Contacts of the helix formed by residues 1045 - 1064 (chain A) in PDB entry 4QUU
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 THR1045 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989A LEU* 3.8 8.9 - - - +
993A LEU* 4.7 0.3 - - - +
1043A TYR* 3.4 6.5 - - - +
1044A LEU* 1.3 86.1 - - - +
1046A VAL* 1.3 63.6 + - - +
1047A LYS* 3.3 5.4 + - - +
1048A ASP* 3.0 31.8 + - - +
1049A TYR* 3.3 17.0 + - - +
1098A GLU* 3.4 14.8 - - - -
1101A CYS* 3.9 2.7 - - - +
1102A GLU* 3.7 31.0 - - + +
1105A GLN* 3.4 27.7 + - - +
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Residues in contact with VAL1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LEU* 3.4 24.7 - - + -
992A PHE* 4.3 4.3 - - + -
993A LEU* 4.3 12.8 - - + -
1045A THR* 1.3 70.9 - - - +
1047A LYS* 1.3 59.9 + - - +
1049A TYR* 3.2 6.2 + - + +
1050A LEU* 2.8 29.0 + - + +
1089A ILE* 3.7 34.1 - - + -
1093A LEU* 3.8 35.9 - - + -
1097A PHE* 5.5 0.2 - - + -
1098A GLU* 2.9 22.5 + - - +
1205A EDO 4.1 5.4 - - - -
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Residues in contact with LYS1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045A THR* 3.2 7.9 + - - +
1046A VAL* 1.3 75.6 - - - +
1048A ASP* 1.3 59.7 + - - +
1050A LEU* 3.3 7.3 + - + +
1051A ARG* 3.0 47.6 + - - +
1098A GLU* 3.4 5.5 + - - +
1102A GLU* 2.7 33.3 + - + +
1205A EDO 2.6 38.5 + - - +
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Residues in contact with ASP1048 (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 LYS 5.1 0.2 - - - +
1043A TYR* 3.7 16.3 - - + -
1044A LEU 4.7 2.4 + - - -
1045A THR* 3.0 24.3 + - - +
1046A VAL 3.2 0.2 - - - -
1047A LYS* 1.3 74.7 - - - +
1049A TYR* 1.3 64.4 + - - +
1051A ARG* 2.4 50.0 + - - +
1052A ASP* 3.5 8.0 + - - +
1105A GLN* 2.9 28.3 + - - +
1206A EDO 3.2 30.1 + - - +
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Residues in contact with TYR1049 (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 LEU* 3.5 52.7 - - + -
996A VAL* 3.7 19.8 - - + +
997A THR* 2.8 32.2 + - - -
1000A LEU* 4.1 2.4 - - - +
1034A VAL* 3.5 23.1 - - + -
1038A ILE* 4.4 0.4 - - + -
1043A TYR* 3.6 16.8 - + + -
1045A THR 3.3 5.2 + - - +
1046A VAL 3.2 8.0 + - - +
1048A ASP* 1.3 77.0 - - - +
1050A LEU* 1.3 69.5 + - + +
1052A ASP* 2.9 20.8 + - - +
1053A ILE* 3.1 40.1 + - + +
1085A ALA* 5.2 0.9 - - + -
1089A ILE* 4.0 20.4 - - + -
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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 VAL 2.8 21.7 + - - +
1047A LYS* 3.8 6.7 - - + +
1049A TYR* 1.3 82.0 - - + +
1051A ARG* 1.3 56.7 + - - +
1053A ILE* 3.3 10.7 + - + +
1054A ASP* 2.8 36.0 + - - +
1085A ALA* 4.5 4.7 - - + -
1086A TYR* 3.9 50.9 - - + +
1089A ILE* 3.5 32.5 - - + -
1205A EDO 3.9 29.2 - - - +
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Residues in contact with ARG1051 (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 LYS* 3.0 31.2 + - - +
1048A ASP* 2.4 43.4 + - - +
1049A TYR 3.2 0.6 - - - -
1050A LEU* 1.3 76.2 - - - +
1052A ASP* 1.3 61.2 + - - +
1054A ASP* 3.5 11.6 - - - +
1055A LEU* 3.0 26.2 + - - +
1206A EDO 6.5 0.2 - - - -
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Residues in contact with ASP1052 (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 MET* 3.6 17.3 - - + +
1034A VAL* 4.3 4.3 - - + -
1037A LYS* 2.7 29.5 + - - +
1043A TYR* 2.6 34.4 + - + +
1048A ASP 3.5 3.4 + - - -
1049A TYR 2.9 9.8 + - - +
1051A ARG* 1.3 78.6 - - - +
1053A ILE* 1.3 65.2 + - - +
1055A LEU* 3.2 21.1 + - - +
1056A ILE* 3.0 27.2 + - - +
1206A EDO 4.8 3.5 - - - -
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Residues in contact with ILE1053 (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* 4.3 7.0 - - + -
1031A LEU* 4.1 24.5 - - + -
1034A VAL* 4.7 5.8 - - + -
1049A TYR* 3.1 50.8 + - + +
1050A LEU* 3.7 13.7 - - + +
1052A ASP* 1.3 75.0 - - - +
1054A ASP* 1.3 65.4 + - - +
1056A ILE* 3.1 12.5 + - + +
1057A CYS* 3.1 21.0 + - - +
1081A LEU* 4.5 8.8 - - + +
1082A ARG* 4.1 21.8 - - + +
1085A ALA* 3.8 21.8 - - + -
1086A TYR* 5.1 0.4 - - + -
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Residues in contact with ASP1054 (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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1050A LEU 2.8 25.8 + - - +
1051A ARG* 3.5 12.4 - - - +
1053A ILE* 1.3 72.7 - - - +
1055A LEU* 1.3 50.4 + - - +
1057A CYS* 3.3 7.7 + - - +
1058A SER* 2.8 36.9 + - - -
1082A ARG* 3.9 12.1 - - - +
1086A TYR* 2.8 39.8 + - - -
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Residues in contact with LEU1055 (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 GLN* 3.7 52.3 - - + +
1029A MET* 4.0 15.9 - - + -
1051A ARG 3.0 14.3 + - - +
1052A ASP* 3.4 26.9 - - - +
1053A ILE 3.2 0.4 - - - -
1054A ASP* 1.3 73.1 - - - +
1056A ILE* 1.3 65.4 + - - +
1057A CYS 3.2 0.2 - - - -
1058A SER* 3.5 9.2 - - - +
1059A ASN* 2.9 52.6 + - - +
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Residues in contact with ILE1056 (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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1009A PHE* 3.6 25.6 - - + -
1029A MET* 3.6 29.6 - - + +
1030A ASP 3.7 26.0 - - - +
1031A LEU* 3.8 22.7 - - + +
1034A VAL* 4.2 7.6 - - + -
1052A ASP 3.0 20.8 + - - +
1053A ILE* 3.1 13.9 + - + +
1055A LEU* 1.3 75.2 - - - +
1057A CYS* 1.3 62.7 + - - +
1059A ASN* 3.9 4.1 - - - +
1060A ALA* 3.2 22.5 + - - +
1081A LEU* 3.6 22.4 - - + -
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Residues in contact with CYS1057 (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 ILE 3.1 9.7 + - - +
1054A ASP* 3.6 8.3 - - - +
1056A ILE* 1.3 79.3 - - - +
1058A SER* 1.4 66.0 + - - +
1060A ALA* 3.1 5.4 + - - +
1061A LEU* 3.1 36.8 + - - +
1078A ALA* 3.5 40.6 - - - +
1079A CYS* 3.9 3.1 - - - -
1081A LEU* 5.7 1.1 - - + -
1082A ARG* 3.8 38.1 - - + -
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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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1054A ASP 2.8 22.9 + - - -
1055A LEU* 3.4 18.4 + - - +
1057A CYS* 1.4 72.8 - - - +
1059A ASN* 1.3 65.7 + - - +
1061A LEU* 3.2 11.0 + - - +
1062A GLU* 2.9 26.0 + - - +
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Residues in contact with ASN1059 (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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1021A TYR* 3.8 16.2 + - - +
1025A ILE* 3.5 31.8 - - + +
1027A GLN* 2.8 26.5 + - - +
1028A PRO* 3.7 0.2 - - - +
1029A MET 3.7 17.4 + - - +
1055A LEU* 2.9 40.3 + - - +
1056A ILE* 3.9 4.0 - - - +
1058A SER* 1.3 78.4 + - - +
1060A ALA* 1.3 58.3 + - - +
1062A GLU* 4.5 2.9 - - - +
1063A TYR* 2.8 33.7 + - - +
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Residues in contact with ALA1060 (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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1009A PHE* 3.9 15.5 - - + -
1056A ILE 3.2 9.6 + - - +
1057A CYS 3.1 9.0 + - - +
1059A ASN* 1.3 79.7 - - - +
1061A LEU* 1.3 60.1 + - - +
1064A ASN* 3.0 43.5 + - - +
1074A ILE* 4.1 11.8 - - + +
1075A ARG* 4.3 2.2 - - - +
1078A ALA* 3.6 22.7 - - + -
5B ALY 4.3 7.0 - - + +
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Residues in contact with LEU1061 (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 CYS* 3.1 27.4 + - - +
1058A SER* 3.2 9.6 + - - +
1060A ALA* 1.3 77.3 - - - +
1062A GLU* 1.3 60.9 + - - +
1065A PRO* 3.6 25.1 - - - +
1075A ARG* 3.7 50.1 - - + +
1078A ALA* 4.3 3.6 - - + -
1079A CYS* 4.0 19.1 - - - -
1082A ARG* 5.0 4.3 - - - +
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Residues in contact with GLU1062 (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 VAL* 4.1 21.8 - - + +
1025A ILE* 3.3 21.9 - - + +
1026A LYS 5.6 0.3 + - - -
1058A SER 2.9 17.3 + - - +
1059A ASN* 3.8 5.4 - - - +
1061A LEU* 1.3 78.0 - - - +
1063A TYR* 1.3 62.8 + - - +
1065A PRO* 3.4 13.1 - - - +
3B ARG* 3.8 10.4 + - - -
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Residues in contact with TYR1063 (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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1018A VAL* 3.5 14.5 - - + +
1020A ASP* 2.7 39.8 + - - +
1021A TYR* 3.6 49.8 - + + -
1024A VAL* 3.8 24.9 - - + -
1025A ILE* 4.0 4.9 - - + +
1059A ASN 2.8 21.6 + - - +
1062A GLU* 1.3 73.9 - - - +
1064A ASN* 1.3 76.6 + - - +
1065A PRO* 3.3 2.0 - - - +
3B ARG* 3.1 18.1 + - + +
4B GLY* 2.9 45.8 + - - -
5B ALY 3.9 19.1 - - + +
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Residues in contact with ASN1064 (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 ALA* 3.0 23.1 + - - +
1061A LEU 3.8 3.4 - - - -
1063A TYR* 1.3 84.6 - - - +
1065A PRO* 1.3 59.4 - - - +
1066A ASP 3.4 2.2 - - - -
1071A ASP* 3.4 29.8 - - + +
1074A ILE* 3.8 18.5 - - + +
1075A ARG* 2.8 27.0 + - + +
4B GLY* 3.6 2.5 - - - -
5B ALY 2.9 65.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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