Contacts of the helix formed by residues 1016 - 1033 (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 THR1016 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961B ILE* 3.9 15.8 - - - +
989B GLN 3.9 7.2 - - - +
990B GLU* 3.5 33.4 - - + +
1008B GLU* 4.5 5.9 + - + +
1014B VAL* 5.4 1.1 - - + -
1015B TYR* 1.3 80.8 - - - +
1017B THR* 1.3 65.0 + - - +
1018B ASN* 3.2 24.0 + - - +
1019B SER* 2.8 27.3 + - - -
1020B ASP* 3.0 12.3 + - - -
1079B PRO* 5.4 0.9 - - - +
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Residues in contact with THR1017 (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* 6.2 0.2 - - + -
956B SER* 2.9 32.2 + - - +
959B GLN* 5.7 1.2 - - - -
960B PHE 4.0 13.7 + - - -
961B ILE* 4.5 6.4 - - - +
989B GLN 5.2 0.8 + - - -
1016B THR* 1.3 74.4 - - - +
1018B ASN* 1.3 66.3 + - - +
1020B ASP* 3.1 12.8 + - - +
1021B VAL* 3.0 24.3 + - + +
1084B SER* 6.2 1.6 - - - -
1085B PHE* 4.0 16.8 - - + +
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Residues in contact with ASN1018 (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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1008B GLU* 4.6 0.2 - - - +
1016B THR* 3.0 13.8 + - - +
1017B THR* 1.3 83.2 - - - +
1019B SER* 1.3 60.4 + - - +
1021B VAL* 3.1 18.8 + - - +
1022B TRP 3.2 5.7 + - - -
1079B PRO* 3.2 48.6 + - + +
1080B TYR* 4.4 7.2 - - - +
1082B ARG* 3.1 21.9 + - - +
1083B PRO 5.3 2.6 - - - +
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Residues in contact with SER1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006B ALA* 3.7 14.8 + - - +
1008B GLU* 3.6 15.5 + - - -
1009B SER* 3.8 12.7 + - - -
1015B TYR* 3.4 14.8 - - - +
1016B THR* 2.8 35.9 + - - -
1018B ASN* 1.3 75.2 - - - +
1020B ASP* 1.3 65.9 + - - +
1022B TRP* 3.2 4.0 + - - +
1023B SER* 3.1 24.5 + - - -
1082B ARG* 3.7 9.6 - - - +
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Residues in contact with ASP1020 (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* 3.6 9.4 - - + +
960B PHE 4.3 1.0 - - - +
961B ILE* 3.5 10.6 - - - +
962B HIS* 2.8 33.9 + - - +
963B ARG* 3.0 27.2 + - - -
964B ASP 4.7 0.3 + - - -
965B LEU* 3.5 11.9 - - + +
1016B THR 3.0 13.6 + - - +
1017B THR* 3.3 13.6 - - - +
1019B SER* 1.3 79.7 + - - +
1021B VAL* 1.3 57.2 + - - +
1023B SER* 3.2 8.9 + - - -
1024B TYR 2.8 24.3 + - - -
1085B PHE* 3.9 16.6 - - + -
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Residues in contact with VAL1021 (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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1017B THR* 3.0 22.6 + - + +
1018B ASN* 3.1 13.0 + - - +
1020B ASP* 1.3 74.8 - - - +
1022B TRP* 1.3 66.2 + - - +
1024B TYR* 3.1 4.9 + - - +
1025B GLY 3.0 17.3 + - - -
1074B CYS* 3.3 32.4 - - + +
1082B ARG* 4.0 9.0 - - + -
1083B PRO* 3.5 28.3 - - + +
1084B SER* 4.8 0.7 - - - -
1085B PHE* 3.7 32.5 - - + +
1088B ILE* 3.9 7.2 - - + -
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Residues in contact with TRP1022 (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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1003B ARG 5.3 0.8 + - - -
1004B TRP 3.6 16.0 + - - -
1005B MET 3.3 15.3 + - - -
1006B ALA* 3.5 22.2 - - + -
1007B ILE* 3.5 33.7 - - + -
1018B ASN 3.2 3.0 + - - -
1019B SER 3.2 9.7 + - - +
1021B VAL* 1.3 77.7 - - - +
1023B SER* 1.3 65.0 + - - +
1025B GLY 3.0 9.5 + - - -
1026B VAL* 3.4 11.5 + - + +
1039B TYR* 4.7 9.1 + - - -
1051B LEU* 4.5 15.3 - - + -
1056B ARG* 3.6 27.8 - - - -
1074B CYS 3.2 13.2 + - - +
1075B TRP* 3.1 55.1 + + + -
1076B ARG 4.2 0.9 - - - -
1082B ARG* 3.5 30.5 - - - +
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Residues in contact with SER1023 (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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963B ARG 5.3 4.7 + - - -
964B ASP* 5.7 0.3 - - - -
965B LEU* 3.5 36.0 + - - +
1004B TRP* 2.7 28.9 + - - +
1005B MET* 4.7 1.4 - - - -
1006B ALA 5.0 0.2 + - - -
1019B SER 3.1 13.5 + - - -
1020B ASP* 3.5 11.3 + - - -
1022B TRP* 1.3 78.7 - - - +
1024B TYR* 1.3 61.1 + - - +
1026B VAL* 3.1 8.0 + - - +
1027B LEU* 2.9 21.3 + - - +
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Residues in contact with TYR1024 (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* 2.6 39.0 + - + +
948B VAL* 3.6 33.9 - - + -
949B ALA* 3.8 7.2 - - + -
965B LEU* 4.0 7.6 - - + +
1020B ASP 2.8 14.4 + - - +
1021B VAL* 3.1 9.4 + - - +
1023B SER* 1.3 77.0 - - - +
1025B GLY* 1.3 59.4 + - - +
1027B LEU* 3.1 18.0 + - + +
1028B LEU* 2.8 43.5 + - + +
1074B CYS* 4.3 6.1 - - - -
1085B PHE* 3.7 23.8 - + + -
1088B ILE* 3.6 35.7 - - + -
1092B LEU* 3.3 12.0 - - - +
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Residues in contact with GLY1025 (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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1021B VAL 3.0 10.3 + - - -
1022B TRP 3.0 6.0 + - - -
1024B TYR* 1.3 79.7 - - - +
1026B VAL* 1.3 60.3 + - - +
1028B LEU* 3.3 7.6 + - - +
1029B TRP* 3.1 17.5 + - - +
1071B MET* 3.9 6.8 - - - +
1074B CYS* 3.9 18.4 - - - -
1075B TRP* 3.5 23.0 - - - -
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Residues in contact with VAL1026 (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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1003B ARG 3.6 23.6 - - - +
1004B TRP* 3.6 28.0 - - + +
1022B TRP* 3.6 26.9 - - + +
1023B SER 3.1 6.8 + - - +
1025B GLY* 1.3 73.2 - - - +
1027B LEU* 1.3 60.1 + - - +
1029B TRP* 3.2 5.5 + - + +
1030B GLU* 2.9 27.4 + - - +
1038B PRO* 3.7 22.7 - - + -
1039B TYR* 5.0 2.2 - - - +
1057B LEU* 4.2 9.4 - - + -
1075B TRP* 3.6 18.6 - - + +
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Residues in contact with LEU1027 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910B LEU* 4.3 11.0 - - + -
945B ALA* 5.3 0.2 - - - -
948B VAL* 4.5 14.6 - - + -
965B LEU* 4.7 3.8 - - + +
966B ALA* 3.7 11.0 - - - +
967B ALA* 3.2 41.7 - - + +
970B ILE* 4.4 7.2 - - + -
1004B TRP* 4.4 0.2 - - - +
1023B SER 2.9 13.0 + - - +
1024B TYR* 3.1 33.6 + - + +
1026B VAL* 1.3 78.0 - - - +
1028B LEU* 1.3 59.8 - - - +
1030B GLU* 3.0 15.1 + - - +
1031B ILE* 3.0 42.5 + - + +
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Residues in contact with LEU1028 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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942B LEU* 5.2 4.0 - - + -
945B ALA* 3.7 28.0 - - + -
1024B TYR* 2.8 27.9 + - + +
1025B GLY* 3.5 9.9 - - - +
1027B LEU* 1.3 80.5 - - - +
1029B TRP* 1.3 57.6 + - - +
1031B ILE* 3.3 6.8 + - + +
1032B VAL* 2.9 43.7 + - + +
1067B VAL* 4.2 17.7 - - + -
1070B LEU* 4.0 32.8 - - + -
1071B MET* 3.9 21.1 - - + +
1074B CYS* 6.0 0.7 - - - -
1092B LEU* 4.9 4.3 - - + -
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Residues in contact with TRP1029 (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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1025B GLY 3.1 12.4 + - - +
1026B VAL* 3.3 13.0 - - - +
1028B LEU* 1.3 75.8 - - - +
1030B GLU* 1.3 64.6 + - - +
1032B VAL* 3.9 0.5 - - - +
1033B SER* 2.9 53.9 + - - -
1036B GLY 3.4 20.2 - - - -
1037B THR 3.7 17.7 - - - -
1038B PRO* 3.8 19.1 - - + -
1039B TYR 4.8 1.3 - - - -
1057B LEU* 3.8 33.2 - - + +
1058B GLU 3.0 28.6 + - - -
1060B PRO* 3.6 17.0 - - + +
1071B MET* 3.7 28.9 - - - +
1075B TRP* 4.4 1.1 - + + -
1114B ALA* 4.7 9.0 - - + -
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Residues in contact with GLU1030 (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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911B LEU* 3.7 16.3 - - - +
914B LEU* 3.7 3.5 - - + +
967B ALA* 3.0 43.8 + - + +
968B ARG* 4.7 0.7 + - - -
1004B TRP* 2.7 42.3 + - - +
1026B VAL 2.9 15.1 + - - +
1027B LEU* 3.0 13.2 + - - +
1029B TRP* 1.3 79.3 - - - +
1031B ILE* 1.3 60.6 + - - +
1033B SER* 3.4 6.1 + - - -
1034B LEU 3.2 2.9 + - - -
1035B GLY* 2.7 32.2 + - - -
1036B GLY 4.2 8.4 - - - +
1038B PRO* 4.2 15.8 - - + +
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Residues in contact with ILE1031 (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* 4.1 20.4 - - + -
914B LEU* 3.7 12.2 - - + +
941B LEU* 3.6 49.7 - - + +
942B LEU* 6.5 0.2 - - + -
944B PHE* 4.1 11.2 - - + +
945B ALA* 3.9 28.7 - - + +
948B VAL* 5.5 0.2 - - + -
1027B LEU* 3.0 37.6 + - + +
1028B LEU* 3.6 11.4 - - + +
1030B GLU* 1.3 76.6 - - - +
1032B VAL* 1.3 67.7 + - + +
1034B LEU* 3.1 14.9 + - - +
1103B VAL* 6.1 0.4 - - + -
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Residues in contact with VAL1032 (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* 5.8 0.2 - - + -
1028B LEU* 2.9 26.5 + - + +
1029B TRP 3.9 3.1 - - - +
1031B ILE* 1.3 78.1 - - + +
1033B SER* 1.3 59.3 + - - +
1034B LEU* 3.1 6.6 + - - +
1060B PRO* 3.8 14.1 - - + -
1062B ASN* 3.1 30.3 + - - +
1063B CYS* 3.6 30.5 - - + -
1067B VAL* 3.9 17.9 - - + -
1071B MET* 3.8 16.6 - - + -
1103B VAL* 4.0 30.3 - - + +
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Residues in contact with SER1033 (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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918B ARG* 3.0 18.7 + - - -
1029B TRP* 2.9 42.1 + - - -
1030B GLU* 3.4 2.8 + - - -
1031B ILE 3.3 0.2 - - - -
1032B VAL* 1.3 75.7 - - - +
1034B LEU* 1.3 66.4 + - - +
1036B GLY 3.1 16.8 + - - -
1060B PRO* 4.5 10.8 - - - -
1062B ASN* 4.8 4.9 - - - +
1113B TYR* 5.8 0.3 - - - -
1114B ALA* 3.8 22.6 + - - +
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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