Contacts of the helix formed by residues 937 - 957 (chain B) in PDB entry 1FVR
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935B THR 4.1 0.2 + - - -
936B LEU* 1.3 74.6 - - - +
938B SER* 1.3 66.2 + - - +
939B GLN* 3.4 10.1 + - - +
940B GLN* 2.7 38.1 + - - +
941B LEU* 3.1 26.6 + - - +
1105B THR* 4.5 4.7 - - - -
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Residues in contact with SER 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B SER* 1.3 72.5 - - - +
939B GLN* 1.3 64.3 + - - +
941B LEU* 3.2 4.9 + - - +
942B LEU* 3.0 27.2 + - - +
1100B LYS 5.1 0.7 + - - -
1101B THR* 4.1 16.3 - - - -
1102B TYR* 3.2 11.7 + - - +
1103B VAL* 2.9 52.8 + - - +
1105B THR* 4.6 4.0 + - - -
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Residues in contact with GLN 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B SER* 3.2 9.1 - - - +
938B SER* 1.3 80.2 - - - +
940B GLN* 1.3 62.1 + - + +
942B LEU* 3.3 3.9 + - - +
943B HIS* 3.0 43.7 + - + -
1095B MET 4.6 0.7 - - - +
1096B LEU* 3.3 52.7 + - - +
1098B GLU 4.0 7.4 - - - +
1099B ARG 4.5 6.8 - - - +
1100B LYS 4.9 2.8 - - - +
1102B TYR* 6.1 0.2 - - - -
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Residues in contact with GLN 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935B THR 3.8 6.1 + - - +
936B LEU* 3.2 30.0 - - + +
937B SER* 2.7 46.4 + - - +
939B GLN* 1.3 78.8 - - + +
941B LEU* 1.3 63.8 + - - +
943B HIS* 3.3 10.2 + - + +
944B PHE* 3.2 31.0 + - + -
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Residues in contact with LEU 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914B LEU* 3.7 30.5 - - + -
936B LEU* 3.9 21.3 - - + +
937B SER 3.1 19.8 + - - +
938B SER 3.2 5.8 + - - +
940B GLN* 1.3 77.3 - - - +
942B LEU* 1.3 63.1 + - - +
944B PHE* 3.2 11.1 + - + +
945B ALA* 3.2 16.8 + - - +
1031B ILE* 3.6 26.8 - - + +
1034B LEU* 4.1 13.7 - - + -
1103B VAL* 3.7 32.8 - - + -
1105B THR* 4.0 19.7 - - + -
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Residues in contact with LEU 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B SER* 3.0 19.8 + - - +
939B GLN* 5.2 3.1 - - - +
941B LEU* 1.3 77.4 - - - +
943B HIS* 1.3 57.7 + - - +
945B ALA* 3.2 8.2 + - + +
946B ALA* 2.8 29.1 + - - +
1028B LEU* 5.2 4.0 - - + -
1031B ILE* 6.5 0.2 - - + -
1067B VAL* 4.6 15.3 - - + -
1092B LEU* 4.5 20.7 - - + +
1095B MET* 4.0 27.4 - - + -
1096B LEU* 3.3 32.8 - - + +
1102B TYR* 4.1 18.2 - - + -
1103B VAL* 3.8 23.3 - - + -
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Residues in contact with HIS 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B GLN* 3.0 45.9 + - + +
940B GLN* 3.5 9.0 - - - +
941B LEU 3.2 0.2 - - - -
942B LEU* 1.3 75.4 - - - +
944B PHE* 1.3 60.9 + - + +
946B ALA* 3.7 5.8 - - - +
947B ASP* 2.8 41.6 + - - +
950B ARG* 5.5 3.6 + - - -
1096B LEU* 3.6 25.1 - - + +
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Residues in contact with PHE 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910B LEU* 4.0 20.4 - - + -
913B PHE* 3.8 34.1 - + - -
914B LEU* 4.9 1.3 - - + -
936B LEU* 4.2 19.7 - - + -
940B GLN* 3.2 24.6 + - + -
941B LEU* 3.2 20.4 + - + +
943B HIS* 1.3 75.6 - - + +
945B ALA* 1.3 64.0 + - - +
947B ASP* 3.3 7.6 + - - +
948B VAL* 3.1 27.1 + - - +
972B VAL* 4.4 14.1 - - + -
976B TYR* 3.3 33.2 - + + -
978B ALA* 4.0 17.4 - - + +
1031B ILE* 4.1 13.0 - - + -
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Residues in contact with ALA 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941B LEU 3.2 8.9 + - - +
942B LEU* 3.2 14.0 + - + +
944B PHE* 1.3 80.2 - - - +
946B ALA* 1.3 56.4 + - - +
948B VAL* 3.3 3.1 + - - -
949B ALA* 3.0 18.7 + - - +
1024B TYR* 2.6 31.0 + - - +
1028B LEU* 3.7 25.6 - - + -
1031B ILE* 3.9 12.9 - - + +
1092B LEU* 3.5 9.0 - - + -
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Residues in contact with ALA 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942B LEU 2.8 17.0 + - - +
943B HIS* 3.7 5.4 - - - +
945B ALA* 1.3 72.7 - - - +
947B ASP* 1.3 56.3 + - - +
949B ALA 3.2 0.3 + - - -
950B ARG* 2.7 49.2 + - - +
1089B LEU* 3.6 19.6 - - + +
1092B LEU* 3.4 17.2 - - + +
1093B ASN* 4.4 1.3 - - - +
1096B LEU* 4.1 19.5 - - + -
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Residues in contact with ASP 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884B ASN* 3.3 27.5 + - - +
943B HIS* 2.8 27.5 + - - +
944B PHE* 3.3 7.2 + - - +
946B ALA* 1.3 77.2 - - - +
948B VAL* 1.3 56.6 + - - +
950B ARG* 2.8 25.1 + - - +
951B GLY 2.9 23.7 + - - -
976B TYR 4.3 3.5 - - - +
977B VAL* 3.9 8.9 - - - +
978B ALA* 3.1 34.8 + - + +
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Residues in contact with VAL 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910B LEU* 5.2 2.9 - - + -
944B PHE 3.1 13.4 + - - +
945B ALA 3.8 6.5 - - - +
947B ASP* 1.3 76.9 - - - +
949B ALA* 1.3 58.2 + - - +
951B GLY 3.3 0.3 + - - -
952B MET* 2.8 39.0 + - + +
965B LEU* 4.7 5.6 - - + -
970B ILE* 3.7 48.0 - - + -
978B ALA* 4.4 5.2 - - + -
980B ILE* 3.6 9.7 - - + +
1024B TYR* 3.6 24.7 - - + -
1027B LEU* 4.5 13.9 - - + -
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Residues in contact with ALA 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945B ALA 3.0 17.7 + - - +
946B ALA 3.6 3.8 - - - +
948B VAL* 1.3 73.5 - - - +
950B ARG* 1.3 61.3 + - - +
952B MET 3.2 0.9 + - - -
953B ASP* 2.9 30.4 + - - +
1024B TYR* 3.8 16.3 - - + +
1085B PHE* 3.8 16.9 - - + +
1088B ILE* 4.0 19.7 - - + -
1089B LEU* 4.3 13.0 - - + -
1092B LEU* 4.1 6.3 - - + -
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Residues in contact with ARG 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B HIS* 3.9 15.9 + - + +
883B PRO* 6.3 0.7 - - - -
884B ASN* 2.8 35.1 + - - +
943B HIS* 5.5 4.8 + - - -
946B ALA* 2.7 38.2 + - - +
947B ASP* 2.8 32.4 + - - +
949B ALA* 1.3 71.6 - - - +
951B GLY* 1.3 63.3 + - - +
953B ASP* 3.3 6.5 + - - +
954B TYR* 3.1 21.5 + - - +
1089B LEU* 3.8 31.4 - - + +
1093B ASN* 4.9 5.9 + - - +
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Residues in contact with GLY 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B HIS* 4.1 8.3 - - - -
884B ASN* 3.8 19.5 - - - +
885B ILE* 4.2 1.5 - - - +
947B ASP 2.9 15.2 + - - -
948B VAL 3.7 2.9 - - - -
950B ARG* 1.3 79.7 - - - +
952B MET* 1.3 56.5 + - - +
954B TYR* 3.4 4.7 + - - +
955B LEU* 3.1 30.1 + - - +
980B ILE* 3.5 11.7 - - - -
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Residues in contact with MET 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948B VAL* 2.8 25.9 + - + +
949B ALA 3.9 0.2 - - - +
951B GLY* 1.3 70.9 - - - +
953B ASP* 1.3 57.4 + - - +
955B LEU* 3.8 18.6 - - + +
956B SER* 2.7 39.9 + - - +
960B PHE* 5.3 3.6 - - + +
962B HIS* 4.1 10.1 - - + +
965B LEU* 3.9 34.5 - - + -
980B ILE* 3.5 20.9 - - + -
1017B THR* 6.2 0.2 - - + -
1020B ASP* 3.6 24.5 - - - +
1085B PHE* 3.6 40.2 - - + -
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Residues in contact with ASP 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949B ALA 2.9 17.5 + - - +
950B ARG* 3.5 8.7 - - - +
952B MET* 1.3 76.8 - - - +
954B TYR* 1.3 59.2 + - - +
956B SER* 3.7 2.1 - - - -
957B GLN* 2.9 65.8 + - - +
1085B PHE* 3.7 15.5 - - + +
1086B ALA* 3.7 28.4 + - - +
1089B LEU* 5.4 5.9 - - + +
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Residues in contact with TYR 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879B LEU 2.8 28.3 + - - -
880B GLY* 3.6 2.3 - - - -
881B HIS 3.2 30.2 + - - -
882B HIS* 3.5 42.6 - + + +
885B ILE* 4.2 6.3 - - + -
950B ARG 3.1 6.4 + - - +
951B GLY 3.4 8.5 - - - +
953B ASP* 1.3 85.5 + - - +
955B LEU* 1.3 77.3 + - + +
957B GLN* 3.7 4.6 + - - +
958B LYS* 2.8 52.5 + - + +
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Residues in contact with LEU 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879B LEU* 3.8 27.4 - - + -
885B ILE* 3.9 23.8 - - + -
951B GLY 3.1 17.4 + - - +
952B MET* 4.1 24.9 - - + +
954B TYR* 1.3 90.7 - - + +
956B SER* 1.3 66.2 + - - +
958B LYS* 3.0 10.4 + - - -
960B PHE* 3.0 43.9 + - + +
962B HIS* 6.2 0.2 - - + -
980B ILE* 4.3 14.6 - - + -
982B ASP* 4.9 2.5 - - + -
985B LEU* 4.4 15.9 - - + -
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Residues in contact with SER 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952B MET* 2.7 27.1 + - - +
953B ASP* 3.7 5.2 - - - -
955B LEU* 1.3 73.3 - - - +
957B GLN* 1.3 58.7 + - - +
959B GLN* 2.9 25.1 + - - -
960B PHE 4.0 11.2 - - - -
1017B THR* 2.9 35.6 + - - +
1085B PHE* 4.0 13.9 - - - -
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Residues in contact with GLN 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953B ASP* 2.9 50.2 + - - +
954B TYR* 4.0 6.3 - - - +
955B LEU 3.3 0.4 - - - -
956B SER* 1.3 76.6 - - - +
958B LYS* 1.3 60.8 + - + +
959B GLN* 3.4 9.7 + - - +
1086B ALA* 5.2 3.8 - - - +
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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