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Residues in contact with ALA 194 (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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192A ASN* 3.2 19.6 + - - +
193A PRO* 1.3 76.5 - - - +
195A VAL* 1.3 60.9 + - + +
197A PHE* 3.2 8.2 + - - +
198A GLY* 2.9 25.8 + - - -
424A THR* 5.1 4.0 - - - +
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Residues in contact with VAL 195 (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* 4.0 39.0 - - + +
190A LEU* 4.4 1.8 - - + -
192A ASN* 3.1 33.3 + - + +
194A ALA* 1.3 75.0 - - + +
196A THR* 1.3 55.3 + - - +
198A GLY* 3.4 1.8 + - - +
199A THR* 2.6 42.2 + - - +
1208A OLC 4.2 28.3 - - + +
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Residues in contact with THR 196 (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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190A LEU* 2.8 42.1 + - + +
192A ASN 2.9 10.7 + - - -
193A PRO* 3.5 11.6 - - - +
195A VAL* 1.3 78.2 - - - +
197A PHE* 1.3 57.0 + - - +
199A THR* 3.4 3.5 + - - -
200A ALA* 2.9 26.2 + - - +
416A TYR* 6.0 0.4 - - - +
420A VAL* 3.9 17.7 - - + -
423A ASN* 5.8 0.7 - - - -
1201A 0HK 3.5 23.4 - - + +
1205A P6G 4.6 16.4 + - - +
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Residues in contact with PHE 197 (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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193A PRO 2.9 17.5 + - - +
194A ALA* 3.2 5.6 + - - +
196A THR* 1.3 75.4 - - - +
198A GLY* 1.3 60.6 + - - +
200A ALA* 3.1 3.1 + - - +
201A ILE* 2.9 55.8 + - + +
205A TYR* 4.2 15.7 - + - -
420A VAL* 3.8 13.0 - - + +
421A LEU* 3.6 46.0 - - + -
424A THR* 3.6 20.0 - - + -
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Residues in contact with GLY 198 (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 ALA 2.9 15.5 + - - -
195A VAL* 3.9 2.2 - - - -
197A PHE* 1.3 77.7 - - - +
199A THR* 1.3 56.8 + - - +
201A ILE* 3.2 14.8 + - - +
202A ALA* 2.9 28.6 + - - +
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Residues in contact with THR 199 (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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164A TRP* 3.4 39.3 - - + -
189A PHE* 4.3 5.0 - - - -
190A LEU* 3.6 15.7 - - + +
195A VAL* 2.6 28.0 + - - +
196A THR 3.5 5.6 - - - -
198A GLY* 1.3 77.0 - - - +
200A ALA* 1.3 56.3 + - - +
202A ALA* 3.3 6.6 + - - +
203A ALA* 2.9 33.1 + - - +
1201A 0HK 3.6 8.1 - - + -
1208A OLC 4.2 17.2 - - + +
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Residues in contact with ALA 200 (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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196A THR 2.9 15.3 + - - +
197A PHE* 3.1 9.4 + - + +
199A THR* 1.3 75.5 - - - +
201A ILE* 1.3 57.0 + - - +
204A PHE* 2.7 30.0 + - - +
205A TYR* 3.1 20.6 + - + -
417A ASN* 4.0 15.7 - - - +
420A VAL* 3.9 19.3 - - + -
1201A 0HK 3.8 15.2 - - + -
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Residues in contact with ILE 201 (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 PHE* 2.9 54.4 + - + +
198A GLY* 3.3 13.0 - - - +
200A ALA* 1.3 76.8 - - - +
202A ALA* 1.3 63.2 + - + +
203A ALA 3.4 0.5 + - - -
205A TYR* 3.8 16.4 - - + -
206A LEU* 3.1 49.4 + - + +
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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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198A GLY 2.9 14.9 + - - +
199A THR* 3.9 6.5 - - - +
201A ILE* 1.3 79.2 - - + +
203A ALA* 1.3 59.3 + - - +
206A LEU* 4.4 12.8 - - + +
207A PRO* 4.0 8.3 - - - +
1208A OLC 3.4 34.0 - - + +
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Residues in contact with ALA 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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117A ASN* 4.3 1.0 - - - +
120A VAL* 3.6 14.7 - - - +
164A TRP* 4.8 1.1 - - + -
199A THR 2.9 18.0 + - - +
200A ALA 4.3 0.4 - - - +
202A ALA* 1.3 80.7 - - - +
204A PHE* 1.3 59.9 + - - +
207A PRO* 3.2 17.3 - - - +
1201A 0HK 3.7 37.8 - - + +
1208A OLC 3.9 25.7 - - + +
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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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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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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