Contacts of the helix formed by residues 1018 - 1032 (chain A) in PDB entry 1M8X
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 LEU1018 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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983A PRO* 3.6 28.9 - - + -
984A GLN* 4.3 17.9 - - + +
1017A CYS* 1.3 72.7 - - - +
1019A PRO* 1.3 68.0 - - + -
1020A ASP* 4.3 6.5 - - + +
1021A GLN* 2.6 48.7 + - + +
1022A THR* 2.8 17.2 + - - -
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Residues in contact with PRO1019 (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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1017A CYS 4.5 1.3 - - - +
1018A LEU* 1.3 94.1 - - + +
1020A ASP* 1.3 59.3 + - - +
1022A THR* 3.6 8.7 + - - +
1023A LEU* 2.9 35.8 + - - +
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Residues in contact with ASP1020 (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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987A GLN* 5.7 2.9 + - - +
990A ILE* 5.5 0.5 - - - +
994A LYS* 5.5 2.6 + - - -
1018A LEU* 3.2 5.1 - - + +
1019A PRO* 1.3 80.8 - - - +
1021A GLN* 1.3 61.7 + - + +
1023A LEU* 4.4 9.5 - - - +
1024A PRO* 3.4 18.3 - - - +
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Residues in contact with GLN1021 (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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983A PRO* 3.2 28.7 + - - +
984A GLN* 4.5 1.8 - - - +
987A GLN* 2.9 43.9 + - - +
990A ILE* 3.8 30.3 - - + +
1017A CYS* 3.2 17.2 - - + +
1018A LEU* 2.6 52.2 + - + +
1020A ASP* 1.3 75.7 - - + +
1022A THR* 1.3 60.5 + - - +
1023A LEU 3.3 1.6 - - - -
1024A PRO* 3.3 13.1 - - - +
1025A ILE* 3.3 16.1 - - - +
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Residues in contact with THR1022 (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 ILE* 3.5 25.8 - - + +
1014A LEU* 4.3 18.6 - - - +
1017A CYS* 3.6 25.6 - - + +
1018A LEU 2.8 13.1 + - - +
1019A PRO* 3.6 13.2 + - - +
1021A GLN* 1.3 71.5 - - - +
1023A LEU* 1.3 61.3 + - - +
1024A PRO 3.5 0.2 - - - -
1025A ILE* 3.3 9.1 + - - +
1026A LEU* 2.9 45.8 + - - +
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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 PRO 2.9 18.1 + - - +
1020A ASP* 4.4 9.2 - - - +
1022A THR* 1.3 77.0 + - - +
1024A PRO* 1.3 70.3 - - + +
1026A LEU* 3.2 11.3 + - + +
1027A GLU* 3.0 21.9 + - + +
1054A ARG* 5.4 9.9 - - - +
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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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990A ILE* 4.9 1.8 - - + -
994A LYS* 3.9 36.3 - - + +
1020A ASP 3.4 14.4 - - - +
1021A GLN* 3.3 16.2 - - - +
1023A LEU* 1.3 96.1 - - + +
1025A ILE* 1.3 68.6 + - + +
1027A GLU* 3.4 7.8 + - + +
1028A GLU* 3.3 29.1 + - - +
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Residues in contact with ILE1025 (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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990A ILE* 4.6 15.7 - - + +
993A PHE* 4.0 25.4 - - + -
994A LYS* 5.3 3.4 - - + +
997A VAL* 3.9 33.1 - - + +
1010A ILE* 4.4 16.2 - - + -
1013A ILE* 4.3 15.0 - - + -
1014A LEU* 4.5 9.6 - - + -
1021A GLN 3.3 20.6 - - - +
1022A THR* 3.5 9.2 - - - +
1023A LEU 3.2 0.4 - - - -
1024A PRO* 1.3 80.1 - - + +
1026A LEU* 1.3 63.2 + - - +
1028A GLU* 3.3 3.5 + - - +
1029A LEU* 3.0 32.6 + - + +
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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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1014A LEU* 4.0 22.4 - - + -
1022A THR* 2.9 36.3 + - - +
1023A LEU* 3.6 9.0 - - + +
1025A ILE* 1.3 74.3 - - - +
1027A GLU* 1.3 65.1 + - - +
1029A LEU* 3.1 15.0 + - + +
1030A HIS* 2.9 36.1 + - + +
1049A VAL* 4.3 17.5 - - + -
1054A ARG* 5.4 5.4 - - - +
1057A ASP* 3.6 38.6 - - - +
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Residues in contact with GLU1027 (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 LEU* 3.0 13.7 + - + +
1024A PRO* 3.8 10.8 - - + +
1025A ILE 3.3 0.4 - - - -
1026A LEU* 1.3 75.6 - - - +
1028A GLU* 1.3 61.2 + - + +
1030A HIS* 3.1 14.9 + - - +
1031A GLN* 2.9 37.2 + - + +
1060A LYS* 5.0 9.6 + - - -
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Residues in contact with GLU1028 (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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994A LYS* 3.7 7.6 - - - +
995A GLY* 2.8 36.4 + - - +
997A VAL* 3.1 47.7 + - + +
998A PHE* 4.2 5.2 + - - +
1024A PRO* 3.3 12.8 + - - +
1025A ILE 3.3 4.1 + - - +
1026A LEU 3.3 0.4 - - - -
1027A GLU* 1.3 82.0 - - + +
1029A LEU* 1.3 62.8 + - - +
1031A GLN* 3.3 6.8 + - - -
1032A HIS* 3.2 33.5 + - + +
1036A LEU* 5.0 0.2 - - - +
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Residues in contact with LEU1029 (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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997A VAL* 3.8 9.9 - - + -
1001A SER* 3.5 25.6 - - - +
1010A ILE* 4.5 0.7 - - + -
1014A LEU* 4.2 17.0 - - + -
1025A ILE* 3.0 26.4 + - + +
1026A LEU* 3.1 22.4 + - + +
1028A GLU* 1.3 77.6 - - - +
1030A HIS* 1.3 63.6 + - + +
1032A HIS 3.5 1.6 + - - -
1033A THR* 2.8 27.5 + - - -
1036A LEU* 3.6 23.0 - - + +
1045A VAL* 3.5 28.0 - - + -
1046A ILE* 4.4 9.5 - - + +
1049A VAL* 4.3 7.2 - - + -
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Residues in contact with HIS1030 (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* 2.9 36.7 + - + +
1027A GLU* 3.6 14.4 - - - +
1029A LEU* 1.3 80.5 - - + +
1031A GLN* 1.3 61.2 + - - +
1033A THR* 3.2 19.3 + - - -
1049A VAL* 5.2 0.4 - - + -
1057A ASP* 2.6 59.3 + - + -
1060A LYS* 3.8 37.7 - - + +
1061A ILE* 4.4 15.1 + - + +
1064A GLU* 5.2 5.7 - - - +
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Residues in contact with GLN1031 (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 GLU* 2.9 25.0 + - + +
1028A GLU* 3.7 9.4 - - - +
1029A LEU 3.3 0.4 - - - -
1030A HIS* 1.3 79.5 - - - +
1032A HIS* 1.3 74.7 + - + +
1033A THR 3.9 0.2 + - - -
1034A GLU* 5.4 0.5 + - - +
1035A GLN* 5.1 0.7 - - - +
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Residues in contact with HIS1032 (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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998A PHE* 3.5 51.6 - + + +
1028A GLU* 3.2 27.4 + - + +
1029A LEU 3.7 2.7 - - - -
1031A GLN* 1.3 93.5 + - + +
1033A THR* 1.3 59.9 + - - +
1034A GLU* 3.3 2.7 - - - -
1035A GLN* 3.0 29.6 + - - +
1036A LEU* 2.8 33.2 + - + +
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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