Contacts of the helix formed by residues 978 - 995 (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 GLN 978 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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973A ALA 3.7 0.2 + - - -
974A CYS* 3.2 22.4 + - - +
975A ASP* 4.5 7.2 + - - +
976A VAL* 3.6 8.0 - - - +
977A ASP* 1.3 70.1 - - - +
979A VAL* 1.3 70.2 + - + +
980A THR 3.0 0.2 - - - -
981A ARG* 2.8 59.3 + - - +
982A GLN* 2.9 7.6 + - - +
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Residues in contact with VAL 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A ASP 3.1 0.8 + - - -
978A GLN* 1.3 80.1 - - + +
980A THR* 1.3 66.4 + - - +
982A GLN* 3.0 22.9 - - + +
983A LEU* 3.1 8.9 + - + +
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Residues in contact with THR 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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927A LYS* 5.3 4.4 - - + +
928A VAL* 6.0 3.2 - - - +
931A CYS* 3.8 13.2 - - - -
932A GLU* 4.8 4.6 + - - +
977A ASP* 2.9 34.4 + - - +
979A VAL* 1.3 81.1 - - - +
981A ARG* 1.3 61.4 + - - +
982A GLN 2.9 1.7 + - - -
983A LEU* 3.0 4.6 + - - +
984A TYR* 2.7 52.3 + - + -
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Residues in contact with ARG 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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970A LEU* 4.0 8.9 + - + +
973A ALA* 3.6 15.0 - - + -
974A CYS* 3.0 51.0 + - - +
977A ASP* 2.9 25.1 - - + +
978A GLN* 2.8 49.4 + - - +
980A THR* 1.3 72.4 - - - +
982A GLN* 1.3 80.1 + - - +
984A TYR* 3.6 11.0 - - - +
985A GLU* 2.8 20.4 + - - +
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Residues in contact with GLN 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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978A GLN 2.9 10.2 + - - +
979A VAL* 3.0 19.7 - - + +
980A THR 2.9 0.4 + - - -
981A ARG* 1.3 94.0 + - + +
983A LEU* 1.3 54.9 + - + +
985A GLU* 2.8 17.7 + - - +
986A PRO* 2.6 46.0 - - - +
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Residues in contact with LEU 983 (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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935A HIS* 5.0 8.7 - - + -
979A VAL* 3.1 5.6 + - + +
980A THR* 3.0 7.8 + - - +
982A GLN* 1.3 83.3 - - + +
984A TYR* 1.3 64.3 + - + +
985A GLU 3.3 0.2 + - - -
986A PRO* 3.3 13.7 - - + +
987A LEU* 3.1 59.9 + - + +
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Residues in contact with TYR 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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931A CYS* 2.6 34.6 - - + -
932A GLU* 2.7 33.5 + - - -
935A HIS* 3.2 40.2 - + + -
966A PHE* 4.2 9.3 - + + -
969A LEU* 3.9 29.8 - - + -
970A LEU* 4.9 5.2 - - + -
977A ASP* 4.1 2.0 - - - -
980A THR* 2.7 55.6 + - + -
981A ARG* 3.6 10.8 - - - +
982A GLN 3.1 0.2 + - - -
983A LEU* 1.3 73.5 - - + +
985A GLU* 1.3 69.6 + - - +
987A LEU* 3.4 6.4 - - - +
988A VAL* 3.1 25.2 + - - +
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Residues in contact with GLU 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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591A GLN* 4.7 9.2 + - - -
970A LEU* 4.3 19.5 - - + +
981A ARG 2.8 10.8 + - - +
982A GLN* 2.8 28.9 + - - +
984A TYR* 1.3 69.0 - - - +
986A PRO* 1.4 77.7 - - + +
988A VAL* 2.8 21.6 + - - +
989A MSE 3.0 29.6 + - + +
1026A ARG* 5.8 1.4 + - - -
1031A ARG* 3.2 27.9 + - - +
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Residues in contact with PRO 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 GLN* 2.6 39.3 - - - +
983A LEU* 3.3 20.9 - - + +
985A GLU* 1.4 90.0 - - + +
987A LEU* 1.3 58.2 + - + +
989A MSE 3.4 11.4 - - + -
990A GLN* 2.7 48.0 + - + +
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Residues in contact with LEU 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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935A HIS* 3.0 42.0 - - + +
938A VAL* 6.4 0.7 - - + -
939A MSE 4.2 22.9 - - + -
966A PHE* 4.4 4.0 - - + -
983A LEU* 3.1 41.0 + - + +
984A TYR* 3.4 6.7 - - - +
985A GLU 2.9 0.8 + - - -
986A PRO* 1.3 78.7 - - + +
988A VAL* 1.3 62.5 + - - +
990A GLN* 3.3 7.9 + - + +
991A LEU* 3.0 37.3 + - + +
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Residues in contact with VAL 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A LYS* 5.6 1.8 - - - -
966A PHE* 3.4 55.2 - - + +
967A PRO* 4.6 7.4 - - + -
970A LEU* 4.3 8.5 - - + -
984A TYR 3.1 17.6 + - - +
985A GLU* 2.8 14.3 + - - +
987A LEU* 1.3 72.6 - - - +
989A MSE 1.3 59.1 + - - +
991A LEU* 3.1 5.7 + - - +
992A ILE* 2.9 35.6 + - + +
1031A ARG* 3.2 36.8 - - - +
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Residues in contact with MSE 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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591A GLN* 5.0 5.2 - - - +
985A GLU* 3.0 24.8 + - + +
986A PRO* 2.9 17.0 + - + +
988A VAL* 1.3 76.0 - - - +
990A GLN* 1.3 73.0 + - - +
992A ILE* 3.0 12.3 - - - +
993A HIS* 2.9 23.0 + - - +
1030A GLY* 3.1 31.0 - - - +
1031A ARG* 3.2 35.9 - - - +
1034A ARG* 3.7 44.0 - - + +
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Residues in contact with GLN 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A PRO* 2.7 45.0 + - + +
987A LEU* 3.7 10.1 - - + +
989A MSE 1.3 78.5 - - - +
991A LEU* 1.3 65.3 + - + +
993A HIS* 2.9 42.4 + - + +
994A TRP* 3.0 18.6 + - - +
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Residues in contact with LEU 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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938A VAL* 4.1 11.9 - - + -
939A MSE 4.7 6.7 - - + -
942A LEU* 3.4 35.0 - - + -
959A TYR* 3.2 28.2 + - + +
963A LYS* 4.3 8.3 - - - -
966A PHE* 3.4 33.9 - - + -
987A LEU* 3.0 20.7 + - + +
988A VAL* 3.1 10.0 + - - +
990A GLN* 1.3 85.3 - - + +
992A ILE* 1.3 56.7 + - - +
994A TRP* 4.0 9.7 + - + +
995A PHE* 3.3 12.8 - - - -
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Residues in contact with ILE 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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963A LYS* 4.4 4.0 - - - +
967A PRO* 6.2 1.1 - - + -
988A VAL* 2.9 18.5 + - + +
989A MSE 3.0 24.8 + - + +
991A LEU* 1.3 77.2 - - - +
993A HIS* 1.3 61.2 + - + +
994A TRP 3.3 0.4 - - - -
995A PHE* 4.2 10.1 - - - -
996A THR* 3.2 20.6 - - - +
1006A THR* 3.4 33.9 - - + +
1031A ARG* 3.2 40.4 - - + +
1034A ARG* 3.9 9.9 - - + +
1035A GLU* 3.3 33.3 - - + +
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Residues in contact with HIS 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 MSE 2.9 10.0 + - - +
990A GLN* 2.9 50.5 + - - +
992A ILE* 1.3 82.3 - - + +
994A TRP* 1.3 93.0 + + + +
995A PHE 3.5 0.2 - - - -
996A THR* 2.7 23.2 + - - -
997A ASN* 3.0 7.3 + - + +
1034A ARG* 5.2 2.0 - - + +
1038A LYS* 3.2 48.0 - - + +
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Residues in contact with TRP 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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942A LEU* 5.2 17.5 + - + +
959A TYR* 6.2 0.2 - - - -
990A GLN 3.0 13.9 + - - +
991A LEU* 4.2 10.1 - - + +
992A ILE 3.3 1.0 - - - -
993A HIS* 1.3 102.6 + + + +
995A PHE* 1.3 62.7 + + + +
997A ASN* 2.8 39.8 + - + -
998A ASN* 3.1 36.5 + - + +
1002A GLU* 4.6 14.2 + - - -
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Residues in contact with PHE 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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959A TYR* 3.3 25.4 - + - -
963A LYS* 3.8 0.9 - - - -
991A LEU 3.3 16.2 - - - -
992A ILE 4.2 8.5 - - - -
993A HIS 3.5 0.2 - - - -
994A TRP* 1.3 81.2 - + + +
996A THR* 1.3 59.3 + - + +
998A ASN* 4.1 8.3 - - - -
999A LYS 2.5 28.7 - - - +
1002A GLU* 3.0 54.1 - - + +
1003A SER* 3.2 24.3 - - - -
1006A THR* 3.0 41.3 - - + -
1035A GLU* 3.8 18.4 - - - -
1054A VAL* 5.8 1.2 - - - +
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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
------------------------------------------------------------
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