Contacts of the helix formed by residues 998 - 1013 (chain A) in PDB entry 4LJP
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 CYS 998 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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969A CYS* 3.3 8.8 - - + +
986A CYS* 3.8 4.3 - - - -
988A LYS* 3.7 24.2 - - + -
989A GLU 3.4 20.9 - - - +
994A TYR* 4.3 2.7 - - - -
997A LEU* 1.3 76.3 - - - +
999A GLN* 1.3 61.4 + - - +
1000A ALA* 3.8 8.3 - - - -
1001A HIS* 3.3 19.9 + - - -
1002A TYR* 2.8 28.8 + - - +
1104A ZN 2.4 33.9 - - - -
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Residues in contact with GLN 999 (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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939A ALA 5.9 0.3 + - - -
989A GLU 4.3 3.0 + - - -
991A PRO* 4.3 7.7 - - + +
994A TYR* 3.8 33.4 + - + -
998A CYS* 1.3 73.5 - - - +
1000A ALA* 1.3 64.6 + - - +
1002A TYR* 3.8 1.7 - - - +
1003A LYS* 3.2 52.3 + - - +
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Residues in contact with ALA1000 (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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935A ARG* 6.2 0.2 - - - +
988A LYS* 6.1 3.8 - - + -
998A CYS* 3.4 9.2 - - - -
999A GLN* 1.3 82.1 - - - +
1001A HIS* 1.3 66.4 + - + +
1003A LYS* 3.5 10.7 + - - +
1004A GLU* 3.1 27.6 + - - +
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Residues in contact with HIS1001 (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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863A TYR* 3.3 23.3 + - - +
882A ARG* 5.1 5.9 - - - +
883A GLY 5.8 0.2 + - - -
969A CYS* 3.6 5.0 - - - -
971A VAL* 3.7 34.5 - - + +
973A GLU* 3.4 28.3 + - - +
986A CYS* 3.6 7.6 - - - -
988A LYS* 5.8 1.3 - - - -
997A LEU* 3.7 5.1 - - + +
998A CYS* 3.3 7.4 + - - +
1000A ALA* 1.3 80.8 - - + +
1002A TYR* 1.3 66.5 + - - +
1004A GLU* 3.1 21.3 + - - +
1005A TYR* 3.0 21.8 + - - +
1104A ZN 2.1 37.0 - - - -
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Residues in contact with TYR1002 (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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939A ALA* 4.2 9.2 - - + -
943A GLN* 2.8 32.6 + - - -
953A PHE* 4.1 0.5 - - - -
954A ASN 2.9 29.8 + - - -
955A THR* 3.6 2.1 - - - +
993A GLY 3.4 14.8 + - - -
994A TYR* 3.2 58.3 - + + -
995A ALA* 3.9 5.6 - - + -
997A LEU* 3.7 11.1 - - + +
998A CYS 2.8 18.1 + - - +
999A GLN 3.8 1.1 - - - +
1001A HIS* 1.3 76.1 - - - +
1003A LYS* 1.3 56.8 + - - +
1005A TYR* 3.1 21.5 + + - +
1006A LEU* 3.0 50.0 + - + +
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Residues in contact with LYS1003 (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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931A LEU* 5.1 0.7 - - + -
935A ARG* 3.6 28.7 + - + +
936A ASP 4.8 2.2 + - - -
937A TRP 2.9 29.1 + - - +
938A THR* 4.3 2.8 - - - +
939A ALA* 4.0 22.4 - - + +
942A LEU* 3.7 23.5 - - + +
999A GLN* 3.2 45.4 + - + +
1000A ALA* 3.6 10.8 - - - +
1002A TYR* 1.3 73.4 - - - +
1004A GLU* 1.3 60.3 + - - +
1006A LEU* 3.4 4.5 + - - +
1007A VAL* 2.8 35.8 + - - +
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Residues in contact with GLU1004 (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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863A TYR* 3.0 28.8 + - + +
882A ARG* 3.9 12.5 + - - -
931A LEU* 4.0 38.6 - - + +
1000A ALA* 3.1 19.0 + - - +
1001A HIS* 3.1 25.5 + - - +
1003A LYS* 1.3 75.3 - - - +
1005A TYR* 1.3 58.1 + - - +
1007A VAL* 3.2 3.8 + - - +
1008A SER* 2.9 28.1 + - - -
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Residues in contact with TYR1005 (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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859A GLY* 3.6 6.2 - - - -
860A LEU* 3.3 50.0 + - + -
863A TYR* 3.8 30.2 - - + -
953A PHE* 3.7 5.9 - - - -
954A ASN* 2.9 53.0 + - + +
995A ALA* 5.4 0.2 - - + -
997A LEU* 4.0 5.6 - - + -
1001A HIS 3.0 11.3 + - - +
1002A TYR* 3.3 25.4 - + - +
1004A GLU* 1.3 73.1 - - - +
1006A LEU* 1.3 77.7 + - + +
1008A SER* 2.7 22.1 + - - -
1009A LEU* 3.3 23.0 + - + +
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Residues in contact with LEU1006 (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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939A ALA* 3.7 27.6 - - + +
942A LEU* 3.9 21.5 - - + -
943A GLN* 3.7 12.6 - - + +
946A LEU* 4.0 22.3 - - + +
953A PHE* 4.2 11.4 - - + -
1002A TYR* 3.0 52.4 + - + +
1003A LYS* 3.8 6.3 - - - +
1005A TYR* 1.3 91.1 - - + +
1007A VAL* 1.3 56.2 + - - +
1009A LEU* 3.2 7.2 + - - +
1010A ILE* 3.0 33.0 + - - +
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Residues in contact with VAL1007 (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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931A LEU* 4.2 34.3 - - + +
934A LEU* 3.8 31.9 - - + +
942A LEU* 4.0 17.0 - - + -
1003A LYS* 2.8 24.3 + - + +
1004A GLU 3.6 5.4 - - - +
1005A TYR 3.2 0.4 - - - -
1006A LEU* 1.3 73.2 - - - +
1008A SER* 1.3 58.4 + - - +
1010A ILE* 3.6 5.8 - - - +
1011A ASN* 2.9 49.2 + - - +
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Residues in contact with SER1008 (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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859A GLY 4.9 1.4 + - - -
863A TYR* 4.3 15.0 - - - +
1004A GLU 2.9 12.8 + - - -
1005A TYR* 2.7 29.0 + - - -
1007A VAL* 1.3 77.3 - - - +
1009A LEU* 1.3 61.6 + - - +
1011A ASN* 4.0 5.9 - - - +
1012A ALA* 3.0 30.0 + - - +
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Residues in contact with LEU1009 (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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859A GLY* 4.0 26.5 - - - +
946A LEU* 3.7 19.7 - - + +
951A VAL* 4.7 4.3 - - + -
952A MET 3.8 11.9 - - - +
953A PHE* 3.6 31.0 - - + -
1005A TYR* 3.3 30.3 + - + +
1006A LEU* 3.2 7.3 + - - +
1008A SER* 1.3 79.2 + - - +
1010A ILE* 1.3 66.7 + - - +
1012A ALA* 3.3 5.2 + - + +
1013A HIS* 3.1 37.4 + - + +
1070A ARG* 5.8 5.2 - - - +
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Residues in contact with ILE1010 (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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929A ASP* 5.4 0.7 - - + -
934A LEU* 4.3 16.4 - - + -
942A LEU* 3.7 44.9 - - + +
945A LEU* 3.9 30.5 - - + -
946A LEU* 3.7 20.6 - - + -
1006A LEU 3.0 23.2 + - - +
1007A VAL* 3.3 8.7 + - + +
1009A LEU* 1.3 77.5 - - - +
1011A ASN* 1.3 63.7 + - - +
1013A HIS 3.5 0.2 + - - -
1014A SER 3.2 3.8 + - - -
1015A LEU* 3.0 46.2 + - + +
1017A PRO* 5.4 0.2 - - + -
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Residues in contact with ASN1011 (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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900A GLY 4.5 7.5 + - - -
929A ASP* 2.9 39.2 + - - +
931A LEU* 5.0 2.2 - - - +
1007A VAL* 2.9 32.0 + - - +
1008A SER* 4.0 5.9 - - - +
1010A ILE* 1.3 78.1 - - - +
1012A ALA* 1.3 64.8 + - - +
1014A SER 3.0 5.4 + - - -
1015A LEU 5.8 0.2 - - - -
1067A ILE* 3.7 29.9 - - + +
1068A PRO 4.4 2.7 - - - +
1069A ARG* 2.9 30.3 + - - +
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Residues in contact with ALA1012 (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 SER 3.0 20.6 + - - +
1009A LEU* 3.3 7.8 + - + +
1011A ASN* 1.3 76.3 - - - +
1013A HIS* 1.3 60.4 + - - +
1014A SER* 3.7 0.5 + - - -
1068A PRO 4.4 7.0 - - - +
1069A ARG* 3.8 1.6 - - - +
1070A ARG* 2.8 69.6 + - - +
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Residues in contact with HIS1013 (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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951A VAL* 3.4 37.3 - - + +
952A MET* 6.4 0.6 - - - -
1009A LEU* 3.1 29.6 + - + +
1010A ILE 3.5 0.2 + - - -
1011A ASN 3.1 0.2 - - - -
1012A ALA* 1.3 77.1 - - + +
1014A SER* 1.3 71.6 + - - +
1015A LEU* 3.3 25.5 + - + +
1070A ARG* 3.4 30.1 + - + -
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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