Contacts of the helix formed by residues 979 - 1002 (chain A) in PDB entry 4TU4
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 SER 979 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980A MET* 1.3 63.8 + - - +
981A GLN* 3.4 17.7 + - - +
982A GLU* 3.2 46.2 + - - +
983A GLU* 3.1 32.2 + - - +
1108A ARG* 4.7 4.2 - - - +
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Residues in contact with MET 980 (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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979A SER* 1.3 73.8 - - - +
981A GLN* 1.3 66.0 + - - +
983A GLU* 3.4 20.4 + - - +
984A ASP* 2.9 60.6 + - - +
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Residues in contact with GLN 981 (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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979A SER* 3.2 16.9 + - - +
980A MET* 1.3 81.4 + - - +
982A GLU* 1.3 64.7 + - + +
984A ASP* 3.2 13.5 + - - +
985A THR* 3.0 25.1 + - - -
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Residues in contact with GLU 982 (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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979A SER* 3.2 28.1 + - - +
980A MET 3.4 0.2 - - - -
981A GLN* 1.3 73.8 - - + +
983A GLU* 1.3 65.3 + - - +
985A THR* 3.1 5.2 + - - -
986A PHE* 3.1 28.3 + - - -
1104A ILE* 3.7 40.1 - - + +
1107A SER* 4.8 7.4 + - - -
1108A ARG* 3.1 27.8 + - - +
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Residues in contact with GLU 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A SER 3.1 20.2 + - - +
980A MET* 3.7 26.6 - - - +
981A GLN 3.3 0.2 - - - -
982A GLU* 1.3 76.0 - - + +
984A ASP* 1.3 56.8 + - - +
986A PHE* 3.4 9.6 + - + +
987A ARG* 2.9 30.0 + - - +
990A ARG* 5.0 2.1 + - - -
1108A ARG* 5.6 7.4 - - - +
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Residues in contact with ASP 984 (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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980A MET* 2.9 48.0 + - - +
981A GLN* 3.2 15.8 + - - +
983A GLU* 1.3 76.5 - - - +
985A THR* 1.3 56.6 + - - +
987A ARG* 3.4 8.8 + - - +
988A GLU* 3.0 29.0 + - - +
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Residues in contact with THR 985 (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 GLN 3.0 14.7 + - - -
982A GLU 3.1 8.9 + - - -
984A ASP* 1.3 72.7 - - - +
986A PHE* 1.3 66.6 + - + +
988A GLU* 3.2 9.8 + - - +
989A LEU* 3.0 18.9 + - - +
1097A PHE* 3.5 14.5 - - + -
1100A LEU* 3.8 26.6 - - + +
1101A CYS* 3.9 21.5 - - - -
1104A ILE* 3.9 22.9 - - + +
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Residues in contact with PHE 986 (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 GLU 3.1 21.1 + - - +
983A GLU* 3.4 7.4 + - + +
985A THR* 1.3 78.4 - - + +
987A ARG* 1.3 57.7 + - - +
989A LEU* 3.3 6.4 + - + +
990A ARG* 2.9 46.0 + - - +
1043A TYR 5.3 1.7 - - - +
1044A LEU* 3.3 62.4 - - + -
1101A CYS* 4.0 18.6 - - - -
1104A ILE* 3.4 39.7 - - + -
1105A GLN 4.2 5.8 - - - -
1108A ARG* 3.8 24.0 - - - -
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Residues in contact with ARG 987 (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 GLU 2.9 17.8 + - - +
984A ASP* 3.7 10.8 - - - +
985A THR 3.2 0.2 - - - -
986A PHE* 1.3 75.5 - - - +
988A GLU* 1.3 63.4 + - - +
990A ARG* 3.2 19.0 + - - +
991A ILE* 3.0 43.4 + - + +
1201A SO4 2.8 40.0 + - - +
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Residues in contact with GLU 988 (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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984A ASP 3.0 15.1 + - - +
985A THR* 3.2 9.7 + - - +
987A ARG* 1.3 77.8 - - - +
989A LEU* 1.3 61.4 + - - +
991A ILE* 3.3 11.6 + - + +
992A PHE* 3.0 22.9 + - - +
1097A PHE* 3.8 21.1 - - + -
1202A GOL 2.8 33.1 + - - +
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Residues in contact with LEU 989 (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 THR 3.0 13.0 + - - +
986A PHE* 3.3 11.4 + - + +
988A GLU* 1.3 75.3 - - - +
990A ARG* 1.3 57.6 + - - +
992A PHE* 3.3 8.3 + - + +
993A LEU* 2.8 48.9 + - + +
1043A TYR 3.7 13.2 - - - +
1044A LEU* 3.3 37.2 - - - +
1045A THR* 3.5 9.4 - - - +
1046A VAL* 3.5 32.1 - - + +
1097A PHE* 3.7 21.9 - - + -
1101A CYS* 4.1 7.2 - - - -
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Residues in contact with ARG 990 (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 GLU 5.0 2.0 + - - -
986A PHE* 2.9 37.6 + - + +
987A ARG* 3.2 27.9 + - - +
989A LEU* 1.3 76.1 - - + +
991A ILE* 1.3 52.2 + - - +
993A LEU* 3.2 3.6 + - + +
994A ARG* 2.8 43.9 + - - +
1038A ILE* 3.2 40.7 - - + +
1041A HIS* 3.3 47.0 + - - +
1043A TYR 5.0 11.0 - - - +
1044A LEU* 6.3 0.8 - - - +
1201A SO4 2.8 39.4 + - - +
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Residues in contact with ILE 991 (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 ARG* 3.0 51.7 + - + +
988A GLU* 3.7 11.7 - - + +
989A LEU 3.3 0.2 - - - -
990A ARG* 1.3 73.9 - - - +
992A PHE* 1.3 63.6 + - - +
994A ARG* 3.4 22.0 + - - +
995A ASN* 3.1 24.2 + - + +
1201A SO4 4.6 4.5 - - - +
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Residues in contact with PHE 992 (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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988A GLU 3.0 13.6 + - - +
989A LEU* 3.5 13.5 - - + +
991A ILE* 1.3 78.4 - - - +
993A LEU* 1.3 73.0 + - + +
995A ASN* 3.2 10.7 + - + +
996A VAL* 3.0 54.6 + - + +
1046A VAL* 4.7 1.8 - - + -
1088A ILE* 5.1 0.4 - - + -
1089A ILE* 4.1 21.1 - - + -
1092A GLU* 4.2 31.2 - - + -
1093A LEU* 4.1 35.4 - - + -
1202A GOL 3.9 26.0 - - - +
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Residues in contact with LEU 993 (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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989A LEU* 2.8 43.5 + - + +
990A ARG* 3.8 4.9 - - + +
992A PHE* 1.3 92.6 - - + +
994A ARG* 1.3 62.5 + - - +
996A VAL* 3.4 3.5 + - + +
997A THR* 2.7 33.4 + - - -
1038A ILE* 3.7 16.2 - - + -
1043A TYR* 3.9 24.0 - - + +
1045A THR 4.7 0.9 - - - +
1046A VAL* 4.4 7.2 - - + -
1049A TYR* 3.6 51.9 + - + -
1089A ILE* 5.3 0.4 - - + -
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Residues in contact with ARG 994 (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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990A ARG* 2.8 40.7 + - - +
991A ILE* 3.7 18.0 - - - +
993A LEU* 1.3 74.9 - - - +
995A ASN* 1.3 57.3 + - - +
997A THR* 3.8 0.9 - - - -
998A HIS* 2.9 31.9 + - - +
1035A ILE* 4.3 16.8 - - + +
1038A ILE* 3.8 23.5 - - + +
1039A ASP* 2.8 34.4 + - - +
1041A HIS* 5.9 0.2 - - - -
1201A SO4 2.8 43.1 + - - -
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Residues in contact with ASN 995 (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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991A ILE* 3.1 15.5 + - + +
992A PHE* 3.6 12.6 - - + +
994A ARG* 1.3 74.2 - - - +
996A VAL* 1.3 66.7 + - - +
998A HIS* 3.5 9.2 + - - +
999A ARG* 2.9 59.6 + - - +
1092A GLU* 4.7 0.2 - - - +
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Residues in contact with VAL 996 (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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992A PHE* 3.0 47.7 + - + +
993A LEU* 3.8 6.1 - - + +
995A ASN* 1.3 77.4 - - - +
997A THR* 1.3 64.9 + - - +
999A ARG* 3.2 13.8 + - - +
1000A LEU* 3.1 31.8 + - + +
1049A TYR* 3.7 21.1 - - + +
1085A ALA* 4.9 5.2 - - - -
1088A ILE* 3.9 31.4 - - + +
1089A ILE* 4.9 6.5 - - + -
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Residues in contact with THR 997 (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 2.7 23.3 + - - -
994A ARG 3.8 0.2 - - - -
996A VAL* 1.3 76.8 - - - +
998A HIS* 1.3 59.3 + - - +
1000A LEU* 3.2 7.3 + - - +
1001A ALA* 2.8 28.5 + - + +
1031A LEU* 3.9 28.4 - - + +
1034A VAL* 4.1 10.5 - - + -
1035A ILE* 3.6 32.3 - - + -
1038A ILE* 3.8 2.9 - - - +
1049A TYR* 2.7 27.5 + - - +
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Residues in contact with HIS 998 (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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994A ARG 2.9 18.6 + - - +
995A ASN* 3.8 9.9 + - - +
997A THR* 1.3 76.0 - - - +
999A ARG* 1.3 68.3 + - - +
1001A ALA* 3.2 7.9 + - + -
1002A ILE* 3.0 57.4 + - + +
1035A ILE* 4.8 4.9 - - + +
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Residues in contact with ARG 999 (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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995A ASN* 2.9 45.6 + - - +
996A VAL* 3.2 10.8 + - - +
998A HIS* 1.3 83.6 - - - +
1000A LEU* 1.3 61.1 - - - +
1002A ILE* 3.3 28.2 + - + +
1003A ASP* 3.5 9.2 + - - +
1088A ILE* 3.9 34.2 - - + +
1092A GLU* 2.5 44.6 + - - -
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Residues in contact with LEU1000 (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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996A VAL* 3.1 20.2 + - + +
997A THR* 3.2 8.0 + - - +
999A ARG* 1.3 76.3 - - - +
1001A ALA* 1.3 62.4 + - - +
1003A ASP* 3.4 7.1 + - - +
1006A PHE* 3.3 32.2 - - + +
1031A LEU* 4.1 8.1 - - + -
1049A TYR* 4.0 15.7 - - - +
1053A ILE* 4.5 7.4 - - + -
1081A LEU* 4.0 26.5 - - + -
1084A THR* 3.5 37.5 - - + -
1085A ALA* 3.9 26.5 - - + +
1088A ILE* 4.4 6.5 - - + -
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Residues in contact with ALA1001 (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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997A THR* 2.8 17.8 + - + +
998A HIS* 3.2 11.2 + - + +
1000A LEU* 1.3 77.9 - - - +
1002A ILE* 1.3 60.7 + - + +
1003A ASP 3.3 4.0 + - - +
1007A ARG* 5.5 0.3 - - - -
1010A THR* 3.6 27.8 - - + +
1031A LEU* 3.9 17.9 - - + +
1035A ILE* 6.6 0.2 - - + -
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Residues in contact with ILE1002 (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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998A HIS* 3.0 48.3 + - + +
999A ARG* 3.3 23.1 - - + +
1001A ALA* 1.3 77.6 - - + +
1003A ASP* 1.3 62.8 + - - +
1004A LYS* 3.5 9.2 + - - +
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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