Contacts of the helix formed by residues 1005 - 1017 (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 TYR1005 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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965A VAL 3.2 14.8 - - - +
966A LYS 3.4 26.2 - - - -
967A ASP 3.3 11.9 - - - -
968A GLN* 3.2 37.6 + - - +
971A ASN* 3.5 24.2 - - + +
972A HIS* 5.9 0.7 - + - -
1003A HIS* 2.9 18.9 + + + -
1004A PRO* 1.3 88.6 - - + +
1006A GLY* 1.3 62.9 + - - +
1007A CYS 3.3 0.2 - - - -
1008A ARG* 2.9 32.0 + - + +
1009A VAL* 3.2 8.9 + - - +
17C U 5.6 8.7 - - - -
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Residues in contact with GLY1006 (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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965A VAL* 4.0 20.1 - - - +
993A PHE* 4.7 0.2 - - - -
1000A LEU* 3.1 22.0 - - - -
1003A HIS* 3.1 14.2 + - - -
1005A TYR* 1.3 78.5 - - - +
1007A CYS* 1.3 61.2 + - - +
1008A ARG 3.1 0.3 + - - -
1009A VAL* 3.1 2.8 + - - +
1010A ILE* 2.9 28.0 + - - +
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Residues in contact with CYS1007 (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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1000A LEU 3.1 8.1 + - - -
1001A SER* 3.4 23.3 - - - +
1003A HIS 3.1 10.0 + - - +
1004A PRO 3.4 19.1 - - - -
1006A GLY* 1.3 75.7 - - - +
1008A ARG* 1.3 60.7 + - - +
1010A ILE* 3.7 2.6 + - - +
1011A GLN* 2.9 34.3 + - - +
1041A TYR* 3.8 18.8 - - - +
1045A VAL* 3.8 16.8 - - + +
16C A 3.8 26.9 - - - -
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Residues in contact with ARG1008 (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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971A ASN* 5.0 0.2 - - - +
975A GLN* 3.6 19.3 - - - +
1004A PRO 3.8 15.0 + - - +
1005A TYR* 2.9 18.7 + - + +
1007A CYS* 1.3 76.4 - - - +
1009A VAL* 1.3 63.1 + - - +
1011A GLN* 3.3 8.4 + - - +
1012A ARG* 3.1 36.0 + - - +
16C A 3.7 58.7 + - - +
17C U 2.8 79.7 + - - +
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Residues in contact with VAL1009 (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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965A VAL* 4.2 16.8 - - + -
971A ASN* 4.2 11.7 - - + +
974A VAL* 3.8 15.0 - - + -
975A GLN* 4.0 17.0 - - + -
978A ILE* 3.4 23.8 - - + -
989A ILE* 5.0 0.2 - - + -
993A PHE* 3.5 27.1 - - + -
1005A TYR 3.2 11.6 + - - +
1006A GLY 3.1 5.9 + - - +
1008A ARG* 1.3 73.0 - - - +
1010A ILE* 1.3 67.3 + - - +
1012A ARG* 3.2 8.5 + - - +
1013A ILE* 2.9 24.7 + - + +
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Residues in contact with ILE1010 (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 PHE* 3.3 34.5 - - + -
997A VAL* 4.4 8.3 - - + -
1000A LEU* 4.6 4.7 - - + -
1001A SER* 3.7 23.8 - - - +
1006A GLY 2.9 23.2 + - - +
1007A CYS* 3.7 7.0 - - - +
1009A VAL* 1.3 75.9 - - - +
1011A GLN* 1.3 61.8 + - - +
1013A ILE* 3.2 8.2 + - + +
1014A LEU* 3.0 29.0 + - + +
1025A ILE* 4.4 25.1 - - + -
1029A LEU* 4.5 1.3 - - + -
1045A VAL* 3.7 26.0 - - + -
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Residues in contact with GLN1011 (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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1007A CYS* 2.9 24.8 + - - +
1008A ARG* 3.7 11.7 - - - +
1009A VAL 3.2 0.6 - - - -
1010A ILE* 1.3 76.7 - - - +
1012A ARG* 1.3 78.2 + - - +
1014A LEU* 3.1 14.8 + - - +
1015A GLU* 3.0 23.6 + - - +
1044A TYR* 3.9 16.9 - - - +
1045A VAL* 4.4 10.5 - - + -
1048A HIS* 3.7 31.8 + - + +
16C A 3.0 43.1 + - - +
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Residues in contact with ARG1012 (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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975A GLN* 3.1 40.0 + - + +
978A ILE* 3.3 23.7 - - + +
979A GLU* 3.8 30.5 - - - -
1008A ARG* 3.1 28.2 + - - +
1009A VAL 3.6 4.9 - - - +
1011A GLN* 1.3 95.5 + - - +
1013A ILE* 1.3 62.9 + - - +
1015A GLU* 3.0 40.5 + - - -
1016A HIS* 3.0 29.6 + - + -
1048A HIS* 4.8 1.2 + - - -
17C U 4.6 10.1 + - - -
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Residues in contact with ILE1013 (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 ILE* 3.6 16.2 - - + -
989A ILE* 4.3 8.5 - - + -
990A ILE* 3.7 31.6 - - + -
993A PHE* 3.9 33.7 - - + -
1009A VAL* 2.9 23.9 + - + +
1010A ILE* 3.2 10.7 + - + +
1012A ARG* 1.3 77.3 - - - +
1014A LEU* 1.3 58.2 + - - +
1017A CYS* 3.0 44.3 + - + +
1022A THR* 3.5 6.9 - - + +
1025A ILE* 4.3 20.6 - - + -
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Residues in contact with LEU1014 (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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1010A ILE* 3.0 26.7 + - + +
1011A GLN* 3.1 9.8 + - - +
1013A ILE* 1.3 76.1 - - - +
1015A GLU* 1.3 59.2 + - - +
1016A HIS 3.6 0.2 - - - -
1017A CYS 5.1 1.0 + - - +
1022A THR* 4.3 20.2 - - - +
1025A ILE* 4.5 16.8 - - + -
1026A LEU* 4.0 30.1 - - + -
1029A LEU* 4.2 10.3 - - + -
1045A VAL* 4.4 5.6 - - + -
1048A HIS* 3.9 21.1 - - + +
1049A VAL* 3.8 25.4 - - + -
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Residues in contact with GLU1015 (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 GLN 3.0 17.0 + - - +
1012A ARG* 3.0 38.1 + - - +
1013A ILE 3.3 0.2 - - - -
1014A LEU* 1.3 79.2 - - - +
1016A HIS* 1.3 82.3 + - + +
1017A CYS 3.9 0.7 - - - -
1048A HIS* 2.9 29.8 + - + +
1052A HIS* 5.1 3.6 + - + -
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Residues in contact with HIS1016 (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 ILE* 3.5 26.2 + - + +
979A GLU* 3.9 41.3 + - + +
983A PRO* 3.5 20.8 - - + +
986A LEU* 6.0 0.4 - - + -
1012A ARG* 3.0 25.0 + - - +
1015A GLU* 1.3 104.9 + - + +
1017A CYS* 1.3 66.5 + - - +
1018A LEU* 5.7 0.2 - - - +
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Residues in contact with CYS1017 (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 ILE* 4.4 10.3 - - - -
983A PRO* 4.4 2.9 - - - -
986A LEU* 4.5 16.6 - - - -
990A ILE* 4.1 12.1 - - - -
1013A ILE* 3.0 42.0 + - + +
1014A LEU 5.2 1.7 - - - +
1015A GLU 5.2 0.7 - - - -
1016A HIS* 1.3 82.8 + - - +
1018A LEU* 1.3 64.7 + - - +
1019A PRO* 4.1 1.2 - - - +
1021A GLN* 3.2 23.1 - - + +
1022A THR* 3.6 17.3 - - + +
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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