Contacts of the helix formed by residues 1060 - 1079 (chain A) in PDB entry 3T8M
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 ASN1060 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021A ARG* 4.6 2.7 - - - -
1058A GLY 4.3 0.2 + - - -
1059A LYS* 1.3 77.6 - - - +
1061A GLU* 1.3 65.0 + - - +
1062A GLU* 3.2 38.4 + - - +
1063A ASP* 2.8 36.8 + - - +
1064A ALA* 3.3 10.6 + - - +
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Residues in contact with GLU1061 (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 LEU* 4.0 29.7 - - + +
1021A ARG* 4.5 8.3 - - - +
1022A HIS* 3.5 27.2 + - + +
1060A ASN* 1.3 75.6 - - - +
1062A GLU* 1.3 70.9 + - + +
1064A ALA* 3.3 9.0 + - - +
1065A LYS* 3.1 24.1 + - - +
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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
----------------------------------------------------------
1060A ASN* 3.2 19.9 + - - +
1061A GLU* 1.3 84.5 - - + +
1063A ASP* 1.3 66.4 + - - +
1065A LYS* 3.5 23.5 + - - +
1066A LYS* 3.1 22.2 + - - +
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Residues in contact with ASP1063 (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* 5.5 1.3 - - - -
1059A LYS* 4.2 23.5 + - + +
1060A ASN* 2.8 30.8 + - - +
1062A GLU* 1.3 76.6 - - - +
1064A ALA* 1.3 58.5 + - - +
1066A LYS* 3.3 14.2 - - + +
1067A TYR* 2.9 29.3 + - - +
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Residues in contact with ALA1064 (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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1017A TYR* 3.7 10.2 - - + -
1018A LEU* 3.7 13.9 - - + -
1021A ARG* 3.7 30.5 - - - +
1056A THR* 3.8 15.4 - - + +
1059A LYS* 5.0 0.2 - - - +
1060A ASN 3.3 10.2 + - - +
1061A GLU 3.3 9.8 + - - +
1062A GLU 3.2 0.2 - - - -
1063A ASP* 1.3 74.6 - - - +
1065A LYS* 1.3 67.1 + - - +
1067A TYR* 3.0 14.1 + - - +
1068A PHE* 3.0 10.7 + - - +
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Residues in contact with LYS1065 (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 VAL* 4.0 37.4 - - + +
1017A TYR* 5.2 1.8 - - - -
1018A LEU* 4.5 5.5 - - + +
1061A GLU 3.1 12.8 + - - +
1062A GLU* 3.9 22.4 + - - +
1064A ALA* 1.3 78.9 - - - +
1066A LYS* 1.3 64.4 + - - +
1068A PHE* 3.3 4.3 + - - +
1069A LEU* 2.9 50.6 + - + +
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Residues in contact with LYS1066 (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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1062A GLU 3.1 12.2 + - - +
1063A ASP* 3.3 15.7 - - - +
1064A ALA 3.1 0.4 - - - -
1065A LYS* 1.3 81.0 - - - +
1067A TYR* 1.3 65.1 + - - +
1069A LEU* 3.3 8.5 + - - +
1070A ASP* 3.0 55.8 + - - +
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Residues in contact with TYR1067 (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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940A PHE* 3.3 39.6 - + - -
1017A TYR* 3.9 15.9 - + - -
1053A ASP* 4.1 17.6 + - - +
1054A ALA* 4.0 8.0 - - - -
1056A THR* 4.6 12.6 - - - +
1063A ASP 2.9 15.2 + - - +
1064A ALA* 3.0 10.7 + - - +
1066A LYS* 1.3 80.2 - - - +
1068A PHE* 1.3 65.7 + - - +
1070A ASP* 3.4 6.7 + - + +
1071A GLN* 3.1 45.8 + - + +
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Residues in contact with PHE1068 (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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936A CYS* 4.5 1.3 - - + -
937A VAL* 3.6 40.6 - - + -
940A PHE* 4.4 20.2 - + + -
985A PHE* 4.4 18.4 - + - -
1013A CYS* 3.5 33.2 - - + -
1014A VAL* 5.1 7.0 - - + -
1017A TYR* 4.0 35.7 - + + -
1064A ALA 3.0 11.0 + - - +
1065A LYS* 3.8 7.9 - - - +
1067A TYR* 1.3 77.1 - - - +
1069A LEU* 1.3 65.2 + - + +
1071A GLN* 3.0 11.8 + - + +
1072A ILE* 3.0 40.5 + - + +
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Residues in contact with LEU1069 (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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1010A GLN* 4.3 30.2 + - + +
1014A VAL* 4.1 17.3 - - + -
1065A LYS* 2.9 47.5 + - + +
1066A LYS* 3.3 6.7 + - - +
1068A PHE* 1.3 75.8 - - - +
1070A ASP* 1.3 65.1 + - - +
1072A ILE* 3.2 20.9 + - + +
1073A GLU* 3.0 27.0 + - + +
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Residues in contact with ASP1070 (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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1066A LYS* 3.0 45.9 + - - +
1067A TYR* 3.6 10.0 - - + +
1069A LEU* 1.3 77.4 - - - +
1071A GLN* 1.3 60.5 + - - +
1073A GLU* 2.9 15.5 + - - +
1074A VAL* 2.8 35.8 + - + +
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Residues in contact with GLN1071 (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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940A PHE* 4.2 24.1 - - + -
984A PRO* 3.4 34.3 - - - +
985A PHE* 3.9 20.5 - - + -
1067A TYR* 3.1 49.6 + - + +
1068A PHE* 3.0 17.4 + - + +
1070A ASP* 1.3 79.6 - - - +
1072A ILE* 1.3 58.1 + - - +
1074A VAL* 3.3 17.0 + - - +
1075A CYS* 3.4 9.4 + - - -
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Residues in contact with ILE1072 (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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985A PHE* 4.1 17.3 - - + -
987A LEU* 3.9 17.5 - - + +
1006A PHE* 4.5 20.9 - - + -
1009A PHE* 4.1 18.8 - - + -
1010A GLN* 4.3 11.7 - - + +
1013A CYS* 4.5 5.6 - - + -
1068A PHE* 3.0 41.5 + - + +
1069A LEU* 3.3 24.7 - - + +
1070A ASP 3.2 0.2 - - - -
1071A GLN* 1.3 75.1 - - - +
1073A GLU* 1.3 70.1 + - - +
1075A CYS* 3.5 6.2 + - - +
1076A ARG* 3.2 22.6 + - + +
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Residues in contact with GLU1073 (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 LYS* 3.1 28.6 + - - -
1006A PHE* 5.0 1.2 - - - -
1010A GLN* 4.6 10.4 + - - -
1069A LEU* 3.0 17.7 + - + +
1070A ASP* 2.9 19.8 + - - +
1072A ILE* 1.3 83.0 - - - +
1074A VAL* 1.3 64.7 + - + +
1076A ARG* 3.0 22.7 + - - +
1077A ASP* 2.9 33.4 + - - +
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Residues in contact with VAL1074 (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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982A ARG 4.8 4.3 - - - +
983A VAL* 5.0 0.7 - - + -
984A PRO* 4.2 17.0 - - + -
1070A ASP* 2.8 24.3 + - + +
1071A GLN* 3.6 17.7 - - - +
1073A GLU* 1.3 75.7 - - + +
1075A CYS* 1.3 61.2 + - - +
1077A ASP* 3.4 8.0 + - - +
1078A LYS* 3.0 55.0 + - + +
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Residues in contact with CYS1075 (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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983A VAL* 3.5 19.3 - - + -
984A PRO* 3.8 8.5 - - - -
985A PHE* 3.1 55.4 - - - -
987A LEU* 3.8 28.4 - - + +
989A PRO* 5.7 0.3 - - - +
1071A GLN 3.4 2.3 + - - -
1072A ILE 3.7 8.1 - - - +
1073A GLU 3.3 0.6 - - - -
1074A VAL* 1.3 78.2 - - - +
1076A ARG* 1.3 56.9 + - - +
1078A LYS* 3.5 1.6 + - - +
1079A GLY* 2.9 29.8 + - - +
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Residues in contact with ARG1076 (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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987A LEU* 5.0 3.4 - - + -
989A PRO* 5.9 0.3 - - - +
992A LEU* 3.8 36.2 - - + +
997A THR* 3.7 12.3 - - - +
1000A LYS* 3.3 66.5 + - + +
1001A LYS 3.3 26.6 + - - +
1006A PHE* 4.4 20.7 - - - -
1072A ILE* 3.2 22.0 - - + +
1073A GLU* 3.0 23.6 + - - +
1075A CYS* 1.3 77.2 - - - +
1077A ASP* 1.3 64.8 + - - +
1079A GLY* 3.1 14.0 + - - -
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Residues in contact with ASP1077 (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 LYS* 2.9 32.6 + - - +
1073A GLU* 2.9 29.0 + - - +
1074A VAL* 3.9 7.7 - - - +
1076A ARG* 1.3 75.0 - - - +
1078A LYS* 1.3 67.9 + - + +
1079A GLY* 3.6 0.3 + - - -
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Residues in contact with LYS1078 (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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981A GLU* 3.6 37.1 + - - +
982A ARG 3.6 22.5 + - - +
983A VAL* 4.7 8.1 - - + -
1074A VAL* 3.0 44.3 + - + +
1075A CYS* 3.9 6.5 - - - +
1077A ASP* 1.3 82.5 - - + +
1079A GLY* 1.3 66.7 + - - +
1080A TRP 3.1 0.2 + - - -
1081A THR* 2.7 34.9 + - - -
1082A VAL* 5.0 6.7 - - + +
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Residues in contact with GLY1079 (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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987A LEU 5.2 0.3 - - - +
988A THR* 4.2 10.2 - - - +
989A PRO* 4.1 25.2 - - - +
1075A CYS 2.9 16.7 + - - +
1076A ARG* 3.1 13.4 + - - -
1077A ASP 3.3 0.4 - - - -
1078A LYS* 1.3 76.3 - - - +
1080A TRP* 1.3 63.2 + - - -
1082A VAL 5.4 0.5 + - - -
1083A GLN* 5.2 1.0 - - - +
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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
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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