Contacts of the helix formed by residues 1002 - 1019 (chain A) in PDB entry 3U9Y
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 ASN1002 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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952A GLY* 3.4 27.5 - - - +
953A THR* 2.7 27.9 + - + +
1000A VAL* 5.3 1.6 - - + -
1001A CYS* 1.3 74.4 - - - +
1003A LYS* 1.3 64.0 + - - +
1004A LYS* 3.2 10.8 + - - +
1005A LEU* 2.9 38.4 + - + +
1006A TRP* 2.9 24.3 + - - +
1040A ILE 4.9 0.4 - - - +
1041A HIS 3.8 13.1 + - - -
1148A TYR* 3.1 10.9 + - + +
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Residues in contact with LYS1003 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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952A GLY 4.7 2.2 + - - -
1001A CYS 4.3 0.2 - - - -
1002A ASN* 1.3 72.2 + - - +
1004A LYS* 1.3 66.5 + - - +
1006A TRP* 3.3 6.9 + - + +
1007A GLU* 2.9 63.4 + - - +
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Residues in contact with LYS1004 (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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1002A ASN* 3.2 7.5 + - - +
1003A LYS* 1.3 87.2 - - - +
1005A LEU* 1.3 60.7 + - + +
1007A GLU* 3.5 5.3 + - - +
1008A ARG* 3.0 48.4 + - - +
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Residues in contact with LEU1005 (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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1000A VAL* 6.0 0.7 - - + -
1002A ASN* 2.9 32.8 + - + +
1004A LYS* 1.3 78.1 - - + +
1006A TRP* 1.3 58.8 + - - +
1008A ARG* 3.4 14.8 + - + +
1009A TYR* 2.9 27.7 + - - +
1039A ILE 4.4 1.6 - - - +
1040A ILE 4.0 17.7 - - - +
1041A HIS 4.3 2.0 - - - +
1042A LYS 3.7 22.0 - - - +
1043A GLY* 3.6 27.8 - - - +
1148A TYR* 3.8 13.7 - - + -
1149A PRO* 4.7 11.9 - - + -
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Residues in contact with TRP1006 (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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1002A ASN 2.9 16.8 + - - +
1003A LYS* 3.3 7.6 + - - +
1005A LEU* 1.3 75.0 - - - +
1007A GLU* 1.3 70.1 + - + +
1009A TYR* 3.1 19.6 + + - +
1010A THR* 2.9 55.1 + - + +
1013A ARG* 4.3 11.7 - - - -
1100A ARG* 3.8 21.5 - - - -
1148A TYR* 3.6 33.8 - + + +
1150A GLU* 3.6 20.0 - - - -
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Residues in contact with GLU1007 (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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1003A LYS* 2.9 58.3 + - - +
1004A LYS* 4.0 4.4 - - - +
1006A TRP* 1.3 81.1 - - + +
1008A ARG* 1.3 64.4 + - - +
1010A THR* 3.4 8.8 + - - +
1011A HIS* 3.1 26.3 + - - +
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Residues in contact with ARG1008 (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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1004A LYS* 3.0 33.6 + - - +
1005A LEU* 3.4 17.7 - - + +
1007A GLU* 1.3 76.9 - - - +
1009A TYR* 1.3 64.2 + - - +
1011A HIS* 3.8 4.7 - - - +
1012A ARG* 3.3 20.6 + - - +
1145A GLU* 3.9 28.5 - - + +
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Residues in contact with TYR1009 (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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1005A LEU 2.9 15.3 + - - +
1006A TRP* 3.1 25.1 + + - +
1008A ARG* 1.3 76.5 - - - +
1010A THR* 1.3 61.7 + - + +
1012A ARG* 3.2 5.9 + - - +
1013A ARG* 3.0 34.0 + - - +
1026A GLU* 2.6 36.8 + - - +
1100A ARG* 3.5 27.3 - - + +
1101A VAL 3.7 0.3 - - - -
1102A THR* 2.9 33.6 + - - -
1145A GLU* 3.3 21.5 - - - +
1146A GLN* 3.5 18.4 - - - -
1147A ALA 3.7 14.4 - - - +
1148A TYR* 3.8 14.4 - - + -
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Residues in contact with THR1010 (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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1006A TRP* 2.9 54.9 + - + +
1007A GLU* 3.4 13.3 + - - +
1009A TYR* 1.3 71.7 - - + +
1011A HIS* 1.3 65.1 + - - +
1013A ARG* 3.5 39.0 + - - +
1014A LYS* 3.3 22.0 + - - +
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Residues in contact with HIS1011 (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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1007A GLU 3.1 19.5 + - - +
1008A ARG* 3.8 6.3 - - - +
1010A THR* 1.3 76.4 + - - +
1012A ARG* 1.3 66.9 + - - +
1013A ARG 3.3 0.2 + - - -
1014A LYS* 3.4 10.9 + - + +
1015A GLU* 3.3 48.0 + - + +
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Residues in contact with ARG1012 (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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1008A ARG 3.3 6.0 + - - +
1009A TYR 3.2 8.8 + - - +
1011A HIS* 1.3 81.4 + - - +
1013A ARG* 1.3 64.0 + - - +
1015A GLU* 3.1 36.4 + - - +
1016A VAL* 3.0 31.5 + - - +
1019A GLU* 4.6 10.9 + - - -
1123A HIS* 4.0 20.0 - - - +
1143A ARG* 3.3 42.2 - - - +
1145A GLU* 3.7 22.0 - - + +
1146A GLN* 3.0 44.0 + - + -
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Residues in contact with ARG1013 (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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1006A TRP* 4.3 14.1 - - - -
1009A TYR* 3.0 26.1 + - + +
1010A THR* 3.5 34.1 + - - +
1011A HIS 3.1 0.4 - - - -
1012A ARG* 1.3 77.0 - - - +
1014A LYS* 1.3 57.2 + - - +
1016A VAL* 3.3 3.2 + - - +
1017A SER* 2.9 31.3 + - - -
1024A ALA* 3.7 23.3 - - + +
1026A GLU* 2.9 37.7 + - - -
1100A ARG* 4.4 1.6 - - - +
1102A THR* 3.7 21.5 - - - +
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Residues in contact with LYS1014 (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 THR 3.3 10.9 + - - +
1011A HIS* 3.6 12.8 - - + +
1012A ARG 3.3 0.4 - - - -
1013A ARG* 1.3 77.4 - - - +
1015A GLU* 1.3 66.4 + - + +
1017A SER* 3.4 7.3 - - - -
1018A GLU* 2.7 64.9 + - + +
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Residues in contact with GLU1015 (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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1011A HIS* 3.3 39.3 + - + +
1012A ARG* 3.1 40.0 + - - +
1014A LYS* 1.3 77.9 - - - +
1016A VAL* 1.3 61.7 + - - +
1018A GLU* 3.1 11.8 + - - +
1019A GLU* 3.1 31.1 + - - +
1143A ARG* 4.2 10.2 + - - -
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Residues in contact with VAL1016 (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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1012A ARG* 3.0 45.0 + - + +
1013A ARG 3.7 6.1 - - - +
1015A GLU* 1.3 71.2 - - - +
1017A SER* 1.3 67.2 + - - +
1019A GLU* 3.0 13.3 + - - +
1020A ASN* 3.1 11.6 + - - +
1023A HIS 4.7 0.2 - - - +
1024A ALA* 4.3 3.1 - - - +
1102A THR* 3.7 22.4 - - + -
1104A GLY* 3.2 34.5 - - - -
1123A HIS* 3.8 24.9 - - + +
1146A GLN* 4.1 6.5 - - - +
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Residues in contact with SER1017 (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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1013A ARG* 2.9 18.8 + - - -
1014A LYS* 3.4 11.9 - - - -
1016A VAL* 1.3 75.4 - - - +
1018A GLU* 1.3 60.1 + - - -
1020A ASN 3.0 10.6 + - - -
1022A ASN* 2.8 49.2 + - - +
1023A HIS 3.7 7.5 + - - +
1024A ALA* 3.9 16.6 + - - +
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Residues in contact with GLU1018 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A LYS* 2.7 52.8 + - + +
1015A GLU* 3.1 8.6 + - - +
1017A SER* 1.3 77.6 - - - +
1019A GLU* 1.3 61.0 + - + +
1020A ASN 3.2 1.4 + - - -
1021A HIS* 4.8 2.3 + - - -
1022A ASN* 4.5 14.0 + - - +
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Residues in contact with GLU1019 (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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1012A ARG* 4.6 11.5 + - - -
1015A GLU* 3.1 17.5 + - - +
1016A VAL 3.0 4.8 + - - +
1018A GLU* 1.3 78.7 - - + +
1020A ASN* 1.3 60.2 + - - +
1021A HIS 4.0 1.3 - - - -
1105A LYS* 5.8 0.2 - - - +
1123A HIS* 2.8 45.4 + - + +
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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