Contacts of the helix formed by residues 1084 - 1098 (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 SER1084 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017B THR* 6.2 1.8 - - - -
1021B VAL* 4.8 2.7 - - - -
1083B PRO* 1.3 73.9 - - - +
1085B PHE* 1.3 65.8 + - - +
1086B ALA* 3.5 9.4 + - - +
1087B GLN* 3.0 34.9 + - - +
1088B ILE* 3.0 25.5 + - - +
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Residues in contact with PHE1085 (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* 3.8 16.0 - - - +
952B MET* 3.6 54.7 - - + -
953B ASP* 3.7 23.6 - - - +
956B SER* 4.0 12.1 - - - -
965B LEU* 4.1 0.9 - - + -
1017B THR* 4.0 14.3 - - + +
1020B ASP* 3.9 10.5 - - + -
1021B VAL* 3.7 35.8 - - + +
1024B TYR* 3.7 29.2 - + + -
1084B SER* 1.3 74.3 - - - +
1086B ALA* 1.3 57.2 + - - +
1088B ILE* 3.3 13.6 + - + +
1089B LEU* 2.9 29.6 + - - +
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Residues in contact with ALA1086 (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* 3.7 25.8 + - - +
957B GLN* 5.2 3.1 - - - +
1084B SER* 3.1 9.9 + - - +
1085B PHE* 1.3 79.8 - - - +
1087B GLN* 1.3 62.7 + - + +
1089B LEU* 3.4 7.9 + - - +
1090B VAL* 3.1 27.0 + - - +
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Residues in contact with GLN1087 (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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1082B ARG 4.8 0.3 - - - +
1083B PRO* 3.3 17.7 - - + +
1084B SER* 3.0 35.4 + - - +
1086B ALA* 1.3 76.4 - - + +
1088B ILE* 1.3 65.7 + - - +
1090B VAL* 3.1 9.9 + - - +
1091B SER* 3.0 26.7 + - - +
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Residues in contact with ILE1088 (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* 4.0 10.8 - - + -
1021B VAL* 3.9 17.3 - - + -
1024B TYR* 3.6 30.7 - - + -
1070B LEU* 4.3 17.5 - - + -
1074B CYS* 3.9 22.0 - - - -
1083B PRO* 3.8 15.9 - - + -
1084B SER 3.0 18.4 + - - +
1085B PHE* 3.5 25.8 - - + +
1087B GLN* 1.3 75.8 - - - +
1089B LEU* 1.3 57.8 + - - +
1091B SER* 3.2 8.0 + - - -
1092B LEU* 3.0 34.6 + - + +
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Residues in contact with LEU1089 (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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946B ALA* 3.6 41.3 - - + +
949B ALA* 4.3 7.0 - - + -
950B ARG* 3.8 37.7 - - + +
953B ASP* 5.4 8.1 - - + +
1085B PHE 2.9 15.7 + - - +
1086B ALA* 3.6 7.6 - - - +
1088B ILE* 1.3 75.4 - - - +
1090B VAL* 1.3 60.6 + - + +
1092B LEU* 3.4 2.1 + - - -
1093B ASN* 2.9 45.4 + - - +
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Residues in contact with VAL1090 (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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1086B ALA 3.1 16.2 + - - +
1087B GLN* 3.1 10.9 + - - +
1089B LEU* 1.3 76.8 - - + +
1091B SER* 1.3 62.8 + - - +
1093B ASN* 3.4 6.6 + - - +
1094B ARG* 3.0 50.9 + - + +
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Residues in contact with SER1091 (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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1066B GLU* 5.0 4.9 - - - +
1070B LEU* 4.3 21.8 - - - +
1073B GLN* 5.3 4.6 + - - -
1087B GLN 3.0 14.2 + - - -
1088B ILE* 3.2 8.9 + - - -
1090B VAL* 1.3 76.3 - - - +
1092B LEU* 1.3 66.8 + - - +
1094B ARG* 3.2 18.2 + - - +
1095B MET* 3.2 21.0 + - - +
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Residues in contact with LEU1092 (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* 4.5 20.0 - - + +
945B ALA* 3.5 13.0 - - + +
946B ALA* 3.4 37.5 - - + +
949B ALA* 4.1 7.9 - - + -
1024B TYR* 3.3 25.8 - - - +
1028B LEU* 4.9 5.6 - - + -
1067B VAL* 6.0 1.1 - - + -
1070B LEU* 3.7 22.4 - - + -
1088B ILE* 3.0 23.3 + - + +
1089B LEU* 3.8 4.0 - - - +
1091B SER* 1.3 74.6 - - - +
1093B ASN* 1.3 59.4 + - - +
1095B MET* 3.2 12.2 + - - +
1096B LEU* 2.9 34.1 + - + +
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Residues in contact with ASN1093 (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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946B ALA* 4.4 3.6 - - - +
950B ARG* 4.9 6.5 + - - +
1089B LEU* 2.9 43.0 + - - +
1090B VAL* 3.7 6.9 - - - +
1091B SER 3.3 0.2 - - - -
1092B LEU* 1.3 76.4 - - - +
1094B ARG* 1.3 64.4 + - + +
1096B LEU* 3.7 20.7 - - - +
1097B GLU* 3.0 26.0 + - - +
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Residues in contact with ARG1094 (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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1066B GLU* 5.5 4.5 - - - +
1090B VAL* 3.0 39.1 + - + +
1091B SER* 3.2 11.6 + - - +
1093B ASN* 1.3 79.0 - - + +
1095B MET* 1.3 63.1 + - + +
1097B GLU* 3.4 12.5 + - - +
1098B GLU* 3.4 21.7 - - - +
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Residues in contact with MET1095 (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* 4.6 1.0 - - - +
942B LEU* 4.0 10.5 - - + -
1066B GLU* 3.1 53.4 - - + +
1067B VAL* 3.3 29.6 - - + +
1070B LEU* 5.3 4.9 - - - -
1091B SER* 3.2 16.9 + - - +
1092B LEU* 3.2 15.7 + - - +
1094B ARG* 1.3 76.0 - - - +
1096B LEU* 1.3 63.8 + - - +
1098B GLU* 3.2 20.6 + - - +
1102B TYR* 3.2 57.6 - - + +
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Residues in contact with LEU1096 (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* 3.3 51.3 + - - +
942B LEU* 3.3 33.9 - - + +
943B HIS* 3.6 29.6 - - + +
946B ALA* 4.1 14.6 - - + -
1092B LEU 2.9 21.0 + - - +
1093B ASN* 3.7 23.6 - - - +
1095B MET* 1.3 77.4 - - - +
1097B GLU* 1.3 62.4 + - - +
1098B GLU 3.1 10.4 + - - +
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Residues in contact with GLU1097 (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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1093B ASN 3.0 18.9 + - - +
1094B ARG* 3.6 8.7 - - - +
1095B MET 3.3 0.2 - - - -
1096B LEU* 1.3 76.0 - - - +
1098B GLU* 1.3 60.8 + - + +
1099B ARG 4.1 0.3 + - - -
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Residues in contact with GLU1098 (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* 4.0 3.3 - - - +
1066B GLU* 4.9 0.7 - - - +
1094B ARG* 3.4 17.7 - - - +
1095B MET* 3.2 10.8 + - - +
1096B LEU 3.1 13.5 - - - +
1097B GLU* 1.3 81.2 - - + +
1099B ARG* 1.3 69.3 + - - +
1100B LYS* 3.9 12.9 - - + +
1102B TYR* 2.5 33.6 + - - -
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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