Contacts of the helix formed by residues 971 - 986 (chain A) in PDB entry 1OY6
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 ARG 971 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A ARG* 3.4 10.5 - - - +
944A LEU* 2.7 38.2 + - + -
945A ILE* 3.3 43.7 - - - +
948A PHE* 3.5 25.9 - - + -
967A ALA* 2.9 35.0 + - - +
968A VAL* 3.0 35.5 + - - +
969A ARG 3.8 0.2 - - - -
970A MET* 1.3 75.5 - - - +
972A LEU* 1.3 70.1 + - - +
973A ARG 3.1 3.3 - - - +
974A PRO* 3.0 19.3 - - + +
975A ILE* 3.4 29.9 - - + +
1025A PHE* 3.6 2.0 - - - -
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Residues in contact with LEU 972 (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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519A MET* 4.2 21.1 - - - -
523A SER* 4.2 18.2 - - - +
527A TYR* 3.9 27.8 - - + -
968A VAL* 3.1 28.5 + - + +
971A ARG* 1.3 76.7 - - - +
973A ARG* 1.3 70.2 + - - +
975A ILE* 3.4 9.4 + - - +
976A LEU* 3.4 32.4 + - + +
1019A ILE* 3.4 30.3 - - + -
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Residues in contact with ARG 973 (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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358A PHE* 3.5 55.3 + - + +
359A LEU* 4.2 13.4 - - - +
414A GLU* 3.3 29.4 + - + +
417A GLU* 3.7 30.9 + - - +
418A ARG* 4.3 14.5 - - - +
516A PHE* 5.5 4.4 - - - -
519A MET* 4.7 20.1 - - + +
520A PHE* 5.8 8.9 - - - -
971A ARG 3.1 1.8 - - - +
972A LEU* 1.3 88.0 - - - +
974A PRO* 1.3 59.8 - - + +
976A LEU* 3.3 2.3 + - - +
977A MET* 2.9 26.2 + - + +
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Residues in contact with PRO 974 (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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410A ILE* 4.1 10.4 - - + +
411A VAL* 5.3 6.3 - - + -
414A GLU* 3.1 39.9 - - + +
418A ARG* 3.7 4.9 - - - +
944A LEU* 5.6 8.3 - - + -
948A PHE* 5.7 2.7 - - + -
971A ARG* 3.0 34.5 - - + +
973A ARG* 1.3 91.5 - - + +
975A ILE* 1.3 60.8 + - + +
977A MET* 3.6 10.7 - - + +
978A THR* 3.2 26.2 + - - -
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Residues in contact with ILE 975 (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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941A ASN* 3.6 46.1 - - + +
944A LEU* 3.7 28.9 - - + -
945A ILE* 5.0 0.9 - - + -
971A ARG* 3.4 33.4 - - - +
972A LEU 3.4 6.9 + - - +
973A ARG 3.2 1.0 - - - -
974A PRO* 1.3 77.1 - - - +
976A LEU* 1.3 70.4 + - + +
978A THR* 3.8 2.8 + - - -
979A SER* 3.2 26.0 + - - -
1015A THR* 4.2 7.6 - - + -
1019A ILE* 3.9 25.6 - - + -
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Residues in contact with LEU 976 (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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358A PHE* 4.4 11.3 - - + -
972A LEU* 3.4 45.5 + - + +
973A ARG 3.3 4.2 + - - +
975A ILE* 1.3 88.3 - - + +
977A MET* 1.3 59.9 + - - +
978A THR 3.4 0.7 - - - -
979A SER* 4.3 6.7 - - - -
980A LEU* 3.1 32.7 + - - +
1015A THR* 5.3 4.9 - - - -
1016A VAL* 6.3 3.8 - - + -
1019A ILE* 4.0 14.4 - - + -
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Residues in contact with MET 977 (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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354A VAL* 3.4 8.9 - - - +
355A MET* 3.6 21.5 - - + +
358A PHE* 3.5 39.3 - - + -
359A LEU* 3.4 40.4 - - + -
410A ILE* 3.4 28.6 - - + +
414A GLU* 4.0 18.8 - - + -
973A ARG* 2.9 18.8 + - - +
974A PRO* 3.6 7.0 - - + +
975A ILE 3.3 0.4 - - - -
976A LEU* 1.3 77.7 - - - +
978A THR* 1.3 59.7 + - - +
981A ALA* 3.2 24.6 + - - +
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Residues in contact with THR 978 (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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403A GLY 4.7 1.6 - - - +
407A ASP* 2.9 51.5 + - + +
410A ILE* 3.3 25.0 - - + +
411A VAL* 5.5 0.2 - - - +
937A LEU* 4.5 11.9 - - + -
941A ASN* 5.6 5.4 - - - +
974A PRO 3.2 14.5 + - - -
975A ILE* 4.0 3.6 - - - -
977A MET* 1.3 77.8 - - - +
979A SER* 1.3 58.4 + - - +
981A ALA* 2.9 6.7 + - - +
982A PHE* 2.6 39.9 + - + +
1011A MET* 5.3 0.9 - - + -
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Residues in contact with SER 979 (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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941A ASN* 5.8 0.2 - - - -
975A ILE 3.2 16.1 + - - -
976A LEU* 4.3 6.3 - - - -
978A THR* 1.3 80.1 - - - +
980A LEU* 1.3 59.8 + - - +
982A PHE* 3.8 0.7 - - - -
983A ILE* 3.0 36.7 + - - +
1011A MET* 3.3 28.1 - - - +
1015A THR* 3.0 31.2 + - - -
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Residues in contact with LEU 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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354A VAL* 3.6 31.2 - - + -
357A LEU* 6.2 3.8 - - + -
358A PHE* 4.2 20.0 - - + -
976A LEU 3.1 19.2 + - - +
978A THR 3.1 0.4 - - - -
979A SER* 1.3 74.5 - - - +
981A ALA* 1.3 66.5 + - - +
982A PHE 3.2 0.9 + - - -
983A ILE* 4.3 1.7 - - - +
984A LEU* 3.2 41.2 + - + +
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Residues in contact with ALA 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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347A ALA 5.2 0.9 - - - +
351A VAL* 3.3 38.7 + - + +
354A VAL* 3.8 17.2 - - + +
355A MET* 4.8 0.7 - - + -
406A VAL* 6.3 0.2 - - + -
410A ILE* 4.5 5.4 - - + -
977A MET 3.2 15.9 + - - +
978A THR* 2.9 12.7 + - - +
980A LEU* 1.3 79.9 - - - +
982A PHE* 1.3 57.8 + - - +
984A LEU* 3.8 2.6 + - - +
985A GLY* 3.5 16.1 + - - -
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Residues in contact with PHE 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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400A LEU* 4.3 11.9 - - + -
403A GLY* 3.3 48.7 - - - +
404A LEU 3.8 3.1 - - - -
933A THR* 4.4 4.0 - - + -
937A LEU* 3.2 33.9 - - + -
978A THR* 2.6 21.5 + - + +
979A SER* 4.0 9.0 - - - +
980A LEU 3.2 0.2 - - - -
981A ALA* 1.3 73.4 - - - +
983A ILE* 1.3 68.4 + - + +
984A LEU 3.3 0.3 + - - -
985A GLY* 3.3 3.6 + - - -
986A VAL* 3.2 41.8 + - + +
1007A VAL* 3.4 31.4 - - + -
1008A MET* 5.8 0.2 - - - -
1011A MET* 3.6 23.8 - - + -
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Residues in contact with ILE 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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979A SER* 3.0 34.1 + - - +
980A LEU* 4.5 2.0 - - - +
982A PHE* 1.3 82.2 - - + +
984A LEU* 1.3 59.9 + - + +
985A GLY 3.5 0.2 - - - -
986A VAL* 3.7 5.9 + - - +
987A MET* 3.3 17.2 + - - +
1008A MET* 3.3 43.9 - - + +
1011A MET* 3.7 29.4 - - + +
1012A VAL* 4.1 22.0 - - + +
1015A THR* 5.2 0.2 - - - +
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Residues in contact with LEU 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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350A LEU* 3.2 30.4 - - + +
354A VAL* 3.4 27.8 - - + -
980A LEU* 3.2 35.6 + - + +
981A ALA 4.1 3.8 - - - +
982A PHE 3.2 0.4 - - - -
983A ILE* 1.3 78.2 - - + +
985A GLY* 1.3 59.3 + - - +
986A VAL 3.2 1.6 - - - -
987A MET* 3.2 27.7 - - + +
988A PRO* 3.2 21.7 - - - +
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Residues in contact with GLY 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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343A THR* 3.7 13.3 - - - +
347A ALA* 3.4 41.5 - - - +
350A LEU* 4.6 1.2 - - - +
399A VAL* 5.2 1.9 - - - +
981A ALA 3.5 8.3 + - - -
982A PHE 3.3 7.1 + - - -
984A LEU* 1.3 77.0 - - - +
986A VAL* 1.3 61.2 + - - +
988A PRO* 3.5 9.7 - - - +
989A LEU* 4.7 0.9 - - - +
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Residues in contact with VAL 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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399A VAL 6.0 1.3 - - - +
400A LEU* 6.0 4.0 - - + +
403A GLY* 6.3 0.4 - - - -
982A PHE* 3.2 44.8 + - + +
983A ILE* 3.8 8.1 - - - +
984A LEU 3.2 0.8 - - - -
985A GLY* 1.3 76.7 - - - +
987A MET* 1.3 63.3 + - - +
988A PRO* 3.5 0.4 - - - -
989A LEU* 3.0 24.4 + - + +
990A VAL* 3.1 26.5 + - + +
1004A GLY* 3.6 23.6 - - - +
1007A VAL* 4.6 5.6 - - + -
1008A MET* 4.2 10.5 - - + +
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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