Contacts of the helix formed by residues 1041 - 1053 (chain A) in PDB entry 4YKN
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 THR1041 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1039A GLU 4.5 5.4 - - - +
1040A ALA* 1.3 76.7 - - - +
1042A LEU* 1.3 60.3 + - - +
1043A ILE* 3.6 7.7 + - - +
1044A THR* 3.1 27.0 + - - +
1045A ILE* 2.9 27.3 + - - +
1085A GLU 3.6 6.5 - - - -
1086A THR* 3.1 29.2 - - + +
1087A ARG 3.4 6.1 - - - +
1088A ARG* 4.2 7.6 - - + +
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Residues in contact with LEU1042 (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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1041A THR* 1.3 70.0 - - - +
1043A ILE* 1.3 60.3 + - - +
1045A ILE* 4.1 12.8 - - + -
1046A LYS* 2.9 32.1 + - - +
1070A PHE* 3.9 28.2 - - + -
1082A PHE* 3.5 40.6 - - + +
1084A ASP 4.1 11.2 - - - +
1085A GLU* 3.2 20.8 + - + +
1087A ARG* 3.2 14.3 + - + +
1089A LEU* 5.2 1.3 - - + -
1092A LEU* 4.0 28.3 - - + -
1099A LEU* 4.2 15.0 - - + -
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Residues in contact with ILE1043 (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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1041A THR* 3.1 8.0 - - - +
1042A LEU* 1.3 76.5 - - - +
1044A THR* 1.3 67.9 + - - +
1046A LYS* 3.9 4.1 - - - +
1047A HIS* 3.1 24.3 + - + +
1085A GLU* 3.1 43.2 + - + +
1086A THR* 4.4 9.9 - - - +
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Residues in contact with THR1044 (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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1040A ALA* 4.5 13.2 - - + -
1041A THR* 3.1 25.4 + - - -
1043A ILE* 1.3 80.0 - - - +
1045A ILE* 1.3 63.5 + - - +
1047A HIS* 3.4 4.7 + - - +
1048A GLU* 3.0 36.6 + - + +
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Residues in contact with ILE1045 (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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1022A VAL* 5.7 0.2 - - + -
1024A CYS* 5.2 2.7 - - - -
1034A LEU* 3.8 10.5 - - + +
1036A CYS* 4.0 31.4 - - - -
1040A ALA* 4.0 16.4 - - + +
1041A THR 2.9 19.5 + - - +
1042A LEU* 3.9 14.8 - - + +
1044A THR* 1.3 77.1 - - + +
1046A LYS* 1.3 59.0 + - - +
1048A GLU* 4.9 2.9 - - - -
1049A LEU* 2.8 31.8 + - + +
1070A PHE* 4.1 16.8 - - + -
1089A LEU* 3.9 36.3 - - + -
1099A LEU* 4.1 12.8 - - + -
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Residues in contact with LYS1046 (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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1042A LEU 2.9 17.2 + - - +
1043A ILE* 3.9 3.8 - - - +
1045A ILE* 1.3 76.8 - - - +
1047A HIS* 1.3 62.0 + - - +
1049A LEU* 3.4 1.0 + - - +
1050A PHE* 3.2 48.4 + - + +
1065A GLU* 3.2 40.7 + - + +
1066A SER* 4.4 5.7 + - - +
1068A TYR* 3.3 18.5 + - + +
1069A ILE* 5.1 1.3 - - - -
1070A PHE* 3.6 24.2 - - + -
1085A GLU* 3.0 38.2 + - - +
1101A VAL* 6.2 0.4 - - + -
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Residues in contact with HIS1047 (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 ILE* 3.1 19.2 + - + +
1044A THR* 3.9 4.9 - - - +
1046A LYS* 1.3 77.5 - - - +
1048A GLU* 1.3 65.2 - - + +
1050A PHE* 3.5 3.3 + - - +
1051A LYS* 3.4 53.2 + - + +
1065A GLU* 3.1 35.8 + - - +
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Residues in contact with GLU1048 (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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1034A LEU* 4.4 14.7 - - + +
1044A THR* 3.0 31.6 + - + +
1045A ILE* 4.1 3.4 - - - +
1047A HIS* 1.3 77.6 - - + +
1049A LEU* 1.3 66.3 + - - +
1051A LYS* 2.9 48.8 + - - +
1052A GLU* 3.1 13.0 + - - +
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Residues in contact with LEU1049 (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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1024A CYS* 3.6 28.7 - - + -
1026A LEU* 4.3 8.3 - - + -
1032A VAL* 3.3 33.4 - - + -
1034A LEU* 3.7 16.3 - - + +
1045A ILE 2.8 19.2 + - - +
1046A LYS 3.5 4.3 - - - +
1047A HIS 3.3 0.2 - - - -
1048A GLU* 1.3 75.9 - - - +
1050A PHE* 1.3 67.3 + - + +
1052A GLU* 3.0 7.7 + - + +
1053A ALA* 2.9 26.1 + - + +
1070A PHE* 3.7 27.6 - - + -
1101A VAL* 3.9 13.9 - - + -
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Residues in contact with PHE1050 (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* 5.2 5.6 - - + -
1046A LYS* 3.2 40.9 + - + +
1047A HIS 4.1 1.3 - - - +
1048A GLU 3.2 0.4 - - - -
1049A LEU* 1.3 92.6 - - + +
1051A LYS* 1.3 62.6 + - - +
1053A ALA* 4.0 9.9 + - + +
1054A ARG* 3.7 17.3 + - - +
1059A HIS* 4.5 7.7 - + - -
1062A LEU* 4.6 21.8 - - + -
1063A GLN 3.7 23.1 - - - -
1065A GLU* 3.8 33.2 - - + +
1068A TYR* 3.4 32.5 - + - -
1101A VAL* 4.3 14.8 - - + -
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Residues in contact with LYS1051 (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 HIS* 3.4 40.7 + - + +
1048A GLU* 2.9 43.7 + - - +
1050A PHE* 1.3 77.3 - - - +
1052A GLU* 1.3 62.5 + - - +
1053A ALA 3.2 0.2 - - - -
1054A ARG* 3.4 21.3 + - - +
1055A LYS* 4.4 7.7 + - - +
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Residues in contact with GLU1052 (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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1032A VAL* 5.2 3.8 - - + -
1033A THR 4.2 16.0 - - - +
1034A LEU* 4.3 16.9 - - + +
1048A GLU 3.1 9.9 + - - +
1049A LEU* 3.0 11.7 + - + +
1051A LYS* 1.3 75.3 - - - +
1053A ALA* 1.3 63.5 + - - +
1055A LYS* 3.1 50.9 + - - +
1056A TYR* 3.2 29.9 + - + -
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Residues in contact with ALA1053 (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* 3.9 19.7 - - + +
1032A VAL* 4.8 2.2 - - + -
1049A LEU* 2.9 16.9 + - + +
1050A PHE* 4.2 11.9 - - + +
1051A LYS 3.2 0.8 - - - -
1052A GLU* 1.3 76.3 - - - +
1054A ARG* 1.3 56.9 + - - +
1055A LYS 3.0 0.4 - - - -
1056A TYR* 3.0 35.4 + - - +
1057A PRO 5.2 0.2 - - - +
1059A HIS* 3.8 9.1 + - + +
1062A LEU* 3.7 27.4 - - + +
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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