Contacts of the helix formed by residues 1061 - 1081 (chain B) in PDB entry 3U5P
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 GLU1061 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060B SER* 1.3 79.7 + - - +
1062B VAL* 1.3 58.0 + - - +
1064B GLN* 3.3 14.4 + - - +
1065B ALA* 2.9 27.2 + - - +
16J PRO* 4.4 16.3 - - + +
17J ARG 5.1 9.9 - - - +
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Residues in contact with VAL1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981B GLU* 3.6 24.9 - - + -
982B PHE* 3.6 9.8 - - + -
1035B CYS* 3.9 7.1 - - - -
1060B SER* 3.2 9.9 + - - +
1061B GLU* 1.3 75.7 - - - +
1063B ALA* 1.3 60.2 + - - +
1065B ALA* 3.2 7.5 + - - +
1066B GLY* 2.8 24.4 + - - -
16J PRO* 4.2 2.7 - - - -
17J ARG 3.5 32.1 - - - +
18J ALY 3.9 43.7 - - + +
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Residues in contact with ALA1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B CYS* 4.0 14.5 - - - +
1036B GLU* 5.7 4.9 - - + +
1039B ASN* 3.5 43.7 - - + +
1060B SER* 3.1 14.5 + - - +
1062B VAL* 1.3 79.8 - - - +
1064B GLN* 1.3 59.1 + - + +
1066B GLY* 3.2 3.1 + - - -
1067B LYS* 2.9 37.7 + - - +
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Residues in contact with GLN1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060B SER 3.0 17.0 + - - +
1061B GLU* 3.4 16.4 - - - +
1063B ALA* 1.3 76.5 - - + +
1065B ALA* 1.3 65.9 + - - +
1067B LYS* 2.9 30.0 + - + +
1068B ALA* 3.1 13.0 + - - +
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Residues in contact with ALA1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978B LEU* 3.8 41.7 - - + +
981B GLU* 6.0 0.4 - - + -
982B PHE* 4.1 7.9 - - + -
1061B GLU 2.9 14.8 + - - +
1062B VAL* 3.2 8.0 + - - +
1064B GLN* 1.3 74.8 - - - +
1066B GLY* 1.3 64.4 + - - +
1068B ALA* 3.1 2.6 + - - +
1069B VAL* 2.9 26.9 + - - +
16J PRO* 4.1 16.4 - - + -
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Residues in contact with GLY1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982B PHE* 3.4 24.8 - - - -
1032B PHE* 3.9 12.5 - - - -
1035B CYS* 4.3 6.1 - - - -
1062B VAL 2.8 12.6 + - - -
1063B ALA 3.5 5.2 - - - -
1064B GLN 3.1 0.2 - - - -
1065B ALA* 1.3 76.2 - - - +
1067B LYS* 1.3 63.0 + - - +
1069B VAL 3.3 0.2 + - - -
1070B ALA* 2.9 28.0 + - - +
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Residues in contact with LYS1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B GLU* 3.6 29.9 + - - +
1039B ASN* 5.5 4.6 - - - +
1063B ALA* 2.9 22.6 + - - +
1064B GLN* 2.9 24.7 + - + +
1066B GLY* 1.3 75.4 - - - +
1068B ALA* 1.3 62.8 + - - +
1070B ALA* 3.7 3.4 - - - +
1071B LEU* 3.1 42.6 + - + +
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Residues in contact with ALA1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B HIS* 4.8 4.0 - - + +
978B LEU* 3.7 23.6 - - + -
1064B GLN 3.1 7.3 + - - +
1065B ALA 3.7 6.1 - - - +
1067B LYS* 1.3 77.6 - - - +
1069B VAL* 1.3 60.8 + - - +
1071B LEU* 3.9 3.9 - - - +
1072B TYR* 2.9 32.4 + - - +
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Residues in contact with VAL1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B LEU* 4.6 17.3 - - + -
976B HIS* 3.6 33.7 - - + +
978B LEU* 3.7 22.7 - - + +
979B SER* 4.2 14.4 - - - +
982B PHE* 4.7 1.3 - - + -
1003B LEU* 6.1 0.4 - - + -
1032B PHE* 3.3 31.4 - - + -
1065B ALA 2.9 17.7 + - - +
1068B ALA* 1.3 76.6 - - - +
1070B ALA* 1.3 56.7 + - - +
1072B TYR* 3.9 5.9 - - - +
1073B PHE* 3.0 27.2 + - - +
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Residues in contact with ALA1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B PHE* 3.7 33.1 - - + -
1066B GLY 2.9 19.0 + - - +
1067B LYS* 3.7 5.6 - - - +
1069B VAL* 1.3 73.8 - - - +
1071B LEU* 1.3 69.4 + - + +
1073B PHE* 3.2 8.4 + - - +
1074B GLU* 3.0 25.3 + - - +
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Residues in contact with LEU1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B LYS* 3.1 38.6 + - + +
1068B ALA* 3.9 4.5 - - - +
1070B ALA* 1.3 80.6 - - + +
1072B TYR* 1.3 60.4 + - - +
1074B GLU* 2.8 32.0 + - + +
1075B ASP* 3.0 16.8 + - - +
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Residues in contact with TYR1072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972B TYR* 3.5 41.8 + - + -
973B LEU* 4.4 7.9 - - + -
976B HIS* 3.4 37.4 - + + +
977B GLU* 6.0 0.7 - - - -
1068B ALA 2.9 20.9 + - - +
1069B VAL 3.9 2.5 - - - +
1071B LEU* 1.3 75.6 - - - +
1073B PHE* 1.3 67.1 + - - +
1075B ASP* 3.5 11.5 + - + +
1076B LYS* 3.3 48.3 + - + +
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Residues in contact with PHE1073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969B LEU* 4.0 33.9 - - + -
973B LEU* 4.0 28.9 - - + -
1024B PHE* 4.6 0.2 - + - -
1025B VAL* 4.5 9.0 - - + -
1028B VAL* 3.4 46.7 - - + -
1029B ARG* 4.3 12.6 - - + -
1032B PHE* 4.9 3.1 - + + -
1069B VAL 3.0 15.5 + - - +
1070B ALA* 3.3 11.9 - - - +
1072B TYR* 1.3 77.8 - - - +
1074B GLU* 1.3 68.0 + - - +
1076B LYS* 3.2 5.9 + - + -
1077B LEU* 2.7 53.9 + - + +
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Residues in contact with GLU1074 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029B ARG* 2.8 48.1 + - - +
1070B ALA* 3.0 16.6 + - + +
1071B LEU* 2.8 31.7 + - + +
1073B PHE* 1.3 77.5 - - - +
1075B ASP* 1.3 64.8 - - - +
1077B LEU* 2.9 19.0 + - - +
1078B THR* 3.0 23.8 + - + +
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Residues in contact with ASP1075 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071B LEU* 3.0 13.0 + - - +
1072B TYR* 3.5 15.8 - - + +
1074B GLU* 1.3 72.0 - - - +
1076B LYS* 1.3 63.4 + - + +
1078B THR* 2.7 33.8 + - - -
1079B GLU* 2.8 16.4 + - - +
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Residues in contact with LYS1076 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969B LEU* 3.3 24.5 - - + +
972B TYR* 3.6 46.5 + - + -
973B LEU* 6.1 0.4 - - + -
1072B TYR* 3.3 52.0 + - + +
1073B PHE* 3.2 11.1 + - + +
1075B ASP* 1.3 82.9 - - + +
1077B LEU* 1.3 60.4 + - - +
1079B GLU* 3.8 28.5 + - + +
1080B ILE* 3.2 18.9 + - + +
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Residues in contact with LEU1077 (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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969B LEU* 3.5 28.0 - - + -
1025B VAL* 3.5 32.1 - - + -
1029B ARG* 3.4 28.7 - - - +
1073B PHE* 2.7 22.4 + - + +
1074B GLU* 2.9 21.7 + - - +
1075B ASP 2.9 0.2 + - - -
1076B LYS* 1.3 80.1 - - - +
1078B THR* 1.3 57.7 + - + +
1079B GLU 3.2 1.1 - - - -
1081B TYR* 2.8 33.3 + - + +
1086B PHE* 4.0 22.2 - - + -
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Residues in contact with THR1078 (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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1074B GLU* 3.4 18.1 + - + +
1075B ASP* 2.7 21.5 + - - -
1077B LEU* 1.3 75.3 - - + +
1079B GLU* 1.3 60.3 + - - +
1081B TYR 3.6 11.0 - - - +
1082B SER* 3.7 21.5 - - - -
1085B THR* 6.3 3.8 - - + -
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Residues in contact with GLU1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972B TYR* 5.0 4.7 + - - -
1075B ASP* 2.8 15.1 + - - +
1076B LYS* 4.0 33.3 + - - +
1078B THR* 1.3 80.5 + - - +
1080B ILE* 1.3 70.4 + - + +
1081B TYR* 4.8 0.2 - - - -
1082B SER* 4.7 6.4 + - - -
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Residues in contact with ILE1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934B ILE* 5.2 7.2 - - + -
965B LYS* 3.6 41.9 + - + +
968B ARG* 4.5 23.6 - - + +
969B LEU* 4.4 12.1 - - + -
972B TYR* 4.4 22.9 - - + -
1076B LYS* 3.2 22.4 + - - +
1077B LEU 4.3 0.2 - - - +
1079B GLU* 1.3 92.2 - - + +
1081B TYR* 1.3 85.9 + - + +
1082B SER 3.9 1.5 + - - -
1083B ASP* 5.1 0.2 - - - +
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Residues in contact with TYR1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962B ASP* 3.3 34.5 + - - +
965B LYS* 3.7 30.9 - - + +
966B CYS* 4.4 4.2 - - - -
969B LEU* 4.5 11.2 - - + -
1021B PRO* 3.7 12.9 - - + +
1025B VAL* 5.8 0.7 - - + -
1077B LEU* 2.8 29.3 + - + +
1078B THR* 3.6 11.5 - - - +
1080B ILE* 1.3 92.3 - - + +
1082B SER* 1.3 60.0 + - - +
1083B ASP* 3.4 10.5 - - - +
1084B ARG* 3.2 49.6 - - + +
1085B THR* 5.5 0.5 - - - +
1086B PHE* 3.7 30.3 - + + -
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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
------------------------------------------------------------
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