Contacts of the helix formed by residues 1013 - 1025 (chain A) in PDB entry 5M5X
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 THR1013 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A PRO* 4.0 26.5 - - + -
595A LEU* 5.6 2.7 - - + -
1009A THR* 3.7 13.4 + - - +
1010A ALA* 5.2 2.7 - - - -
1011A VAL 3.2 0.4 - - - -
1012A LYS* 1.3 85.8 - - - +
1014A SER* 1.3 60.5 + - - +
1016A SER* 3.1 20.5 + - - +
1017A GLY* 3.8 5.0 + - - -
1198A THR* 4.4 10.2 - - + +
15T C 3.0 27.9 + - + +
16T G 5.5 3.8 - - + +
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Residues in contact with SER1014 (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 ALA 3.5 10.7 + - - -
1011A VAL* 2.9 13.2 + - - -
1013A THR* 1.3 77.4 - - - +
1015A ARG* 1.3 75.4 + - - +
1016A SER 3.2 4.0 + - - -
1017A GLY 3.8 4.3 + - - -
1018A TYR* 4.5 4.5 + - - +
1223A ARG* 4.9 0.9 + - - -
15T C 3.1 62.4 + - - +
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Residues in contact with ARG1015 (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 VAL* 3.0 31.7 + - + +
1012A LYS 3.8 0.9 + - - +
1013A THR 3.4 0.4 - - - -
1014A SER* 1.3 92.9 + - - +
1016A SER* 1.3 55.3 + - - +
1019A LEU* 3.8 1.4 - - - +
1197A SER* 4.9 0.8 + - - -
1201A THR* 3.7 28.3 - - + -
1219A ILE* 3.8 22.9 - - + +
1223A ARG* 2.5 47.3 + - - +
513B LYS* 4.9 31.9 + - - +
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Residues in contact with SER1016 (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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595A LEU* 4.5 12.0 - - - +
1012A LYS 3.7 8.1 + - - -
1013A THR* 3.1 18.7 + - - +
1015A ARG* 1.3 79.1 - - - +
1017A GLY* 1.3 66.3 + - - +
1018A TYR 3.4 1.3 - - - -
1019A LEU* 3.2 9.2 + - - +
1020A GLN* 3.0 28.1 + - - +
1194A GLY 4.5 7.2 - - - -
1197A SER* 5.0 4.3 - - - -
1198A THR* 3.2 33.5 + - - +
1201A THR* 5.5 0.2 - - - -
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Residues in contact with GLY1017 (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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595A LEU* 5.5 3.4 - - - -
1013A THR 3.8 7.7 + - - -
1014A SER 3.8 4.2 + - - -
1015A ARG 3.8 0.2 - - - -
1016A SER* 1.3 80.5 + - - +
1018A TYR* 1.3 61.4 + - - +
1020A GLN* 3.1 11.4 + - - +
1021A ARG* 3.3 11.6 + - - +
1074B MET* 3.3 30.2 - - - +
15T C 4.7 13.5 - - - -
16T G 5.9 0.2 - - - -
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Residues in contact with TYR1018 (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 SER 4.5 6.3 + - - +
1017A GLY* 1.3 71.4 - - - +
1019A LEU* 1.3 65.5 + - - +
1021A ARG* 3.9 25.1 - - - +
1022A CYS* 3.1 38.9 + - + +
1223A ARG* 3.8 35.3 - - - +
1227A MET* 4.6 11.1 - - + +
1599A ASN* 5.8 2.1 - - - +
1615A TYR* 2.7 30.7 + + - -
1616A GLU* 5.2 1.9 + - - -
13T T 5.0 1.6 + - - -
14T A 3.2 49.8 + - - +
15T C 4.7 7.6 - - - -
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Residues in contact with LEU1019 (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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1015A ARG 3.8 4.5 - - - +
1016A SER* 3.2 10.7 + - - +
1017A GLY 3.2 0.6 - - - -
1018A TYR* 1.3 79.6 - - - +
1020A GLN* 1.3 63.1 + - - +
1023A LEU* 3.2 37.2 + - + +
1193A VAL* 4.3 8.1 - - + +
1194A GLY* 3.7 29.6 - - - +
1197A SER* 4.6 4.3 - - - +
1219A ILE* 3.7 26.2 - - + -
1222A LEU* 4.1 16.2 - - + -
1223A ARG* 3.4 25.2 - - + +
1226A VAL* 6.1 0.2 - - + -
1227A MET* 3.6 29.4 - - + +
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Residues in contact with GLN1020 (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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594A THR 5.6 0.6 + - - -
595A LEU* 3.6 34.8 + - + +
1016A SER* 3.0 17.7 + - - +
1017A GLY 3.1 7.4 + - - +
1019A LEU* 1.3 79.6 - - - +
1021A ARG* 1.3 59.2 + - - +
1023A LEU* 3.7 2.0 - - - +
1024A THR* 2.4 38.7 + - - +
1190A SER 3.2 18.7 + - - +
1191A GLN* 3.6 30.0 - - - +
1194A GLY* 3.2 27.4 + - - +
1074B MET* 4.1 14.9 - - - -
1077B ASP* 4.4 9.1 + - - +
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Residues in contact with ARG1021 (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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468A ARG* 2.9 50.5 - - - +
1017A GLY 3.3 10.8 + - - +
1018A TYR* 3.9 28.7 - - - +
1020A GLN* 1.3 80.1 - - - +
1022A CYS* 1.3 64.0 + - - +
1024A THR* 4.3 5.4 - - - -
1025A LYS* 3.2 25.0 + - + +
1614A SER 5.2 1.2 + - - -
1615A TYR* 3.5 30.7 + - - +
1073B GLU* 3.0 41.8 + - + +
1074B MET* 4.7 11.4 - - + -
1076B ARG* 5.8 4.9 - - - +
14T A 4.2 5.7 + - - -
15T C 5.5 3.4 + - - -
16T G 5.8 2.8 + - - -
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Residues in contact with CYS1022 (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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1018A TYR* 3.1 31.1 + - + +
1020A GLN 3.3 0.2 - - - -
1021A ARG* 1.3 79.2 - - - +
1023A LEU* 1.3 58.7 + - - +
1025A LYS* 4.1 10.9 - - - -
1026A GLN* 4.1 1.6 - - - +
1227A MET* 3.6 36.3 - - + -
1598A PHE* 3.5 31.7 - - - +
1599A ASN* 5.1 3.8 - - - -
1615A TYR* 3.2 33.2 - - - +
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Residues in contact with LEU1023 (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 LEU* 3.2 33.2 - - + +
1020A GLN 3.7 2.5 - - - +
1021A ARG 3.3 0.2 - - - -
1022A CYS* 1.3 74.2 - - - +
1024A THR* 1.3 69.1 + - - +
1025A LYS 3.2 1.8 - - - -
1026A GLN* 3.3 4.3 + - - +
1027A LEU* 3.1 31.2 + - + +
1190A SER* 3.6 35.9 - - - +
1193A VAL* 4.3 12.1 - - + -
1222A LEU* 5.9 1.8 - - + -
1226A VAL* 4.3 14.8 - - + -
1227A MET* 3.7 17.7 - - + -
1585A ILE* 5.3 7.0 - - + -
1598A PHE* 3.6 27.1 - - + -
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Residues in contact with THR1024 (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 GLN* 2.4 34.5 + - - +
1021A ARG* 4.2 4.0 - - - -
1023A LEU* 1.3 75.4 - - - +
1025A LYS* 1.3 61.0 + - - +
1027A LEU* 3.5 1.1 - - - +
1028A GLU* 2.9 30.2 + - + +
1187A ILE* 3.7 8.7 - - + -
1190A SER* 3.2 31.6 + - - +
1076B ARG* 5.7 6.1 - - - +
1077B ASP* 3.2 41.1 + - + +
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Residues in contact with LYS1025 (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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1021A ARG* 3.2 19.3 + - + +
1022A CYS 4.1 9.9 - - - +
1023A LEU 3.2 0.2 - - - -
1024A THR* 1.3 77.2 - - - +
1026A GLN* 1.3 76.7 + - - +
1028A GLU* 3.1 32.6 - - - +
1598A PHE 3.8 5.3 + - - -
1599A ASN 4.9 1.0 - - - -
1603A MET* 3.2 34.0 - - + +
1611A MET* 3.8 19.1 - - + +
1614A SER* 5.6 1.6 - - - -
1615A TYR* 2.9 60.3 - - + +
1638A SER* 5.5 2.0 - - - -
1076B ARG* 5.2 7.5 - - - +
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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