Contacts of the helix formed by residues 196 - 207 (chain A) in PDB entry 3H44
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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192A LYS 4.3 5.6 + - - +
193A ASN* 3.1 20.7 + - - +
194A VAL 3.1 1.0 - - - -
195A MET* 1.3 78.0 - - - +
197A ASP* 1.3 66.0 + - - +
198A ALA* 3.2 12.5 + - - +
199A TRP* 2.7 61.0 + - + +
200A ARG* 3.2 13.2 + - - +
677A GLN* 5.5 2.7 - - - +
786A HIS* 5.5 1.3 - - + -
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Residues in contact with ASP 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 MET 3.6 2.7 + - - +
196A ASN* 1.3 73.6 + - - +
198A ALA* 1.3 60.3 + - - +
200A ARG* 3.8 10.0 + - - +
201A LEU* 3.2 35.2 + - + +
306A PRO* 3.4 9.2 - - - +
307A ILE* 2.7 31.6 + - - +
308A LYS* 2.8 43.8 + - + +
310A ILE* 4.0 22.2 - - + +
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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* 3.0 12.9 + - - +
197A ASP* 1.3 77.1 - - - +
199A TRP* 1.3 58.5 + - + +
201A LEU* 3.6 8.7 + - - +
202A PHE* 3.0 26.3 + - - +
2000A DIO 4.1 4.2 - - - +
16C LYS* 4.1 19.6 - - - +
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Residues in contact with TRP 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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192A LYS* 5.4 1.7 - - - +
193A ASN* 3.3 53.6 + - + +
196A ASN* 2.7 35.7 - - - +
198A ALA* 1.3 74.7 - - + +
200A ARG* 1.3 65.7 + - - +
202A PHE* 3.1 23.0 + + - +
203A GLN* 3.0 25.1 + - - +
220A THR* 4.2 11.7 - - - -
496A TYR* 3.5 27.0 - - + -
16C LYS* 3.3 41.4 - - + +
17C ARG* 3.8 18.8 - - + -
18C SER* 4.2 15.7 - - - -
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Residues in contact with ARG 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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194A VAL 2.7 39.8 + - - +
195A MET* 4.1 7.7 - - - +
196A ASN 3.3 22.0 - - - +
197A ASP* 3.9 11.2 + - - +
199A TRP* 1.3 76.4 - - - +
201A LEU* 1.3 59.8 + - + +
203A GLN* 3.4 1.4 + - - +
204A LEU* 2.8 31.9 + - - +
305A VAL 4.9 5.5 + - - -
306A PRO* 5.6 0.2 - - - +
307A ILE* 3.5 40.1 - - - +
493A GLU* 5.3 0.3 - - - +
496A TYR* 3.4 34.2 + - + -
497A GLY 3.7 8.3 + - - -
498A THR* 3.5 49.2 + - + +
499A GLN* 4.7 2.8 - - - +
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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 ASP* 3.2 29.7 + - + +
198A ALA* 3.7 5.6 - - - +
200A ARG* 1.3 82.9 - - + +
202A PHE* 1.3 61.3 + - - +
204A LEU* 3.8 6.3 - - + +
205A GLU* 3.1 22.7 + - - +
304A ILE* 4.1 25.4 - - + -
306A PRO* 6.4 1.1 - - + -
310A ILE* 5.4 2.7 - - + -
314A TYR* 3.6 29.2 - - + +
481A VAL* 4.1 28.5 - - + -
498A THR* 5.2 1.3 - - + -
2000A DIO 3.1 30.0 - - - +
2002A DIO 4.1 3.9 - - - +
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Residues in contact with PHE 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 TRP* 3.1 30.2 + + - +
201A LEU* 1.3 78.0 - - - +
203A GLN* 1.3 71.3 + - + +
205A GLU* 3.7 6.7 + - - +
206A LYS* 3.2 51.2 + - + +
215A PHE* 5.7 0.8 - + - -
219A GLY 6.4 0.2 - - - -
496A TYR* 5.3 0.4 - - - -
2000A DIO 3.8 21.8 - - - -
16C LYS* 4.1 48.5 - - + -
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Residues in contact with GLN 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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199A TRP 3.0 7.4 + - - +
200A ARG 4.1 0.4 - - - +
202A PHE* 1.3 83.2 - - + +
204A LEU* 1.3 59.0 + - - +
205A GLU 3.1 1.8 - - - -
206A LYS* 2.8 33.0 + - - +
207A ALA* 2.8 29.5 + - + +
216A SER 3.9 6.1 + - - -
217A LYS 3.1 27.3 + - - +
218A PHE* 3.7 29.1 - - - +
219A GLY 4.5 1.9 + - - -
493A GLU* 3.6 21.1 - - - +
495A TRP* 4.2 6.5 - - + -
496A TYR* 3.4 34.2 + - + -
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Residues in contact with LEU 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 ARG 2.8 19.9 + - - +
201A LEU* 3.8 7.6 - - + +
203A GLN* 1.3 72.8 - - - +
205A GLU* 1.3 66.7 + - - +
207A ALA* 3.3 7.2 + - + +
208A THR* 3.3 18.4 + - + +
302A TYR* 5.2 0.2 - - + -
304A ILE* 3.2 45.5 - - + -
493A GLU* 3.9 23.6 - - + +
498A THR* 4.3 8.3 - - + +
500A TYR* 3.7 44.0 - - + +
2002A DIO 3.4 15.5 - - - +
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Residues in contact with GLU 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 LEU 3.1 16.8 + - - +
202A PHE* 3.8 6.4 - - - +
203A GLN 3.1 0.2 - - - -
204A LEU* 1.3 74.8 - - - +
206A LYS* 1.3 64.2 + - - +
207A ALA 3.0 1.4 + - - -
208A THR* 3.0 17.7 + - - -
209A GLY 3.7 4.3 + - - -
215A PHE* 3.9 16.6 - - + -
293A PHE* 3.6 33.8 - - + -
316A THR* 4.1 15.1 + - - +
364A LYS* 3.4 26.6 + - - -
372A PHE* 4.5 3.0 - - - -
477A ARG* 4.3 1.3 - - - +
2000A DIO 4.0 12.5 - - - +
2002A DIO 3.4 32.0 + - - +
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Residues in contact with LYS 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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97A LEU* 4.7 9.1 - - - +
202A PHE* 3.2 50.3 - - - +
203A GLN* 2.8 38.2 + - - +
205A GLU* 1.3 75.5 - - - +
207A ALA* 1.3 57.9 + - - +
208A THR 3.2 3.9 + - - -
209A GLY* 3.6 8.5 + - - -
215A PHE* 3.0 67.3 + - + +
216A SER* 3.3 22.2 - - - -
217A LYS 3.8 6.8 + - - +
219A GLY 6.3 0.4 - - - +
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Residues in contact with ALA 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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203A GLN* 2.8 17.1 + - - +
204A LEU* 4.0 4.9 - - + +
205A GLU 3.0 1.0 + - - -
206A LYS* 1.3 75.9 - - + +
208A THR* 1.3 64.0 + - + +
209A GLY 3.7 4.3 - - - +
211A PRO* 5.9 3.1 - - - +
216A SER* 4.9 7.2 - - - +
493A GLU* 4.1 27.4 - - + +
495A TRP* 6.1 0.4 - - + -
500A TYR* 4.7 5.7 + - - +
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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