Contacts of the helix formed by residues 191 - 202 (chain A) in PDB entry 3QTC
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ALA 3.6 4.0 + - - +
190A LEU* 1.3 76.0 - - - +
192A LYS* 1.3 57.9 + - - +
193A SER* 3.5 10.5 + - - -
194A GLN* 2.9 41.1 + - - +
195A THR* 2.9 29.1 + - - +
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Residues in contact with LYS 192 (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 3.9 0.4 + - - -
191A THR* 1.3 72.4 - - - +
193A SER* 1.3 57.1 + - - +
195A THR* 2.8 27.3 + - - +
196A ASP* 2.9 51.0 + - - +
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Residues in contact with SER 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 THR* 3.2 8.8 + - - -
192A LYS* 1.3 80.4 - - - +
194A GLN* 1.3 63.0 + - - +
196A ASP* 3.4 10.5 + - - +
197A ARG* 3.1 21.7 + - - +
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Residues in contact with GLN 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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189A ALA 4.5 1.6 - - - +
190A LEU* 3.5 13.1 - - + +
191A THR* 2.9 46.0 + - + +
193A SER* 1.3 74.3 - - - +
195A THR* 1.3 66.3 + - - +
197A ARG* 3.2 5.3 + - - +
198A LEU* 3.0 28.4 + - - +
216A PHE* 3.5 54.7 - - + +
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Residues in contact with THR 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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190A LEU* 3.6 31.4 - - + +
191A THR 2.9 18.0 + - - +
192A LYS* 2.8 35.0 + - - +
194A GLN* 1.3 77.4 - - - +
196A ASP* 1.3 60.3 + - - +
198A LEU* 3.3 8.5 + - - +
199A GLU* 2.8 38.1 + - - +
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Residues in contact with ASP 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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192A LYS* 2.9 51.4 + - - +
193A SER* 3.5 12.0 - - - +
194A GLN 3.3 0.2 - - - -
195A THR* 1.3 75.8 + - - +
197A ARG* 1.3 61.8 + - - +
199A GLU* 3.3 11.9 + - - +
200A VAL* 3.1 27.8 + - + +
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Residues in contact with ARG 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 SER 3.1 13.1 + - - +
194A GLN* 3.2 8.9 + - - +
196A ASP* 1.3 77.5 - - - +
198A LEU* 1.3 61.8 + - - +
200A VAL* 3.3 32.2 + - - +
201A LEU* 3.5 26.4 + - + +
216A PHE* 3.9 16.6 - - + -
220A GLU* 3.1 29.3 + - + +
224A LEU* 3.5 25.7 - - - +
453A ASN* 3.1 34.2 + - - +
454A LEU* 4.6 3.0 + - - +
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Residues in contact with LEU 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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190A LEU* 3.8 28.7 - - + -
194A GLN 3.0 18.4 + - - +
195A THR* 3.8 7.6 - - + +
197A ARG* 1.3 75.4 - - - +
199A GLU* 1.3 59.1 + - + +
201A LEU* 3.0 8.7 + - + +
202A LEU* 2.9 30.0 + - + +
216A PHE* 3.8 20.2 - - + -
219A LEU* 4.0 21.8 - - + -
220A GLU* 3.7 37.5 - - + +
223A LEU* 3.6 16.8 - - + +
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Residues in contact with GLU 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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195A THR* 2.8 29.3 + - - +
196A ASP* 3.6 10.5 - - - +
197A ARG 3.2 0.2 - - - -
198A LEU* 1.3 73.4 - - + +
200A VAL* 1.3 55.5 + - - +
202A LEU* 3.3 30.2 + - + +
435A LYS* 3.5 28.7 + - - +
439A ARG* 2.7 29.8 + - - -
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Residues in contact with VAL 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 ASP* 3.1 16.9 + - + +
197A ARG* 3.4 26.9 - - - +
198A LEU 3.3 0.2 - - - -
199A GLU* 1.3 75.5 - - - +
201A LEU* 1.3 58.4 + - + +
227A ARG* 5.8 0.2 - - - -
439A ARG* 3.1 21.0 + - - +
446A TYR* 3.8 21.9 - - + +
451A SER* 3.4 35.4 + - - +
453A ASN* 5.6 2.5 - - + +
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Residues in contact with LEU 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 ARG* 3.7 41.5 - - + +
198A LEU* 3.0 11.7 + - - +
200A VAL* 1.3 74.8 - - - +
202A LEU* 1.3 52.7 + - - +
220A GLU* 4.0 18.4 - - + +
223A LEU* 3.8 19.5 - - + +
224A LEU* 3.8 27.6 - - + -
227A ARG* 2.8 46.9 + - + +
439A ARG* 5.2 0.2 - - - -
451A SER* 4.1 9.9 - - - -
454A LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 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 LEU* 2.9 12.9 + - + +
199A GLU* 3.3 31.9 + - + +
201A LEU* 1.3 78.4 - - - +
203A ASN* 1.3 61.5 + - - +
204A PRO* 4.3 0.7 - - - +
206A ASP* 3.7 24.9 - - + +
207A GLU 5.7 2.0 - - - +
223A LEU* 4.0 19.7 - - + -
227A ARG* 5.3 0.2 - - - -
435A LYS* 5.6 3.4 - - + +
439A ARG* 2.8 36.5 + - - -
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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