Contacts of the helix formed by residues 937 - 957 (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 SER 937 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935X THR 4.1 0.4 + - - -
936X LEU* 1.3 76.4 - - - +
938X SER* 1.3 58.9 - - - +
939X GLN* 3.5 10.8 + - - +
940X GLN* 3.0 37.1 + - - +
941X LEU* 3.0 29.4 + - - +
1105X THR* 4.7 6.1 - - - -
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Residues in contact with SER 938 (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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936X LEU 4.1 0.2 + - - -
937X SER* 1.3 72.1 - - - +
939X GLN* 1.3 56.9 + - - +
941X LEU* 3.4 4.3 + - - +
942X LEU* 3.0 35.8 + - - +
1101X THR* 3.7 15.3 - - - -
1102X TYR* 3.2 14.7 + - - +
1103X VAL* 3.0 54.6 + - - +
1105X THR* 4.7 4.2 + - - +
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Residues in contact with GLN 939 (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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937X SER* 3.1 10.1 + - - +
938X SER* 1.3 80.7 + - - +
940X GLN* 1.3 57.5 + - + +
942X LEU* 5.6 1.4 - - - +
943X HIS* 3.0 39.4 + - + +
1095X MET 5.2 0.3 - - - +
1096X LEU* 2.7 59.9 + - + +
1098X GLU 4.7 5.4 + - - +
1100X LYS 5.3 4.0 - - - +
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Residues in contact with GLN 940 (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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935X THR 3.7 5.8 + - - +
936X LEU* 3.4 28.4 - - + +
937X SER* 3.0 38.9 + - - +
939X GLN* 1.3 76.3 - - + +
941X LEU* 1.3 57.2 + - - +
943X HIS* 3.4 8.2 + - - +
944X PHE* 3.1 36.7 + - + -
976X TYR* 6.1 4.9 - - - +
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Residues in contact with LEU 941 (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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914X LEU* 3.7 30.5 - - + -
936X LEU* 3.9 22.4 - - + +
937X SER 3.0 23.3 + - - +
938X SER* 3.7 4.7 - - - +
939X GLN 3.3 0.2 - - - -
940X GLN* 1.3 75.0 - - - +
942X LEU* 1.3 65.4 + - + +
944X PHE* 3.4 7.2 + - + +
945X ALA* 3.2 16.3 + - - +
1031X ILE* 3.3 32.7 - - + +
1034X LEU* 3.9 19.3 - - + -
1103X VAL* 3.8 36.1 - - + -
1105X THR* 4.4 6.5 - - + -
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Residues in contact with LEU 942 (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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938X SER* 3.0 24.1 + - - +
939X GLN* 5.6 1.3 - - - +
941X LEU* 1.3 77.4 - - + +
943X HIS* 1.3 57.3 + - - +
945X ALA* 3.3 5.4 + - - +
946X ALA* 2.9 28.6 + - - +
1028X LEU* 5.0 7.2 - - + -
1031X ILE* 6.1 0.4 - - + -
1032X VAL* 5.2 2.2 - - + -
1067X VAL* 4.3 21.5 - - + -
1092X LEU* 4.1 23.6 - - + +
1095X MET* 4.1 17.0 - - + -
1096X LEU* 3.7 24.9 - - + +
1102X TYR* 3.9 35.2 - - + -
1103X VAL* 4.6 12.1 - - + -
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Residues in contact with HIS 943 (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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939X GLN* 3.0 28.0 + - + +
940X GLN* 3.7 8.7 - - - +
941X LEU 3.2 0.2 - - - -
942X LEU* 1.3 75.4 - - - +
944X PHE* 1.3 59.4 + - + +
946X ALA* 3.7 4.3 - - - +
947X ASP* 2.9 41.4 + - - +
950X ARG* 5.1 7.7 + - - -
1093X ASN* 6.0 0.4 - - - -
1096X LEU* 3.4 39.2 - - + +
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Residues in contact with PHE 944 (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* 3.9 24.2 - - + -
913X PHE* 3.7 34.1 - + - -
914X LEU* 5.0 1.1 - - + -
936X LEU* 4.2 19.5 - - + -
940X GLN* 3.1 26.9 + - + -
941X LEU* 3.6 17.0 - - + +
943X HIS* 1.3 76.1 - - + +
945X ALA* 1.3 62.2 + - - +
947X ASP* 3.3 6.7 + - - +
948X VAL* 3.1 29.2 + - - +
972X VAL* 3.9 19.3 - - + -
976X TYR* 3.5 31.2 - + + -
978X ALA* 4.0 17.0 - - + +
1031X ILE* 4.3 10.5 - - + -
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Residues in contact with ALA 945 (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 3.2 8.2 + - - +
942X LEU* 3.5 11.9 - - - +
943X HIS 3.2 0.6 - - - -
944X PHE* 1.3 79.0 - - - +
946X ALA* 1.3 57.4 + - - +
948X VAL* 3.4 2.5 + - - -
949X ALA* 3.1 18.2 + - - +
1024X TYR* 2.6 32.3 + - - +
1028X LEU* 3.8 18.6 - - + -
1031X ILE* 3.7 23.1 - - + +
1092X LEU* 3.7 7.0 - - + -
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Residues in contact with ALA 946 (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 2.9 17.0 + - - +
943X HIS* 3.7 6.3 - - + +
945X ALA* 1.3 72.5 - - - +
947X ASP* 1.3 56.2 + - - +
949X ALA* 3.2 1.1 + - - -
950X ARG* 2.7 48.1 + - - +
1089X LEU* 3.4 19.5 - - + +
1092X LEU* 3.8 15.5 - - + +
1093X ASN* 4.2 4.7 - - - +
1096X LEU* 4.0 18.6 - - + -
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Residues in contact with ASP 947 (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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884X ASN* 3.2 27.6 + - - +
943X HIS* 2.9 25.7 + - - +
944X PHE* 3.3 9.7 - - - +
946X ALA* 1.3 76.7 - - - +
948X VAL* 1.3 57.0 + - - +
950X ARG* 2.9 27.2 + - - +
951X GLY 2.9 23.7 + - - -
976X TYR 4.1 4.3 - - - +
977X VAL* 3.5 10.6 - - - +
978X ALA* 2.8 35.9 + - + +
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Residues in contact with VAL 948 (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* 5.2 2.5 - - + -
944X PHE 3.1 17.1 + - - +
945X ALA 3.9 5.2 - - - +
946X ALA 3.2 0.2 - - - -
947X ASP* 1.3 72.6 - - - +
949X ALA* 1.3 61.2 + - - +
951X GLY* 3.4 0.7 + - - +
952X MET* 2.9 35.7 + - + +
965X LEU* 4.6 2.2 - - + -
970X ILE* 4.0 46.4 - - + -
978X ALA* 4.2 5.6 - - + -
980X ILE* 3.8 13.8 - - + +
1024X TYR* 4.0 15.0 - - + -
1027X LEU* 4.0 23.8 - - + -
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Residues in contact with ALA 949 (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 3.1 14.3 + - - +
946X ALA 3.5 8.1 - - - +
948X VAL* 1.3 77.2 - - - +
950X ARG* 1.3 55.6 + - - +
952X MET 3.8 0.3 - - - -
953X ASP* 2.9 30.5 + - - +
1024X TYR* 3.8 8.4 - - + +
1085X PHE* 3.8 16.8 - - + +
1088X ILE* 3.9 27.6 - - + -
1089X LEU* 4.0 18.6 - - + +
1092X LEU* 4.3 1.6 - - + -
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Residues in contact with ARG 950 (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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882X HIS* 3.8 16.9 - - + +
884X ASN* 3.0 28.2 + - - +
943X HIS* 5.1 7.7 + - - -
946X ALA* 2.7 35.9 + - - +
947X ASP* 2.9 28.5 + - - +
948X VAL 3.3 0.2 - - - -
949X ALA* 1.3 72.2 - - - +
951X GLY* 1.3 63.7 + - - +
953X ASP* 3.5 4.3 + - - +
954X TYR* 3.1 21.8 + - - +
1089X LEU* 3.9 31.7 - - + +
1093X ASN* 4.4 7.3 + - - +
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Residues in contact with GLY 951 (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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882X HIS* 4.6 2.0 - - - -
884X ASN* 3.8 17.2 - - - +
885X ILE* 4.2 2.7 - - - +
947X ASP 2.9 15.2 + - - -
950X ARG* 1.3 77.5 - - - +
952X MET* 1.3 56.6 + - - +
954X TYR* 3.3 8.3 + - - +
955X LEU* 3.0 30.5 + - - +
980X ILE* 3.3 19.5 - - - -
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Residues in contact with MET 952 (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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948X VAL* 2.9 22.6 + - + +
951X GLY* 1.3 72.6 - - - +
953X ASP* 1.3 62.5 + - - +
955X LEU* 4.0 13.9 - - + +
956X SER* 2.8 35.8 + - - +
960X PHE* 4.9 10.1 - - + +
962X HIS* 3.9 12.1 - - + +
965X LEU* 3.9 39.5 - - + -
980X ILE* 3.6 19.7 - - + -
1020X ASP* 3.4 24.9 - - - +
1085X PHE* 3.5 34.8 - - + -
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Residues in contact with ASP 953 (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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949X ALA 2.9 18.6 + - - +
950X ARG* 3.7 7.2 - - - +
952X MET* 1.3 77.0 - - - +
954X TYR* 1.3 64.5 + - - +
956X SER* 3.3 5.6 + - - -
957X GLN* 3.1 44.1 + - - +
1085X PHE* 3.6 10.8 - - + +
1086X ALA* 3.5 31.9 + - - +
1089X LEU* 5.1 6.6 - - + +
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Residues in contact with TYR 954 (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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879X LEU 2.7 29.0 + - - -
880X GLY* 3.6 1.6 - - - -
881X HIS 3.3 19.3 + - - -
882X HIS* 3.9 45.8 - + + +
885X ILE* 4.1 11.4 - - + -
950X ARG 3.1 10.8 + - - +
951X GLY* 3.4 10.8 - - - +
952X MET 3.3 0.2 - - - -
953X ASP* 1.3 84.0 + - - +
955X LEU* 1.3 73.8 + - + +
957X GLN* 3.6 8.8 + - - +
958X LYS* 2.8 41.1 + - - +
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Residues in contact with LEU 955 (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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1X RAJ 4.4 5.2 - - - -
879X LEU* 3.8 33.4 - - + +
885X ILE* 3.9 21.8 - - + -
951X GLY 3.0 16.3 + - - +
952X MET* 4.0 22.2 - - - +
954X TYR* 1.3 92.7 - - + +
956X SER* 1.3 61.3 + - - +
958X LYS* 2.9 23.3 + - + +
960X PHE* 3.2 52.1 + - + +
980X ILE* 4.1 12.6 - - + -
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Residues in contact with SER 956 (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* 2.8 28.4 + - - +
953X ASP* 3.3 12.6 + - - -
955X LEU* 1.3 74.2 - - - +
957X GLN* 1.3 66.7 + - - +
958X LYS 3.1 0.4 - - - -
959X GLN* 3.0 24.1 + - - +
960X PHE 3.8 13.6 + - - -
1017X THR* 3.8 33.4 + - - +
1085X PHE* 4.0 10.3 + - - +
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Residues in contact with GLN 957 (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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953X ASP* 3.1 37.4 + - - +
954X TYR* 3.9 7.2 - - - +
955X LEU 3.2 0.6 - - - -
956X SER* 1.3 85.5 + - - +
958X LYS* 1.3 58.3 + - + +
959X GLN* 3.2 16.6 + - - +
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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