Contacts of the helix formed by residues 1196 - 1203 (chain A) in PDB entry 3AVS
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 ASN1196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A ASP 5.9 0.2 - - - -
1019A LYS* 3.4 47.8 + - + +
1020A ILE 5.6 2.7 - - - +
1021A TRP* 3.5 16.9 - - + +
1194A TRP 3.5 2.7 + - - +
1195A PRO* 1.3 69.9 - - - +
1197A LEU* 1.3 64.1 + - - +
1198A GLU* 3.0 25.4 + - - +
1199A ASP* 3.0 42.1 + - - +
1200A LEU* 3.2 12.2 + - - +
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Residues in contact with LEU1197 (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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1009A ASP* 3.7 31.7 + - + +
1019A LYS* 5.4 1.3 - - - +
1167A PHE* 4.0 15.7 - - + -
1195A PRO 3.5 5.3 + - - +
1196A ASN* 1.3 73.6 + - - +
1198A GLU* 1.3 58.0 + - + +
1200A LEU* 3.3 14.2 + - + +
1201A TYR* 3.0 29.3 + - - +
1207A VAL* 4.5 13.9 - - + -
1209A ARG* 3.7 28.0 - - - +
1227A TRP* 4.1 27.1 - - + +
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Residues in contact with GLU1198 (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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1010A GLU* 5.6 0.3 - - - +
1019A LYS* 3.2 32.9 + - - +
1196A ASN* 3.0 11.6 + - - +
1197A LEU* 1.3 77.2 - - + +
1199A ASP* 1.3 65.4 + - - +
1201A TYR* 3.6 7.4 + - - +
1202A GLU* 3.2 24.1 + - - +
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Residues in contact with ASP1199 (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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1021A TRP* 3.0 29.5 + - + -
1180A PHE* 3.5 34.4 - - + -
1184A ASN* 5.2 1.4 + - - -
1196A ASN* 3.0 25.7 + - + +
1198A GLU* 1.3 76.8 - - - +
1200A LEU* 1.3 63.8 + - - +
1202A GLU* 3.4 6.0 + - - +
1203A ALA* 3.2 16.1 + - - +
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Residues in contact with LEU1200 (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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1021A TRP* 4.2 11.0 - - + -
1169A VAL* 4.3 5.8 - - + -
1177A LEU* 4.2 17.7 - - + -
1180A PHE* 3.8 26.5 - - + -
1195A PRO* 4.0 10.3 - - + -
1196A ASN 3.2 10.6 + - - +
1197A LEU* 3.7 11.2 - - + +
1198A GLU 3.3 0.2 - - - -
1199A ASP* 1.3 76.5 - - - +
1201A TYR* 1.3 63.5 + - - +
1203A ALA 3.1 7.8 + - - -
1205A VAL* 3.0 38.7 + - + +
1207A VAL* 3.7 29.6 - - + -
1227A TRP* 3.8 25.8 - - + -
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Residues in contact with TYR1201 (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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933A LYS* 2.9 63.9 + - + +
936A LEU* 3.3 32.9 - - + +
937A ASN* 4.2 17.9 - - - -
1197A LEU 3.0 17.2 + - - +
1198A GLU* 3.8 7.0 - - - +
1200A LEU* 1.3 75.9 - - - +
1202A GLU* 1.3 71.8 + - - +
1204A ASN 3.1 7.6 + - - -
1205A VAL 4.6 2.9 + - - -
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Residues in contact with GLU1202 (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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933A LYS* 3.7 22.4 + - - -
1198A GLU 3.2 15.5 + - - +
1199A ASP* 3.9 5.4 - - - +
1200A LEU 3.2 0.2 - - - -
1201A TYR* 1.3 90.5 - - - +
1203A ALA* 1.3 58.5 + - - +
1204A ASN* 3.2 6.3 + - - +
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Residues in contact with ALA1203 (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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926A SER* 4.9 7.3 + - - -
1176A VAL* 4.7 5.6 - - + +
1180A PHE* 3.8 24.5 - - + -
1199A ASP 3.2 14.2 + - - +
1200A LEU 3.1 5.3 + - - +
1202A GLU* 1.3 75.7 - - - +
1204A ASN* 1.3 74.4 + - - +
1205A VAL* 3.2 11.2 + - + +
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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