Contacts of the helix formed by residues 1012 - 1023 (chain A) in PDB entry 3M5M
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 GLY1012 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A GLN* 3.9 16.4 - - - +
1011A ARG* 1.3 76.1 - - - +
1013A GLU* 1.3 61.1 + - - -
1014A GLU* 3.4 7.7 + - - -
1015A GLY* 3.4 4.2 + - - +
1016A CYS* 2.9 27.2 + - - +
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Residues in contact with GLU1013 (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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1012A GLY* 1.3 71.6 - - - -
1014A GLU* 1.3 81.7 + - + +
1016A CYS* 3.5 7.2 - - - +
1017A GLN* 2.9 30.1 + - - +
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Residues in contact with GLU1014 (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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1012A GLY* 4.4 3.8 - - - -
1013A GLU* 1.3 100.5 + - + +
1015A GLY* 1.3 66.1 + - - +
1017A GLN* 3.4 7.5 + - - +
1018A GLU* 3.1 36.8 + - - +
1103B ASP* 3.9 21.1 - - - +
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Residues in contact with GLY1015 (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 ARG* 3.8 22.4 - - - -
1012A GLY 3.4 7.1 + - - +
1014A GLU* 1.3 76.9 + - - +
1016A CYS* 1.3 57.8 + - - +
1018A GLU* 3.4 11.9 + - - +
1019A THR* 2.7 36.7 + - - -
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Residues in contact with CYS1016 (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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993A VAL* 3.6 16.9 - - - +
995A VAL* 3.5 28.7 - - + -
1011A ARG* 3.9 9.7 - - - +
1012A GLY 2.9 18.2 + - - +
1013A GLU* 3.5 9.4 - - - +
1015A GLY* 1.3 76.5 - - - +
1017A GLN* 1.3 58.5 + - - +
1020A SER* 2.9 33.2 + - - -
1037A SER* 4.1 19.5 - - - -
1038A THR 5.3 3.1 - - - -
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Residues in contact with GLN1017 (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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1013A GLU 2.9 16.8 + - - +
1014A GLU* 3.7 6.3 - - - +
1015A GLY 3.4 0.2 - - - -
1016A CYS* 1.3 75.8 - - - +
1018A GLU* 1.3 69.5 + - - +
1020A SER* 3.2 9.0 + - - -
1021A GLN* 3.1 25.0 + - - +
1100B GLY 2.8 23.0 + - - -
1101B SER* 3.4 7.6 + - - -
1102B SER* 2.9 43.7 + - - +
1103B ASP* 4.7 1.0 + - - -
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Residues in contact with GLU1018 (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 ARG* 5.9 0.3 + - - -
1014A GLU* 3.1 29.1 + - - +
1015A GLY* 3.7 9.5 - - - +
1017A GLN* 1.3 78.8 + - - +
1019A THR* 1.3 60.3 + - - +
1021A GLN* 3.1 5.4 + - - +
1022A THR* 3.0 31.9 + - - +
1099B CYS* 3.4 29.2 - - - +
1100B GLY 4.2 3.4 - - - -
1101B SER* 3.7 30.7 + - - +
1146B PRO* 4.5 9.2 - - - +
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Residues in contact with THR1019 (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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993A VAL* 3.8 17.5 - - + -
1011A ARG* 3.3 18.8 + - - +
1015A GLY* 2.7 21.6 + - - -
1016A CYS 3.8 3.1 - - - -
1018A GLU* 1.3 77.7 - - - +
1020A SER* 1.3 58.2 + - - +
1022A THR* 3.8 7.0 - - - -
1023A GLY* 2.8 28.2 + - - -
1024A ARG 3.4 20.4 + - - +
1025A ASP* 3.8 13.0 - - + -
1065A ALA* 3.5 23.3 - - + +
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Residues in contact with SER1020 (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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988A LYS* 4.7 0.9 + - - -
990A GLY* 3.2 14.6 - - - -
991A SER* 2.8 52.1 + - - +
993A VAL* 3.4 11.8 - - - +
1016A CYS* 2.9 19.6 + - - -
1017A GLN* 3.2 8.3 + - - -
1019A THR* 1.3 77.0 - - - +
1021A GLN* 1.3 61.5 + - - +
1023A GLY 4.1 0.3 + - - -
1037A SER 5.8 0.4 - - - -
1038A THR* 5.6 2.3 - - - -
1039A ALA 5.5 4.7 + - - -
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Residues in contact with GLN1021 (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 LYS* 6.0 4.0 - - - +
988A LYS* 2.7 54.9 + - - +
990A GLY* 5.1 4.1 - - - -
1017A GLN* 3.1 14.9 + - - +
1018A GLU 3.1 7.4 + - - +
1020A SER* 1.3 78.7 - - - +
1022A THR* 1.3 62.3 + - + +
1100B GLY* 3.6 33.4 - - - +
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Residues in contact with THR1022 (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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988A LYS* 5.6 2.6 - - - -
1018A GLU 3.0 8.7 + - - +
1019A THR* 3.7 1.7 + - - -
1021A GLN* 1.3 77.4 - - + +
1023A GLY* 1.3 59.7 + - - +
1024A ARG* 3.0 34.8 + - - +
1069A GLY* 5.0 0.3 - - - -
1070A PRO* 3.8 13.0 - - - +
1098B THR 3.4 14.6 - - - +
1099B CYS* 3.2 38.6 - - - +
1100B GLY* 3.8 3.1 - - - +
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Residues in contact with GLY1023 (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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991A SER* 3.8 20.4 - - - -
1019A THR 2.8 15.3 + - - -
1020A SER 4.1 0.8 + - - -
1021A GLN 3.4 1.8 - - - -
1022A THR* 1.3 77.4 - - - +
1024A ARG* 1.3 56.9 + - - +
1065A ALA* 3.2 8.6 - - - -
1066A SER 3.0 13.0 + - - -
1069A GLY* 2.9 26.3 - - - -
1070A PRO* 3.9 8.3 - - - -
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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