Contacts of the helix formed by residues 1053 - 1065 (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 GLY1053 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1049A MET* 2.7 30.6 + - - -
1050A ILE 4.9 0.6 + - - -
1051A HIS 3.7 0.6 - - - -
1052A LEU* 1.3 77.7 - - - +
1054A PHE* 1.3 64.6 + - - -
1055A ASP 3.4 2.7 - - - -
1056A ALA 3.6 0.6 + - - -
1057A MET* 3.3 21.8 + - - +
1083A LEU* 5.2 3.1 - - - -
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Residues in contact with PHE1054 (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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1049A MET* 3.6 25.5 - - + +
1053A GLY* 1.3 71.2 - - - -
1055A ASP* 1.3 73.4 + - - +
1057A MET* 3.1 3.3 + - - +
1058A ASN* 2.8 53.3 + - + +
1073A LEU* 4.5 8.7 - - + -
1076A LEU* 3.8 39.0 - - + -
1077A GLU* 4.3 11.2 - - + -
1080A ARG* 3.7 54.5 - - + +
1083A LEU* 4.7 5.0 - - + +
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Residues in contact with ASP1055 (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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1053A GLY 3.4 0.4 - - - -
1054A PHE* 1.3 92.3 - - - +
1056A ALA* 1.3 57.7 + - - +
1058A ASN* 3.3 5.2 + - - +
1059A ARG* 2.9 51.8 + - + +
1080A ARG* 4.5 6.8 + - - -
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Residues in contact with ALA1056 (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* 6.4 0.7 - - - +
1020A HIS* 4.3 26.1 - - + +
1052A LEU* 3.4 27.8 + - + +
1053A GLY 3.6 1.6 + - - +
1054A PHE 3.3 0.6 - - - -
1055A ASP* 1.3 78.3 - - - +
1057A MET* 1.3 59.3 + - - +
1059A ARG* 3.4 26.2 + - - +
1060A ALA* 3.0 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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1023A VAL* 4.9 4.9 - - + -
1026A LEU* 3.7 20.9 - - + -
1027A TYR* 2.7 29.4 + - + +
1045A VAL* 4.5 5.4 - - + +
1048A ILE* 3.6 24.0 - - + -
1049A MET* 3.5 43.7 - - - -
1052A LEU* 4.1 18.2 - - + -
1053A GLY 3.3 9.1 + - - +
1054A PHE* 3.1 7.7 + - - +
1056A ALA* 1.3 77.4 - - - +
1058A ASN* 1.3 58.3 + - - +
1060A ALA* 3.3 4.8 + - - +
1061A LEU* 3.0 19.1 + - - +
1076A LEU* 3.6 26.2 - - + -
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Residues in contact with ASN1058 (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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1054A PHE* 2.8 37.8 + - + +
1055A ASP* 3.7 5.1 + - - +
1057A MET* 1.3 75.4 - - - +
1059A ARG* 1.3 65.5 + - - +
1061A LEU* 3.2 10.8 + - - +
1062A ASP* 3.1 37.0 + - - +
1073A LEU* 3.6 25.3 - - - +
1076A LEU* 4.0 8.2 - - + +
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Residues in contact with ARG1059 (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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1055A ASP* 2.9 35.3 + - - +
1056A ALA* 3.6 30.4 - - - +
1058A ASN* 1.3 77.5 - - - +
1060A ALA* 1.3 58.4 + - - +
1062A ASP* 3.2 8.8 + - - +
1063A LYS* 2.9 31.8 + - - +
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Residues in contact with ALA1060 (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* 5.4 8.3 - - + +
1023A VAL* 4.0 20.0 - - + -
1027A TYR* 4.2 2.0 - - - -
1056A ALA 3.0 14.5 + - - +
1057A MET* 3.5 9.9 - - - +
1059A ARG* 1.3 76.4 - - - +
1061A LEU* 1.3 57.8 + - - +
1063A LYS* 4.5 6.3 - - - +
1064A GLN* 2.9 55.1 + - - +
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Residues in contact with LEU1061 (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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1027A TYR* 3.8 12.5 - - + +
1057A MET 3.0 13.4 + - - +
1058A ASN* 3.4 17.0 - - - +
1059A ARG 3.2 0.2 - - - -
1060A ALA* 1.3 78.6 - - - +
1062A ASP* 1.3 63.7 + - - +
1065A LYS 3.1 14.0 + - - -
1066A PRO* 3.4 28.5 - - + +
1069A LYS* 2.8 42.4 + - + +
1072A ILE* 3.7 23.3 - - + -
1073A LEU* 4.0 36.6 - - + +
1076A LEU* 4.3 7.2 - - + -
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Residues in contact with ASP1062 (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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1058A ASN* 3.1 34.5 + - - +
1059A ARG* 3.2 10.4 + - - +
1061A LEU* 1.3 81.8 - - - +
1063A LYS* 1.3 60.3 + - - +
1065A LYS* 3.4 25.5 + - - +
1069A LYS* 3.8 15.5 + - - +
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Residues in contact with LYS1063 (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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1059A ARG 2.9 17.8 + - - +
1060A ALA* 4.1 6.5 - - - +
1062A ASP* 1.3 79.9 - - - +
1064A GLN* 1.3 71.3 + - + +
1065A LYS* 3.5 13.9 + - - +
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Residues in contact with GLN1064 (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 5.4 1.2 + - - -
1023A VAL* 4.2 2.9 - - - +
1024A PRO* 3.7 43.3 - - - +
1027A TYR* 4.1 11.3 - - - -
1060A ALA* 2.9 37.1 + - - +
1063A LYS* 1.3 85.3 - - + +
1065A LYS* 1.3 72.4 + - - +
1066A PRO* 3.2 11.4 - - + +
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Residues in contact with LYS1065 (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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1061A LEU 3.1 7.6 + - - -
1062A ASP 3.4 20.0 + - - +
1063A LYS* 3.8 10.1 + - - +
1064A GLN* 1.3 82.0 - - - +
1066A PRO* 1.3 75.1 - - - +
1067A ALA 3.8 0.3 + - - -
1069A LYS* 4.0 12.3 - - - +
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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