Contacts of the helix formed by residues 1015 - 1030 (chain A) in PDB entry 4QMH
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 SER1015 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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975A LYS* 5.6 2.2 + - - +
978A PHE* 3.2 27.0 + - - +
979A GLU* 5.4 3.4 - - - -
1013A SER 4.3 0.2 - - - -
1014A VAL* 1.3 71.2 - - - +
1016A LYS* 1.3 63.1 + - - +
1017A GLU* 3.4 9.9 + - - +
1018A ASP* 3.1 18.6 + - - +
1019A ILE* 3.1 23.4 + - - +
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Residues in contact with LYS1016 (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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1011A PRO* 5.9 2.2 - - + +
1014A VAL* 3.2 7.6 + - - +
1015A SER* 1.3 72.2 + - - +
1017A GLU* 1.3 57.9 + - - +
1019A ILE* 3.2 7.0 + - - +
1020A HIS* 2.9 40.4 + - + -
1051A HIS* 4.1 26.7 - - + +
1052A LEU* 3.6 21.7 + - + +
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Residues in contact with GLU1017 (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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981A GLU* 5.4 3.9 - - - +
1015A SER* 3.2 7.5 + - - +
1016A LYS* 1.3 80.9 - - - +
1018A ASP* 1.3 62.1 + - - +
1020A HIS* 3.2 22.6 + - - +
1021A SER* 3.2 20.1 + - - -
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Residues in contact with ASP1018 (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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977A PHE 4.3 2.3 - - - +
978A PHE* 3.3 45.0 - - + +
979A GLU* 3.5 6.9 + - - +
980A SER 3.6 1.0 + - - -
981A GLU* 2.9 38.6 + - - +
982A MET 5.0 0.5 + - - -
983A ILE* 4.9 3.1 - - - +
984A ALA 5.6 0.3 + - - -
1015A SER* 3.1 14.0 + - - +
1017A GLU* 1.3 75.0 - - - +
1019A ILE* 1.3 64.2 + - - +
1021A SER* 2.5 26.5 + - - -
1022A MET* 3.6 20.5 + - - +
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Residues in contact with ILE1019 (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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978A PHE* 3.7 9.2 - - + -
1006A LEU* 3.9 15.3 - - + -
1014A VAL* 3.4 35.2 - - + -
1015A SER 3.1 6.8 + - - +
1016A LYS* 3.2 6.5 + - - +
1018A ASP* 1.3 73.0 - - - +
1020A HIS* 1.3 65.3 + - - +
1022A MET* 2.9 44.1 + - + +
1023A VAL* 3.5 6.1 + - - +
1048A ILE* 3.7 30.7 - - + +
1051A HIS* 4.4 9.6 - - + -
1052A LEU* 3.7 25.4 - - + -
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Residues in contact with HIS1020 (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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1016A LYS* 2.9 36.1 + - + -
1017A GLU* 3.2 27.3 + - - +
1019A ILE* 1.3 75.5 - - - +
1021A SER* 1.3 61.6 + - - +
1022A MET 3.1 0.2 - - - -
1023A VAL* 3.0 22.3 + - - +
1024A PRO* 3.5 5.4 - - - +
1052A LEU* 3.6 32.7 - - + +
1056A ALA* 4.3 25.7 - - + +
1060A ALA* 5.4 7.4 - - + +
1064A GLN* 5.4 1.9 + - - -
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Residues in contact with SER1021 (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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981A GLU* 3.6 37.1 - - - +
984A ALA* 3.5 18.2 - - - +
1017A GLU* 3.2 12.4 + - - -
1018A ASP* 2.5 25.9 + - - -
1020A HIS* 1.3 75.3 - - - +
1022A MET* 1.3 60.5 + - - +
1023A VAL 3.3 0.2 - - - -
1024A PRO* 3.6 9.0 - - - +
1025A HIS* 3.4 18.5 + - - -
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Residues in contact with MET1022 (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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978A PHE* 3.7 19.7 - - + -
983A ILE* 3.6 35.7 - - + -
984A ALA* 4.6 4.0 - - + +
987A LEU* 4.6 8.5 - - + -
999A TRP* 4.0 3.7 - - + -
1002A LEU* 4.1 16.2 - - + -
1018A ASP* 3.6 22.4 - - - +
1019A ILE* 2.9 39.5 + - + +
1021A SER* 1.3 81.2 - - - +
1023A VAL* 1.3 60.3 + - - +
1024A PRO 3.4 0.7 - - - -
1025A HIS* 3.0 14.3 + - - +
1026A LEU* 2.9 26.4 + - - +
1048A ILE* 4.1 17.9 - - + -
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Residues in contact with VAL1023 (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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1019A ILE 3.8 4.3 - - - +
1020A HIS* 3.0 17.9 + - - +
1022A MET* 1.3 78.1 - - - +
1024A PRO* 1.3 68.6 - - + +
1026A LEU* 3.1 7.7 + - + +
1027A TYR* 2.9 59.6 + - + +
1048A ILE* 4.3 12.1 - - + -
1052A LEU* 3.7 31.0 - - + -
1057A MET* 4.9 5.4 - - + -
1060A ALA* 4.0 16.6 - - + -
1064A GLN* 4.2 4.5 - - - +
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Residues in contact with PRO1024 (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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1020A HIS 3.5 9.6 - - - +
1021A SER* 3.6 9.9 - - - +
1022A MET 3.6 3.1 - - - -
1023A VAL* 1.3 94.1 - - + +
1025A HIS* 1.3 68.9 + - + +
1027A TYR* 3.4 4.3 + - + +
1028A ALA* 3.1 22.7 + - - +
1064A GLN* 3.7 29.6 - - - +
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Residues in contact with HIS1025 (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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984A ALA* 3.5 26.3 + - + +
987A LEU* 4.1 12.7 - - + -
988A LYS* 3.6 41.7 - - + +
999A TRP* 3.7 6.5 - - + -
1021A SER 3.4 25.6 + - - -
1022A MET* 3.0 8.8 + - - +
1024A PRO* 1.3 81.8 - - + +
1026A LEU* 1.3 61.7 + - - +
1028A ALA* 3.3 3.7 + - - -
1029A HIS* 2.8 52.8 + - + -
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Residues in contact with LEU1026 (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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999A TRP* 3.5 34.0 - - + -
1022A MET 2.9 10.4 + - - +
1023A VAL* 3.1 10.7 + - - +
1025A HIS* 1.3 76.4 - - - +
1027A TYR* 1.3 65.8 + - + +
1029A HIS* 4.6 0.4 - - - +
1030A ILE* 3.0 43.8 + - + +
1041A ALA* 3.4 29.2 - - + +
1044A ALA* 4.5 1.3 - - + -
1045A VAL* 4.1 19.5 - - + +
1048A ILE* 4.1 17.3 - - + -
1057A MET* 3.7 29.8 - - + -
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Residues in contact with TYR1027 (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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1023A VAL* 2.9 40.9 + - + +
1024A PRO* 3.9 5.2 - - + +
1026A LEU* 1.3 96.6 - - + +
1028A ALA* 1.3 61.8 + - - +
1030A ILE* 4.2 10.5 - - + +
1031A CYS* 4.4 6.1 - - - +
1057A MET* 2.7 39.5 + - + +
1060A ALA 4.2 1.3 - - - -
1061A LEU* 3.8 27.4 - - + -
1064A GLN* 4.1 9.2 - - - -
1066A PRO* 4.1 23.0 - - + +
1067A ALA 5.0 1.0 - - - +
1072A ILE* 3.5 54.7 - - + +
1076A LEU* 3.8 11.9 - - + +
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Residues in contact with ALA1028 (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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1024A PRO 3.1 16.6 + - - +
1025A HIS* 3.8 4.9 - - - +
1027A TYR* 1.3 78.3 - - - +
1029A HIS* 1.3 69.8 + - + +
1031A CYS* 3.0 23.2 + - - +
1032A ASP* 3.3 8.1 + - - -
1066A PRO* 5.8 0.2 - - - +
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Residues in contact with HIS1029 (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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987A LEU* 3.7 18.3 + - + -
988A LYS 5.3 2.0 + - - -
995A LYS* 3.3 30.4 + - + +
999A TRP* 2.9 32.8 + - - +
1025A HIS* 2.8 35.9 + - + +
1028A ALA* 1.3 83.4 - - + +
1030A ILE* 1.3 61.6 + - - +
1031A CYS 2.9 5.4 - - - -
1032A ASP* 3.0 34.9 + - - +
1037A VAL* 3.8 12.1 - - + -
1038A ARG* 3.5 13.7 + - - -
1041A ALA* 3.8 6.8 - - + +
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Residues in contact with ILE1030 (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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1026A LEU* 3.0 34.6 + - + +
1027A TYR* 4.2 18.4 - - + +
1029A HIS* 1.3 75.7 - - - +
1031A CYS* 1.3 70.0 + - - +
1032A ASP 3.5 0.2 - - - -
1038A ARG* 3.7 11.8 - - - +
1041A ALA* 3.9 2.8 - - - +
1042A ASN* 3.5 43.7 + - - +
1045A VAL* 3.8 25.8 - - + -
1071A ASP* 4.8 14.8 - - + +
1072A ILE* 4.8 10.3 - - + +
1075A ALA* 4.1 12.6 - - + -
1076A LEU* 6.1 0.9 - - + -
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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