Contacts of the helix formed by residues 1056 - 1068 (chain A) in PDB entry 5LUQ
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 THR1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1039A TRP* 3.1 36.1 - - + +
1049A GLN* 4.1 29.3 + - + +
1055A ASN* 1.3 85.9 + - - +
1057A LYS* 1.3 80.1 + - - +
1059A LEU* 2.8 26.9 + - - +
1060A PHE* 2.9 23.6 + - - -
1090A ARG* 6.3 0.2 - - - +
1093A GLU* 5.8 2.9 - - - +
1096A VAL* 5.5 10.1 - - + -
1099A PHE* 6.6 0.2 - - - -
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Residues in contact with LYS1057 (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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1056A THR* 1.3 84.4 + - - +
1058A SER* 1.3 62.6 + - - +
1060A PHE* 3.3 9.0 + - - +
1061A LYS* 3.0 37.5 + - - +
1099A PHE* 4.9 29.3 - - + -
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Residues in contact with SER1058 (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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1053A PRO* 3.8 25.6 - - - -
1054A VAL 2.8 8.8 + - - -
1055A ASN 2.4 48.1 + - - -
1057A LYS* 1.3 75.6 - - - +
1059A LEU* 1.3 63.0 + - - +
1061A LYS* 3.4 11.1 + - - +
1062A ARG* 3.0 18.9 + - - +
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Residues in contact with LEU1059 (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 VAL* 5.4 11.7 - - + -
1032A CYS* 6.1 0.2 - - - -
1036A PHE* 3.2 45.5 - - + -
1054A VAL 4.2 5.6 + - - +
1055A ASN* 3.3 24.7 + - - +
1056A THR* 2.8 19.9 + - - +
1058A SER* 1.3 74.8 + - - +
1060A PHE* 1.3 64.5 + - + +
1062A ARG* 2.5 34.0 + - + +
1063A LEU* 2.9 44.3 + - + +
1082A PHE* 4.1 3.6 - - + -
1086A TYR* 5.8 2.9 - - + -
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Residues in contact with PHE1060 (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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1056A THR* 2.9 34.5 + - - -
1057A LYS 4.0 3.1 - - - +
1059A LEU* 1.3 83.6 - - + +
1061A LYS* 1.3 63.6 + - - +
1063A LEU* 3.3 20.0 - - + -
1064A TYR* 2.7 50.7 + + + -
1082A PHE* 4.6 12.1 - + - -
1083A ASN* 5.7 2.7 - - - -
1086A TYR* 4.6 6.5 - + - -
1090A ARG* 3.5 44.9 - - + -
1096A VAL* 5.0 1.6 - - + -
1099A PHE* 3.3 38.4 - + + -
1100A VAL* 3.9 16.2 - - + -
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Residues in contact with LYS1061 (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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1057A LYS* 3.0 23.5 + - - +
1058A SER* 3.4 14.1 - - - +
1060A PHE* 1.3 77.0 - - - +
1062A ARG* 1.3 54.7 + - - +
1064A TYR* 5.0 1.8 - - - -
1065A SER* 2.6 39.1 + - - -
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Residues in contact with ARG1062 (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 VAL* 5.6 6.1 - - + -
1011A GLU* 2.7 42.7 + - + +
1058A SER 3.0 10.9 + - - +
1059A LEU* 2.5 21.0 + - + +
1061A LYS* 1.3 72.4 - - - +
1063A LEU* 1.3 60.9 + - + +
1065A SER* 3.0 22.7 + - - -
1066A LEU* 2.8 28.6 + - - +
1069A HIS* 4.1 15.0 + - - -
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Residues in contact with LEU1063 (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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1059A LEU* 2.9 41.4 + - + +
1060A PHE* 3.3 20.0 - - + +
1062A ARG* 1.3 78.9 - - + +
1064A TYR* 1.3 57.9 + - + +
1066A LEU* 2.9 20.8 + - + +
1067A ALA* 2.7 32.6 + - - +
1079A SER* 3.9 6.3 + - - +
1082A PHE* 3.1 60.1 - - + -
1107A TYR* 6.0 1.8 - - + +
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Residues in contact with TYR1064 (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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1060A PHE* 2.7 60.0 + + + +
1061A LYS* 4.4 2.0 - - - +
1063A LEU* 1.3 71.2 - - + +
1065A SER* 1.3 61.0 + - - +
1067A ALA* 2.7 25.8 + - - +
1068A LEU* 3.1 19.5 + - + +
1099A PHE* 5.8 1.1 - + - -
1100A VAL* 3.3 18.0 + - + +
1103A ALA* 2.9 52.7 - - + +
1104A LEU* 3.5 3.3 + - - +
1106A ILE* 3.3 29.4 - - + -
1107A TYR* 4.5 22.2 - + + -
1110A SER* 4.6 5.2 - - - -
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Residues in contact with SER1065 (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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1061A LYS 2.6 25.3 + - - -
1062A ARG* 3.0 20.6 + - - -
1064A TYR* 1.3 75.9 - - - +
1066A LEU* 1.3 57.7 + - - +
1068A LEU 3.0 15.0 - - - +
1069A HIS* 2.8 44.0 + - - -
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Residues in contact with LEU1066 (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 GLU* 4.1 12.1 - - + +
1014A LEU* 3.6 44.2 - - + -
1062A ARG 2.8 20.7 + - - +
1063A LEU* 2.9 27.3 + - + +
1065A SER* 1.3 77.2 + - - +
1067A ALA* 1.3 63.7 + - - +
1069A HIS* 3.4 15.5 + - + +
1075A ARG* 3.8 42.8 - - - +
1078A ALA* 4.4 5.6 - - + -
1079A SER* 4.3 13.0 - - - +
1082A PHE* 5.1 2.5 - - + -
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Residues in contact with ALA1067 (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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1063A LEU 2.7 11.0 + - - +
1064A TYR* 2.7 16.5 + - - +
1066A LEU* 1.3 73.5 - - - +
1068A LEU* 1.3 68.2 + - + +
1069A HIS 3.9 0.9 + - - -
1070A PRO* 4.5 3.5 - - - +
1071A ASN 4.2 2.9 - - - +
1075A ARG 5.0 0.2 - - - -
1076A LEU* 3.4 25.3 - - - +
1079A SER* 3.0 31.2 - - - +
1107A TYR* 3.9 6.1 - - + -
1110A SER* 4.3 0.9 - - - -
1111A LEU* 3.3 19.1 - - + -
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Residues in contact with LEU1068 (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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1064A TYR* 3.1 21.2 + - + +
1065A SER* 3.0 14.3 - - - +
1067A ALA* 1.3 79.7 - - + +
1069A HIS* 1.3 62.8 + - - +
1071A ASN 3.6 14.1 - - - +
1106A ILE* 6.0 1.3 - - + -
1109A GLU 5.1 1.1 - - - +
1110A SER* 3.3 49.1 - - - +
1113A LEU* 6.6 0.2 - - + -
1114A ALA* 5.3 4.7 - - + -
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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