Contacts of the helix formed by residues 1047 - 1058 (chain A) in PDB entry 4X7J
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 TYR1047 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906A ILE* 4.7 7.1 - - + +
909A ARG 4.1 16.3 + - - -
911A ARG* 3.7 39.1 + - + +
1018A LEU* 4.0 34.1 + - + +
1043A PHE* 2.8 40.5 + + + +
1044A THR 3.9 0.2 - - - -
1046A LYS* 1.3 121.8 + - + +
1048A PRO* 1.4 59.2 - - - +
1049A CYS 3.4 2.5 - - - -
1050A GLU* 3.4 27.8 - - + +
1051A TYR* 2.8 28.9 + - - +
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Residues in contact with PRO1048 (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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1044A THR 3.6 14.5 - - - +
1045A GLN 3.6 10.8 - - - +
1046A LYS 3.4 9.6 - - - +
1047A TYR* 1.4 88.9 - - - +
1049A CYS* 1.3 69.9 + - - +
1050A GLU* 5.1 0.4 - - - +
1051A TYR* 3.5 7.6 + - + +
1052A VAL* 3.2 28.7 + - - +
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Residues in contact with CYS1049 (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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911A ARG* 4.4 7.4 - - - +
1047A TYR 3.4 0.4 - - - -
1048A PRO* 1.3 88.1 - - - +
1050A GLU* 1.3 68.3 + - - +
1052A VAL* 3.4 8.8 + - - +
1053A MET* 3.2 24.4 + - - +
1074A ASN* 5.8 0.2 + - - -
1076A VAL* 3.7 25.8 - - + -
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Residues in contact with GLU1050 (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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911A ARG* 2.7 45.3 + - - +
915A LEU* 3.6 24.2 - - + +
1014A LEU* 4.7 5.8 - - + -
1018A LEU* 3.8 29.2 - - + -
1043A PHE* 4.5 2.2 - - + -
1047A TYR* 3.4 29.4 - - + +
1048A PRO* 3.4 0.4 - - - +
1049A CYS* 1.3 73.5 + - - +
1051A TYR* 1.3 61.1 + - - +
1053A MET* 3.3 12.7 + - + +
1054A VAL* 3.0 36.4 + - - +
1076A VAL* 3.7 9.2 - - + +
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Residues in contact with TYR1051 (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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1039A PHE* 3.5 38.5 - + - -
1043A PHE* 3.8 16.3 - + + -
1044A THR* 3.7 41.1 - - + +
1047A TYR 2.8 21.2 + - - +
1048A PRO* 3.6 9.6 - - + +
1049A CYS 3.3 0.2 - - - -
1050A GLU* 1.3 76.8 - - - +
1052A VAL* 1.3 67.8 + - + +
1054A VAL* 3.9 1.9 - - - +
1055A GLN* 3.0 53.8 + - + +
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Residues in contact with VAL1052 (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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1048A PRO 3.2 14.9 + - - +
1049A CYS* 3.5 9.9 - - - +
1050A GLU 3.3 0.2 - - - -
1051A TYR* 1.3 85.2 - - + +
1053A MET* 1.3 63.7 + - + +
1055A GLN* 3.3 14.7 + - - +
1056A ASP* 3.2 35.5 + - - +
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Residues in contact with MET1053 (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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1014A LEU* 4.0 13.7 - - + -
1049A CYS 3.2 12.3 + - - +
1050A GLU* 3.4 20.4 - - - +
1052A VAL* 1.3 78.6 - - + +
1054A VAL* 1.3 59.3 + - - +
1056A ASP* 3.5 9.3 + - - +
1057A MET* 3.1 52.3 + - + +
1066A PRO* 5.2 1.2 - - + +
1071A ILE* 4.2 8.5 - - + +
1074A ASN* 3.7 35.2 - - + +
1076A VAL* 4.3 17.9 - - - -
1077A PHE* 3.6 28.9 - - + -
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Residues in contact with VAL1054 (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 GLY* 3.6 23.8 - - - +
1014A LEU* 3.8 23.8 - - + -
1015A PHE* 4.3 13.2 - - + +
1039A PHE* 3.7 19.3 - - + -
1043A PHE* 4.6 6.3 - - + -
1050A GLU 3.0 23.2 + - - +
1051A TYR* 3.9 4.7 - - - +
1053A MET* 1.3 73.9 - - - +
1055A GLN* 1.3 65.5 + - - +
1057A MET* 3.2 6.2 + - - -
1058A LEU* 2.9 47.1 + - + +
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Residues in contact with GLN1055 (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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1037A LEU* 4.0 24.9 + - + +
1039A PHE* 3.8 22.4 - - + -
1051A TYR* 3.0 54.2 + - + +
1052A VAL* 3.3 16.2 + - - +
1054A VAL* 1.3 75.2 - - - +
1056A ASP* 1.3 65.8 + - - +
1058A LEU* 3.2 12.8 + - - +
1059A SER* 3.3 12.1 + - - -
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Residues in contact with ASP1056 (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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1052A VAL* 3.2 28.4 + - - +
1053A MET* 3.8 10.2 - - - +
1054A VAL 3.2 0.2 - - - -
1055A GLN* 1.3 79.6 - - - +
1057A MET* 1.3 61.4 + - - +
1059A SER* 2.9 22.0 + - - -
1064A GLU 4.0 3.2 - - - +
1065A ARG* 3.5 5.7 - - - -
1066A PRO* 3.4 27.7 - - + +
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Residues in contact with MET1057 (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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918A PHE* 4.2 4.3 - - + -
1007A ILE* 3.5 29.7 - - + +
1008A PHE* 3.4 19.6 - - - -
1010A LEU* 4.1 9.4 - - - -
1011A GLY* 3.7 28.0 - - - -
1014A LEU* 4.0 14.4 - - + -
1053A MET* 3.1 46.9 + - + +
1054A VAL* 3.2 5.1 + - - +
1056A ASP* 1.3 75.3 - - - +
1058A LEU* 1.3 58.3 + - - +
1059A SER 3.3 1.1 - - - -
1065A ARG* 3.5 14.6 - - - +
1066A PRO* 4.1 7.0 - - + -
1071A ILE* 3.9 39.5 - - + -
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Residues in contact with LEU1058 (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 PHE* 3.3 59.2 - - + +
1011A GLY* 4.1 2.5 - - - -
1012A LEU* 3.9 19.1 - - + +
1034A VAL* 3.5 37.2 - - + +
1035A ARG* 4.7 5.0 - - - +
1037A LEU* 4.0 15.2 - - + +
1039A PHE* 4.5 4.0 - - + -
1054A VAL* 2.9 40.4 + - + +
1055A GLN 3.2 6.2 + - - +
1057A MET* 1.3 76.9 - - - +
1059A SER* 1.3 65.1 + - - +
1060A PRO* 3.3 6.9 - - - +
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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