Contacts of the helix formed by residues 1063 - 1081 (chain B) in PDB entry 3KZ1
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 THR1063 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A ASP* 3.5 21.5 - - - +
1041B ARG* 3.7 10.3 - - - +
1061B ALA* 3.7 6.4 - - - +
1062B LEU* 1.3 85.7 - - + +
1064B SER* 1.3 65.7 + - - +
1065B SER* 3.6 10.4 + - - -
1066B ASP* 2.9 23.9 + - - +
1067B LYS* 3.1 16.5 + - - +
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Residues in contact with SER1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A LEU* 3.8 25.8 - - - +
873A ASP* 3.0 20.9 + - - +
880A GLN* 5.0 7.3 + - - -
1040B LYS* 3.6 24.0 - - - +
1041B ARG* 3.8 1.8 - - - +
1063B THR* 1.3 71.5 - - - +
1065B SER* 1.3 70.7 + - - +
1067B LYS* 2.8 21.5 + - - +
1068B ASN* 3.1 19.3 + - - +
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Residues in contact with SER1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A GLN* 3.7 26.3 + - - +
1063B THR* 3.7 9.4 - - - -
1064B SER* 1.3 82.8 + - - +
1066B ASP* 1.3 62.0 + - - +
1068B ASN* 3.3 18.5 + - - +
1069B THR* 3.2 19.6 + - - -
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Residues in contact with ASP1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B HIS* 5.1 4.0 - - - -
971B PRO* 4.9 1.4 - - - +
972B LEU* 4.4 2.9 - - - +
1061B ALA* 3.6 8.7 - - + +
1062B LEU* 3.5 30.5 + - + +
1063B THR* 2.9 30.6 + - - +
1064B SER 3.1 0.2 - - - -
1065B SER* 1.3 75.2 - - - +
1067B LYS* 1.3 62.2 + - - +
1069B THR* 3.3 10.5 + - - -
1070B TRP* 3.1 46.8 + - - -
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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
----------------------------------------------------------
1035B SER* 3.7 23.9 + - - -
1036B VAL 3.6 10.3 + - - -
1039B ASP 3.5 13.9 + - - -
1040B LYS* 3.2 33.2 - - + +
1041B ARG 4.0 13.0 - - - +
1042B ALA 3.2 21.6 + - - -
1043B PHE* 4.0 17.4 - - + -
1061B ALA* 3.7 7.8 - - - +
1063B THR 3.1 9.0 + - - +
1064B SER 2.8 9.2 + - - +
1066B ASP* 1.3 78.3 - - - +
1068B ASN* 1.3 67.2 + - - +
1070B TRP* 3.3 4.6 + - - +
1071B MET* 2.9 36.3 + - + +
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Residues in contact with ASN1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064B SER* 3.1 21.4 + - - +
1065B SER* 3.7 9.1 - - - +
1066B ASP 3.3 0.4 - - - -
1067B LYS* 1.3 85.0 - - - +
1069B THR* 1.3 59.5 + - - +
1071B MET* 3.3 9.2 + - - +
1072B GLU* 2.9 44.5 + - + +
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Residues in contact with THR1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B HIS* 4.4 11.4 - - + +
1065B SER* 3.2 14.8 + - - -
1066B ASP* 3.3 14.6 + - - +
1067B LYS 3.3 1.0 - - - -
1068B ASN* 1.3 79.0 - - - +
1070B TRP* 1.3 63.7 + - - +
1072B GLU* 3.4 5.9 + - - +
1073B LEU* 3.1 47.0 + - + +
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Residues in contact with TRP1070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B HIS* 3.5 38.2 - + - -
969B GLU* 4.0 1.8 - - - -
970B GLY* 3.8 21.6 - - - -
971B PRO* 6.1 0.4 - - - +
972B LEU* 3.5 33.5 - - + +
986B VAL* 3.4 43.5 - - + -
988B LEU* 4.6 13.7 - - + -
993B LEU* 4.7 1.8 - - + -
1043B PHE* 3.9 18.8 - + + -
1061B ALA* 4.7 3.6 - - + -
1066B ASP* 3.1 43.7 + - - -
1067B LYS 3.3 6.5 + - - +
1069B THR* 1.3 77.7 - - - +
1071B MET* 1.3 52.3 + - - +
1073B LEU* 4.6 3.6 - - - -
1074B LEU* 2.8 67.0 + - + +
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Residues in contact with MET1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033B ILE* 4.2 16.6 - - + +
1034B ARG* 4.6 2.2 - - - -
1035B SER* 3.5 30.3 - - - +
1043B PHE* 3.8 26.9 - - + -
1067B LYS* 2.9 37.1 + - + +
1068B ASN* 3.5 11.7 - - - +
1070B TRP* 1.3 76.4 - - - +
1072B GLU* 1.3 57.6 + - + +
1074B LEU* 4.0 3.5 - - - +
1075B GLU* 2.9 59.2 + - - +
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Residues in contact with GLU1072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A LYS* 5.5 4.9 + - - -
1068B ASN* 2.9 30.9 + - - +
1069B THR* 4.1 5.4 + - - +
1071B MET* 1.3 73.7 - - + +
1073B LEU* 1.3 68.5 + - + +
1075B GLU* 4.0 9.0 - - - +
1076B GLU* 3.1 25.5 + - - +
1079B ARG* 5.8 0.2 + - - -
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Residues in contact with LEU1073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B ILE* 4.3 18.7 - - + +
968B HIS* 3.4 39.7 - - + +
988B LEU* 3.9 17.4 - - + +
1069B THR* 3.1 32.5 + - + +
1070B TRP* 4.0 3.1 - - - +
1072B GLU* 1.3 80.5 - - + +
1074B LEU* 1.3 54.8 + - - +
1076B GLU* 3.4 6.7 + - + +
1077B ALA* 3.0 30.0 + - - +
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Residues in contact with LEU1074 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988B LEU* 3.4 35.4 - - + -
993B LEU* 4.1 11.0 - - + -
1028B LEU* 5.7 4.0 - - + -
1033B ILE* 4.0 30.7 - - + -
1043B PHE* 3.6 36.8 - - + -
1045B ILE* 3.8 13.5 - - + -
1070B TRP* 2.8 39.9 + - + +
1071B MET 4.0 0.2 - - - +
1073B LEU* 1.3 68.9 - - - +
1075B GLU* 1.3 64.1 + - - +
1076B GLU 3.1 2.8 + - - -
1077B ALA* 3.3 2.9 + - - +
1078B VAL* 3.1 28.2 + - - +
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Residues in contact with GLU1075 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A GLN* 4.5 16.9 + - - +
1033B ILE* 4.3 26.2 - - + +
1071B MET* 2.9 48.2 + - - +
1072B GLU* 4.1 9.2 + - - +
1074B LEU* 1.3 73.6 - - - +
1076B GLU* 1.3 58.7 + - - +
1078B VAL* 4.3 3.4 - - - +
1079B ARG* 3.4 41.8 + - - +
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Residues in contact with GLU1076 (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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1072B GLU 3.1 19.0 + - - +
1073B LEU* 3.6 8.1 - - + +
1074B LEU 3.1 0.8 - - - -
1075B GLU* 1.3 75.4 - - - +
1077B ALA* 1.3 66.7 + - - +
1078B VAL 3.2 1.7 + - - -
1079B ARG* 3.2 29.8 + - - +
1080B ASN* 3.1 37.8 + - - +
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Residues in contact with ALA1077 (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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967B ILE* 3.6 30.0 - - + +
988B LEU* 3.9 16.6 - - + -
989B LEU 4.5 0.2 - - - +
990B GLU 4.2 5.1 - - - +
1028B LEU* 4.1 11.4 - - + +
1073B LEU 3.0 17.4 + - - +
1074B LEU* 3.3 3.1 + - - +
1076B GLU* 1.3 76.5 - - - +
1078B VAL* 1.3 57.1 + - - +
1080B ASN* 3.5 10.1 + - - +
1081B ALA* 3.0 27.9 + - - +
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Residues in contact with VAL1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B LEU* 4.0 29.0 - - + +
1031B VAL* 3.9 31.6 - - + +
1033B ILE* 3.8 23.8 - - + +
1074B LEU 3.1 17.7 + - - +
1075B GLU* 4.3 4.0 - - - +
1077B ALA* 1.3 73.5 - - - +
1079B ARG* 1.3 67.7 + - - +
1080B ASN 3.2 0.2 - - - -
1081B ALA* 2.9 22.7 + - - +
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Residues in contact with ARG1079 (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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714A GLN* 4.8 12.9 - - - +
715A ASN* 5.8 3.8 + - - +
1072B GLU 5.8 0.4 + - - -
1075B GLU* 3.4 33.1 + - - +
1076B GLU* 3.2 32.2 + - - +
1078B VAL* 1.3 79.8 - - - +
1080B ASN* 1.3 64.2 + - - +
1081B ALA 4.4 2.8 - - - -
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Residues in contact with ASN1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B ILE* 6.1 2.2 - - - +
990B GLU 5.7 1.8 - - - +
1076B GLU* 3.1 34.6 + - - +
1077B ALA* 3.6 11.8 - - - +
1078B VAL 3.2 0.2 - - - -
1079B ARG* 1.3 79.9 - - - +
1081B ALA* 1.3 57.4 + - - +
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Residues in contact with ALA1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990B GLU 4.3 9.9 - - - +
991B ASP* 5.0 4.5 - - + -
1028B LEU* 3.9 23.1 - - + -
1029B ASN* 3.2 32.7 - - + +
1077B ALA 3.0 14.7 + - - +
1078B VAL 2.9 15.8 + - - +
1079B ARG 4.4 2.5 - - - -
1080B ASN* 1.3 81.8 - - - +
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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
------------------------------------------------------------
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