Contacts of the helix formed by residues 1041 - 1053 (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 TYR1041 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A SER 3.6 13.4 - - - +
1002A THR 3.5 20.2 - - - +
1003A HIS 4.0 0.9 - - - +
1004A PRO* 3.7 39.0 - - + +
1007A CYS* 3.8 21.5 - - - +
1039A ASP* 2.8 9.2 + - - +
1040A GLN* 1.3 108.7 + - + +
1042A GLY* 1.3 64.0 + - - +
1043A ASN 3.1 1.8 - - - -
1044A TYR* 3.1 23.1 + - - +
1045A VAL 3.8 2.4 + - - -
16C A 3.5 43.6 + - - -
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Residues in contact with GLY1042 (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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1001A SER 3.3 14.1 + - - -
1036A LEU* 3.2 29.5 - - - +
1039A ASP* 2.7 18.0 + - - -
1041A TYR* 1.3 73.8 - - - +
1043A ASN* 1.3 61.6 + - - +
1045A VAL* 3.0 17.6 + - - +
1046A ILE* 3.2 14.9 + - - +
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Residues in contact with ASN1043 (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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1036A LEU 3.0 9.8 + - - -
1037A VAL* 3.2 24.9 - - - +
1039A ASP 3.0 19.9 + - - +
1040A GLN 3.3 10.5 + - - -
1041A TYR 3.1 1.2 - - - -
1042A GLY* 1.3 77.6 - - - +
1044A TYR* 1.3 64.2 + - - +
1046A ILE* 3.6 1.0 + - - +
1047A GLN* 2.6 57.3 + - - +
1077A PHE* 3.7 14.4 - - - +
1081A VAL* 3.8 12.9 - - + +
15C U 2.8 35.5 + - - +
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Residues in contact with TYR1044 (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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1007A CYS* 5.5 0.2 - - - -
1011A GLN* 3.9 6.2 - - - +
1040A GLN 3.8 11.4 - - - -
1041A TYR* 3.1 15.3 + - - +
1042A GLY 3.1 1.0 - - - -
1043A ASN* 1.3 80.2 + - - +
1045A VAL* 1.3 59.5 + - - +
1047A GLN* 3.4 13.5 + - - +
1048A HIS* 2.9 28.2 + - - +
15C U 2.9 71.0 - + + +
16C A 3.4 86.0 + + + +
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Residues in contact with VAL1045 (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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1001A SER* 4.1 16.2 - - - +
1007A CYS* 3.8 40.8 - - + +
1010A ILE* 3.7 18.2 - - + -
1011A GLN* 4.4 4.5 - - + -
1014A LEU* 4.4 5.2 - - + -
1029A LEU* 3.5 38.4 - - + -
1036A LEU* 5.8 0.4 - - + -
1041A TYR 4.2 0.4 - - - +
1042A GLY* 3.0 9.1 + - - +
1044A TYR* 1.3 78.1 - - - +
1046A ILE* 1.3 63.4 + - + +
1048A HIS* 3.2 16.5 + - - +
1049A VAL* 3.2 13.7 + - - +
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Residues in contact with ILE1046 (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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1029A LEU* 4.4 15.3 - - + +
1033A THR* 4.2 17.5 - - + +
1036A LEU* 3.9 33.2 - - + -
1037A VAL* 4.3 15.0 - - + +
1042A GLY 3.2 13.0 + - - +
1043A ASN 4.0 5.8 - - - +
1044A TYR 3.3 0.2 - - - -
1045A VAL* 1.3 74.5 - - - +
1047A GLN* 1.3 64.5 + - - +
1049A VAL* 3.2 7.3 + - + +
1050A LEU* 3.0 19.9 + - + +
1061A ILE* 3.4 40.4 - - + -
1081A VAL* 4.0 16.6 - - + -
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Residues in contact with GLN1047 (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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1043A ASN* 2.6 43.0 + - - +
1044A TYR* 3.7 13.5 - - + +
1046A ILE* 1.3 72.3 - - - +
1048A HIS* 1.3 67.2 + - - +
1050A LEU* 2.8 21.4 + - - -
1051A GLU* 2.8 23.0 + - - +
1080A ASN* 3.8 12.5 - - - +
1081A VAL* 4.1 15.0 - - + +
1084A LYS* 3.1 43.5 + - + +
15C U 2.9 20.2 + - - +
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Residues in contact with HIS1048 (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 GLN* 3.7 40.2 + - + +
1012A ARG* 4.8 1.1 - - - -
1014A LEU* 3.9 20.7 - - + +
1015A GLU* 2.9 45.3 + - + +
1044A TYR 2.9 14.7 + - - +
1045A VAL 3.2 12.1 + - - +
1047A GLN* 1.3 77.5 - - - +
1049A VAL* 1.3 59.3 + - - +
1051A GLU* 3.2 5.2 + - - -
1052A HIS* 2.9 61.8 + + + +
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Residues in contact with VAL1049 (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* 3.8 22.4 - - + -
1026A LEU* 4.3 17.5 - - + -
1029A LEU* 4.3 8.7 - - + -
1030A HIS* 5.2 0.9 - - + -
1045A VAL 3.2 14.3 + - - +
1046A ILE* 3.5 9.2 - - + +
1047A GLN 3.1 0.6 - - - -
1048A HIS* 1.3 76.2 - - - +
1050A LEU* 1.3 58.6 + - - +
1053A GLY* 2.8 33.3 + - - +
1057A ASP* 3.9 28.0 - - + -
1058A LYS* 3.7 5.6 - - - +
1061A ILE* 3.8 20.9 - - + -
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Residues in contact with LEU1050 (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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1046A ILE 3.0 16.6 + - - +
1047A GLN* 2.8 12.6 + - - +
1049A VAL* 1.3 73.1 - - - +
1051A GLU* 1.3 58.4 + - - +
1058A LYS* 3.2 57.8 + - + +
1061A ILE* 4.1 15.3 - - + -
1062A VAL* 4.5 5.2 - - + -
1081A VAL* 3.9 15.9 - - + +
1084A LYS* 3.6 35.2 - - + +
1085A CYS* 3.7 31.2 - - - +
1088A HIS* 3.2 17.3 - - + +
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Residues in contact with GLU1051 (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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1047A GLN* 2.8 25.3 + - - +
1048A HIS* 3.8 5.6 - - - +
1050A LEU* 1.3 81.8 - - - +
1052A HIS* 1.3 87.4 + - + +
1058A LYS* 4.6 5.3 + - - -
1084A LYS* 3.2 34.5 - - + -
1088A HIS* 3.9 29.2 + - + +
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Residues in contact with HIS1052 (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 GLU* 5.1 3.6 + - + -
1048A HIS* 2.9 60.5 + + + +
1051A GLU* 1.3 103.3 + - + +
1053A GLY* 1.3 67.7 + - - +
1058A LYS* 4.8 1.1 - - - +
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Residues in contact with GLY1053 (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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1048A HIS 4.0 0.6 + - - -
1049A VAL* 2.8 32.6 + - - +
1052A HIS* 1.3 83.0 - - - +
1054A ARG* 1.3 64.0 + - - -
1055A PRO* 3.8 1.9 - - - +
1057A ASP* 5.3 0.7 - - - -
1058A LYS* 2.9 20.9 + - - +
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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