Contacts of the helix formed by residues 196 - 208 (chain A) in PDB entry 3D4S
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A TRP 2.7 27.3 + - - +
174A TYR 2.7 17.3 + - - -
175A ARG 3.3 17.7 + - - +
176A ALA* 4.1 8.2 - - - +
177A THR* 5.5 1.6 - - + +
195A THR* 1.3 78.3 + - - +
197A GLN* 1.3 61.5 + - - +
198A ALA* 3.2 10.3 + - - +
199A TYR* 2.7 33.4 + - - +
200A ALA* 3.2 16.7 + - - +
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Residues in contact with GLN 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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195A THR 5.6 0.7 - - - +
196A ASN* 1.3 73.6 - - - +
198A ALA* 1.3 60.8 + - - +
200A ALA* 4.0 2.4 - - - +
201A ILE* 3.4 31.9 + - + +
297A VAL* 3.6 40.6 + - + +
300A ASP* 5.3 7.4 - - - +
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Residues in contact with ALA 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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196A ASN* 3.2 9.9 + - - +
197A GLN* 1.3 76.3 - - - +
199A TYR* 1.3 59.7 + - - +
201A ILE* 3.5 3.3 + - - +
202A ALA* 3.0 33.2 + - - +
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Residues in contact with TYR 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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114A VAL* 4.3 8.1 - - - +
164A THR 5.3 2.3 + - - -
165A SER 4.7 1.6 + - - -
168A PRO* 3.7 31.9 - - + -
169A ILE* 3.8 21.9 - - + +
173A TRP* 4.4 3.8 - - + +
174A TYR* 3.7 30.3 - - + +
193A PHE* 3.8 17.0 - + - -
195A THR* 3.7 16.4 - - + -
196A ASN* 2.7 23.5 + - - +
198A ALA* 1.3 70.0 - - - +
200A ALA* 1.3 62.3 + - - +
202A ALA* 4.6 3.6 - - - -
203A SER* 2.8 56.6 + - - -
401A TIM 3.4 28.1 - - - -
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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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195A THR* 3.6 19.5 - - - +
196A ASN 3.2 9.7 + - - +
197A GLN* 4.0 2.5 - - - +
198A ALA 3.4 0.2 - - - -
199A TYR* 1.3 84.9 - - - +
201A ILE* 1.3 57.1 + - - +
204A SER* 2.6 29.6 + - - -
293A ASN* 3.5 13.3 + - - +
294A ILE* 4.7 2.6 - - - +
297A VAL* 3.5 26.9 - - + +
401A TIM 4.4 7.9 - - - +
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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 GLN* 3.4 16.6 + - + +
198A ALA* 4.1 3.1 - - - +
199A TYR 3.2 0.4 - - - -
200A ALA* 1.3 77.6 - - - +
202A ALA* 1.3 66.7 + - - +
204A SER* 3.3 4.5 + - - -
205A ILE* 3.1 45.6 + - + +
294A ILE* 5.1 18.4 - - + -
297A VAL* 3.8 30.3 - - + -
298A ILE* 5.2 10.5 - - + -
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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 ALA 3.0 19.3 + - - +
199A TYR* 4.1 3.1 - - - +
201A ILE* 1.3 79.0 - - - +
203A SER* 1.3 61.0 + - - +
205A ILE* 3.6 4.0 + - - +
206A VAL* 3.1 33.4 + - + +
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Residues in contact with SER 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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114A VAL* 4.7 3.3 - - - +
164A THR 5.0 4.9 + - - -
199A TYR* 2.8 44.2 + - - -
202A ALA* 1.3 71.7 - - - +
204A SER* 1.3 57.7 + - - +
206A VAL* 4.9 2.0 - - - -
207A SER* 2.7 51.2 + - - +
401A TIM 3.4 26.9 + - - -
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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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200A ALA 2.6 26.4 + - - -
201A ILE 3.3 4.2 + - - -
203A SER* 1.3 77.9 - - - +
205A ILE* 1.3 57.8 + - - +
208A PHE* 3.0 10.2 + - - +
209A TYR* 2.9 38.3 + - - -
290A PHE* 4.0 22.6 - - - -
293A ASN* 2.8 22.1 + - - -
294A ILE* 4.4 8.5 - - - -
401A TIM 4.0 3.8 + - - -
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Residues in contact with ILE 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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201A ILE* 3.1 35.6 + - + +
202A ALA* 4.0 4.5 - - - +
204A SER* 1.3 76.0 - - - +
206A VAL* 1.3 67.7 + - + +
209A TYR* 3.4 20.5 + - + -
210A VAL* 2.8 48.4 + - + +
294A ILE* 4.9 7.4 - - + -
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Residues in contact with VAL 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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122A TRP* 3.3 30.5 + - + +
164A THR* 5.0 18.4 - - + +
202A ALA* 3.1 19.5 + - + +
203A SER* 4.3 2.2 - - - +
205A ILE* 1.3 81.8 - - + +
207A SER* 1.3 63.0 + - - +
210A VAL* 4.5 8.0 - - + +
211A PRO* 3.7 2.3 - - - +
404A OLC 5.8 7.9 - - + -
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Residues in contact with SER 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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114A VAL* 5.0 2.1 - - - +
118A THR* 3.4 35.9 + - - +
121A ILE* 3.1 23.2 - - - +
122A TRP* 3.7 4.9 + - - +
164A THR* 4.7 11.6 + - - -
165A SER* 5.2 0.3 + - - -
203A SER* 2.7 35.2 + - - -
206A VAL* 1.3 77.0 - - - +
208A PHE* 1.3 55.9 + - - -
211A PRO* 3.6 4.4 - - - +
401A TIM 3.8 15.1 + - - -
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Residues in contact with PHE 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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117A VAL* 4.9 1.8 - - + -
121A ILE* 3.8 14.5 - - + +
204A SER 3.0 13.0 + - - +
206A VAL 3.6 0.2 - - - -
207A SER* 1.3 79.2 - - - +
209A TYR* 1.3 73.7 + + - +
210A VAL 3.5 1.8 - - - -
211A PRO* 3.3 5.0 - - - +
212A LEU* 3.1 56.3 + - + +
282A PHE* 3.7 33.0 - + - -
283A THR* 5.2 1.3 - - - -
286A TRP* 3.7 10.3 - - + -
287A LEU* 3.9 26.9 - - + -
290A PHE* 3.4 61.5 - + + -
401A TIM 5.3 0.2 - - - -
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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