Contacts of the helix formed by residues 1016 - 1033 (chain X) in PDB entry 2OO8
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 THR1016 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961X ILE* 3.8 17.3 - - - +
1008X GLU* 4.6 2.8 + - - -
1014X VAL* 3.8 21.3 - - + +
1015X TYR* 1.3 79.3 - - - +
1017X THR* 1.3 63.5 + - - +
1018X ASN* 3.1 23.6 + - - +
1019X SER* 2.8 28.3 + - - -
1020X ASP* 3.0 9.7 + - - +
1079X PRO* 5.2 2.0 - - + +
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Residues in contact with THR1017 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956X SER* 3.8 34.5 + - - +
959X GLN* 5.7 2.1 - - - -
960X PHE 4.3 8.0 + - - -
961X ILE* 4.4 6.3 - - - +
1016X THR* 1.3 74.7 - - - +
1018X ASN* 1.3 61.0 + - - +
1020X ASP* 3.2 11.9 - - - +
1021X VAL* 2.9 30.5 + - + +
1084X SER* 6.0 3.1 - - - -
1085X PHE* 3.9 17.9 - - + +
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Residues in contact with ASN1018 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016X THR* 3.1 12.6 + - - +
1017X THR* 1.3 83.8 - - - +
1019X SER* 1.3 59.4 + - - +
1021X VAL* 3.3 6.3 + - - +
1022X TRP 3.2 13.3 + - - -
1079X PRO* 3.2 46.9 + - + +
1080X TYR* 3.9 7.1 + - - +
1082X ARG* 2.9 31.5 + - - +
1083X PRO 4.8 5.1 + - - -
1084X SER* 6.1 0.6 - - - +
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Residues in contact with SER1019 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006X ALA* 3.8 9.2 + - - +
1008X GLU* 3.7 12.8 - - - -
1009X SER* 3.6 21.6 + - - -
1014X VAL 4.2 2.2 - - - -
1015X TYR* 3.4 11.1 - - - +
1016X THR* 2.8 38.3 + - - -
1018X ASN* 1.3 72.6 - - - +
1020X ASP* 1.3 66.8 + - - +
1021X VAL 3.2 0.4 - - - -
1022X TRP* 3.2 4.3 + - - +
1023X SER* 3.1 25.2 + - - -
1082X ARG* 3.6 8.0 - - - +
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Residues in contact with ASP1020 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952X MET* 3.4 11.4 - - - +
960X PHE 4.4 1.4 - - - +
961X ILE* 3.5 11.1 - - - +
962X HIS* 2.8 30.6 + - - +
963X ARG* 3.0 28.3 + - - -
964X ASP 4.7 0.2 + - - -
965X LEU* 3.3 16.3 + - + +
1016X THR 3.0 13.9 + - - +
1017X THR* 3.2 15.7 - - - +
1019X SER* 1.3 79.2 + - - +
1021X VAL* 1.3 53.8 + - - -
1023X SER* 3.5 4.9 + - - -
1024X TYR* 2.9 23.6 + - - +
1085X PHE* 3.7 15.4 - - + -
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Residues in contact with VAL1021 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017X THR* 2.9 21.4 + - + +
1018X ASN* 3.5 12.1 - - - +
1019X SER 3.2 0.4 - - - -
1020X ASP* 1.3 72.2 - - - +
1022X TRP* 1.3 67.4 + - - +
1024X TYR* 3.1 4.3 + - - +
1025X GLY 2.9 18.7 + - - -
1074X CYS* 3.4 32.6 - - - +
1082X ARG* 4.0 9.0 - - + -
1083X PRO* 3.6 28.3 - - + +
1084X SER* 4.8 0.2 - - - -
1085X PHE* 3.6 34.1 - - + +
1088X ILE* 3.9 7.0 - - + -
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Residues in contact with TRP1022 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003X ARG 5.1 1.0 + - - -
1004X TRP 3.4 20.0 + - - -
1005X MET 3.4 17.6 + - - -
1006X ALA* 3.5 20.4 - - + -
1007X ILE* 3.6 30.1 - - + -
1018X ASN 3.2 9.7 + - - +
1019X SER 3.3 11.2 - - - +
1021X VAL* 1.3 75.1 - - - +
1023X SER* 1.3 56.5 + - - +
1025X GLY 2.9 17.5 + - - -
1026X VAL* 3.1 19.1 + - + +
1039X TYR* 4.7 6.5 + - - -
1051X LEU* 4.2 20.0 - - + -
1056X ARG* 3.7 16.8 - - - -
1074X CYS 3.2 13.5 + - - +
1075X TRP* 3.1 60.5 + + + -
1076X ARG 3.9 1.3 - - - -
1082X ARG* 3.5 26.2 - - - +
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Residues in contact with SER1023 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963X ARG 5.5 3.8 + - - -
964X ASP* 5.8 0.6 - - - -
965X LEU* 3.5 35.0 + - - +
1004X TRP* 2.6 29.1 + - - +
1005X MET* 4.5 3.1 - - - -
1006X ALA 4.8 0.2 + - - -
1019X SER 3.1 11.4 + - - -
1020X ASP* 3.6 10.8 + - - -
1022X TRP* 1.3 77.9 - - - +
1024X TYR* 1.3 56.4 + - - +
1026X VAL* 3.1 6.6 + - - +
1027X LEU* 2.9 26.2 + - - +
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Residues in contact with TYR1024 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945X ALA* 2.6 38.1 + - + +
948X VAL* 4.0 21.1 - - + -
949X ALA* 3.8 13.9 - - - -
965X LEU* 4.3 7.0 - - + +
1020X ASP 2.9 15.7 + - - +
1021X VAL 3.1 8.0 + - - +
1023X SER* 1.3 73.1 - - - +
1025X GLY* 1.3 58.7 + - - +
1027X LEU* 3.1 15.7 + - + +
1028X LEU* 2.7 53.2 + - + +
1074X CYS* 4.3 2.9 - - - -
1085X PHE* 3.6 24.9 - + + -
1088X ILE* 3.6 34.1 - - + -
1092X LEU* 3.1 17.8 - - - +
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Residues in contact with GLY1025 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021X VAL 2.9 12.1 + - - -
1022X TRP 2.9 5.5 + - - -
1024X TYR* 1.3 79.1 - - - +
1026X VAL* 1.3 56.8 + - - +
1028X LEU* 3.4 7.7 + - - +
1029X TRP 3.0 21.3 + - - -
1071X MET* 4.0 5.6 - - - +
1074X CYS* 3.7 19.5 - - - -
1075X TRP* 3.3 23.3 - - - -
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Residues in contact with VAL1026 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003X ARG 3.8 17.0 - - - +
1004X TRP* 3.6 21.5 - - + +
1022X TRP* 3.1 22.8 + - + +
1023X SER 3.1 5.8 + - - +
1025X GLY* 1.3 74.4 - - - +
1027X LEU* 1.3 58.7 + - - +
1029X TRP* 3.0 4.9 + - - +
1030X GLU* 2.9 26.4 + - - +
1038X PRO* 3.6 36.3 - - + -
1039X TYR* 4.8 2.2 - - - +
1057X LEU* 4.3 8.7 - - + -
1075X TRP* 3.6 23.1 - - + +
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Residues in contact with LEU1027 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910X LEU* 4.5 6.3 - - + -
948X VAL* 4.0 31.0 - - + -
965X LEU* 4.4 9.6 - - + -
966X ALA* 3.8 21.8 - - - +
967X ALA* 3.9 13.0 - - - +
970X ILE* 3.9 20.2 - - + -
1004X TRP* 4.4 0.4 - - - -
1023X SER 2.9 12.0 + - - +
1024X TYR* 3.2 18.4 - - + +
1026X VAL* 1.3 75.8 - - - +
1028X LEU* 1.3 57.7 + - - +
1030X GLU* 3.0 17.7 + - - +
1031X ILE* 2.9 55.1 + - + +
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Residues in contact with LEU1028 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942X LEU* 5.0 3.8 - - + -
945X ALA* 3.8 27.4 - - + -
1024X TYR* 2.7 33.1 + - + +
1025X GLY* 3.5 9.9 - - - +
1027X LEU* 1.3 71.8 - - - +
1029X TRP* 1.3 63.8 + - - +
1031X ILE* 3.2 11.2 + - + +
1032X VAL* 3.1 34.2 + - + +
1067X VAL* 4.3 12.6 - - + +
1070X LEU* 4.1 31.6 - - + -
1071X MET* 3.8 27.8 - - + +
1074X CYS* 5.7 0.7 - - - -
1092X LEU* 4.7 5.2 - - + -
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Residues in contact with TRP1029 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025X GLY 3.0 13.5 + - - +
1026X VAL 3.0 11.9 + - - +
1028X LEU* 1.3 77.0 - - - +
1030X GLU* 1.3 60.2 + - - +
1032X VAL* 3.5 1.4 + - - +
1033X SER* 2.8 52.0 + - - -
1036X GLY 3.5 18.2 - - - -
1037X THR 3.5 20.0 - - - -
1038X PRO* 3.6 18.8 - - + -
1039X TYR 4.8 1.1 - - - -
1040X CYS* 5.7 0.9 - - + -
1057X LEU* 3.8 37.3 - - + +
1058X GLU 3.3 23.3 + - - -
1060X PRO* 3.6 18.8 - - + +
1068X TYR* 5.5 0.2 - + - -
1071X MET* 3.8 27.9 - - - +
1075X TRP* 4.3 1.3 - + + -
1114X ALA* 4.5 13.0 - - + -
1115X GLY 5.8 0.2 - - - -
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Residues in contact with GLU1030 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911X LEU* 3.6 15.8 - - + +
914X LEU* 4.0 4.0 - - + -
967X ALA* 2.9 42.0 + - + +
968X ARG 4.6 1.6 + - - -
1004X TRP* 2.8 45.1 + - + +
1026X VAL 2.9 12.5 + - - +
1027X LEU* 3.2 15.0 - - - +
1029X TRP* 1.3 77.2 - - - +
1031X ILE* 1.3 63.1 + - - +
1033X SER* 3.3 6.1 + - - -
1034X LEU 3.0 3.8 + - - -
1035X GLY* 2.8 31.1 + - - +
1036X GLY 4.1 15.8 - - - +
1038X PRO* 4.4 6.3 - - + -
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Residues in contact with ILE1031 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910X LEU* 4.1 24.0 - - + -
914X LEU* 3.8 16.1 - - + +
941X LEU* 3.3 43.2 - - + +
942X LEU* 6.1 0.4 - - + -
944X PHE* 4.3 5.4 - - + -
945X ALA* 3.7 35.9 - - + +
1027X LEU* 2.9 37.4 + - + +
1028X LEU* 3.2 11.4 + - + +
1030X GLU* 1.3 75.1 - - + +
1032X VAL* 1.3 68.0 + - + +
1034X LEU* 3.0 20.1 + - - +
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Residues in contact with VAL1032 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941X LEU* 5.2 0.4 - - - -
942X LEU* 5.2 2.5 - - + -
1028X LEU* 3.1 23.2 + - + +
1029X TRP 4.1 1.6 - - - +
1031X ILE* 1.3 79.0 - - + +
1033X SER* 1.3 58.7 + - - +
1034X LEU* 3.5 4.0 + - - +
1060X PRO* 4.0 9.9 - - + -
1062X ASN* 2.9 35.2 + - - +
1063X CYS* 3.7 32.1 - - + -
1067X VAL* 3.9 23.1 - - + -
1071X MET* 3.9 6.3 - - + -
1103X VAL* 3.9 32.8 - - + +
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Residues in contact with SER1033 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918X ARG* 3.0 23.6 + - - -
1029X TRP* 2.8 44.5 + - - -
1030X GLU* 3.3 6.1 + - - -
1032X VAL* 1.3 75.4 - - - +
1034X LEU* 1.3 62.4 + - - +
1036X GLY 3.3 12.3 + - - -
1060X PRO* 5.1 7.4 - - - -
1062X ASN* 4.7 5.4 - - - +
1113X TYR* 5.4 1.0 - - - -
1114X ALA* 3.8 25.0 + - - +
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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
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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