Contacts of the helix formed by residues 1063 - 1080 (chain E) in PDB entry 3T06
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041E ARG* 4.3 13.9 - - - +
1061E ALA* 3.6 6.2 - - - +
1062E LEU* 1.3 86.0 - - + +
1064E SER* 1.3 64.8 + - - +
1065E SER 3.3 3.8 + - - -
1066E ASP* 3.0 22.9 + - + +
1067E LYS* 3.1 17.3 + - - +
96F PRO 3.8 15.7 - - - +
97F GLU* 3.3 35.3 + - - +
101F PRO* 4.2 11.8 - - + +
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Residues in contact with SER1064 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040E LYS* 3.6 52.1 - - - +
1041E ARG* 4.7 3.2 - - - +
1063E THR* 1.3 73.6 - - - +
1065E SER* 1.3 49.9 + - - +
1067E LYS* 3.1 18.6 + - - +
1068E ASN* 2.2 28.0 + - - +
97F GLU* 2.7 21.7 + - - -
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Residues in contact with SER1065 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063E THR* 3.2 1.3 - - - -
1064E SER* 1.3 74.5 + - - +
1066E ASP* 1.3 64.4 + - - +
1068E ASN* 2.9 11.1 - - - +
1069E THR* 3.1 27.2 + - - -
97F GLU* 2.9 43.3 + - - +
98F LYS* 4.8 6.8 - - - +
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Residues in contact with ASP1066 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968E HIS* 5.3 2.4 + - - -
971E PRO* 4.5 4.3 - - - +
1061E ALA* 3.5 8.1 - - + +
1062E LEU* 3.1 34.4 + - + +
1063E THR* 3.0 29.1 + - + +
1065E SER* 1.3 75.1 + - - +
1067E LYS* 1.3 58.2 + - - +
1069E THR* 3.4 10.6 - - - +
1070E TRP* 2.9 49.1 + - - -
101F PRO* 6.4 1.3 - - + -
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Residues in contact with LYS1067 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035E SER* 2.2 31.8 + - - -
1036E VAL 4.2 8.3 + - - -
1037E ALA* 5.2 2.0 - - - +
1040E LYS* 2.7 25.9 + - - +
1041E ARG 3.2 18.6 - - - +
1042E ALA 3.5 20.8 + - - +
1043E PHE* 4.5 4.7 - - + -
1061E ALA* 3.3 7.3 - - - +
1063E THR 3.1 5.8 + - - +
1064E SER* 3.1 12.2 + - - +
1066E ASP* 1.3 79.7 - - - +
1068E ASN* 1.3 55.8 + - - +
1070E TRP* 3.0 7.9 + - - +
1071E MET* 2.6 58.5 + - + +
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Residues in contact with ASN1068 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064E SER* 2.2 34.2 + - - +
1065E SER* 2.9 16.0 - - - +
1067E LYS* 1.3 75.5 - - + +
1069E THR* 1.3 58.4 + - - +
1071E MET* 4.0 13.2 - - + +
1072E GLU* 2.7 38.2 + - + +
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Residues in contact with THR1069 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968E HIS* 4.3 15.9 - - + +
1065E SER* 3.1 17.1 + - - -
1066E ASP* 3.4 16.9 - - - +
1068E ASN* 1.3 75.8 - - - +
1070E TRP* 1.3 61.6 + - - +
1072E GLU* 4.4 2.5 - - - +
1073E LEU* 3.2 40.9 + - + +
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Residues in contact with TRP1070 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968E HIS* 3.7 35.9 + + - -
969E GLU* 4.1 4.3 - - - -
970E GLY* 4.0 22.3 - - - -
971E PRO 4.7 1.6 + - - -
972E LEU* 3.6 25.6 - - + +
986E VAL* 3.2 41.1 - - + -
988E LEU* 4.4 11.7 - - + -
993E LEU* 4.5 2.0 - - + -
1043E PHE* 4.2 20.9 - + + -
1061E ALA* 4.4 2.5 - - + -
1066E ASP* 2.9 44.2 + - - -
1067E LYS 3.1 8.5 - - - +
1069E THR* 1.3 75.6 - - - +
1071E MET* 1.3 56.1 + - - +
1073E LEU* 3.4 3.9 + - + +
1074E LEU* 2.7 67.5 + - + +
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Residues in contact with MET1071 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033E ILE* 4.1 21.0 - - + +
1034E ARG 4.2 2.0 - - - +
1035E SER* 3.5 26.2 - - - +
1043E PHE* 4.0 20.9 - - + -
1067E LYS* 2.6 55.4 + - + +
1068E ASN* 3.0 10.7 + - + +
1070E TRP* 1.3 73.6 - - - +
1072E GLU* 1.3 54.2 + - - +
1074E LEU* 3.5 6.3 - - - +
1075E GLU* 2.7 54.6 + - - +
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Residues in contact with GLU1072 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068E ASN* 2.7 21.4 + - + +
1069E THR* 4.4 2.9 - - - +
1071E MET* 1.3 72.0 - - - +
1073E LEU* 1.3 66.2 + - - +
1075E GLU* 3.3 16.3 + - - +
1076E GLU* 3.0 32.7 + - - +
1079E ARG* 5.8 1.1 + - - +
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Residues in contact with LEU1073 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925E LYS* 5.3 6.3 - - - +
967E ILE* 4.2 19.0 - - + +
968E HIS* 3.5 40.2 - - + +
988E LEU* 4.1 12.8 - - + +
1069E THR* 3.2 33.4 + - + +
1070E TRP* 3.7 3.6 - - + +
1072E GLU* 1.3 80.5 + - - +
1074E LEU* 1.3 66.7 + - + +
1076E GLU* 3.4 5.8 + - + +
1077E ALA* 3.1 23.6 + - - +
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Residues in contact with LEU1074 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988E LEU* 3.4 34.1 - - + -
993E LEU* 4.4 8.5 - - + -
1028E LEU* 5.9 4.0 - - + -
1033E ILE* 3.7 31.6 - - + -
1043E PHE* 3.5 35.9 - - + -
1045E ILE* 4.0 8.1 - - + -
1070E TRP* 2.7 39.0 + - + +
1071E MET* 3.5 4.9 - - - +
1073E LEU* 1.3 70.6 - - - +
1075E GLU* 1.3 67.8 + - - +
1077E ALA* 3.0 13.7 + - - +
1078E VAL* 3.0 15.6 + - - +
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Residues in contact with GLU1075 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033E ILE* 4.7 18.0 - - + +
1071E MET* 2.7 47.9 + - - +
1072E GLU* 3.3 18.1 + - - +
1074E LEU* 1.3 70.7 - - - +
1076E GLU* 1.3 63.2 + - - +
1078E VAL* 2.8 26.7 - - - +
1079E ARG* 3.1 33.2 + - - +
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Residues in contact with GLU1076 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072E GLU* 3.0 20.6 + - - +
1073E LEU* 3.7 7.4 - - + +
1074E LEU 3.2 0.2 - - - -
1075E GLU* 1.3 74.9 - - - +
1077E ALA* 1.3 65.7 + - - +
1079E ARG* 3.0 38.3 + - - +
1080E ASN* 2.9 44.3 + - - +
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Residues in contact with ALA1077 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967E ILE* 5.3 7.9 - - + -
988E LEU* 4.1 16.4 - - + -
989E LEU 5.2 0.4 - - - +
990E GLU 4.7 8.0 - - - +
1028E LEU* 3.8 25.3 - - + +
1073E LEU 3.1 11.2 + - - +
1074E LEU* 3.0 8.8 + - - +
1076E GLU* 1.3 79.3 - - - +
1078E VAL* 1.3 62.4 + - - +
1080E ASN* 3.4 10.8 + - - +
1081E ALA* 3.4 18.9 + - - +
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Residues in contact with VAL1078 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028E LEU* 3.3 29.5 - - + +
1029E ASN* 5.2 2.2 - - - -
1031E VAL* 3.7 21.5 - - + +
1032E LEU* 5.0 7.6 - - + -
1033E ILE* 4.7 13.0 - - + -
1074E LEU 3.0 14.2 + - - +
1075E GLU* 2.8 30.3 - - - +
1077E ALA* 1.3 74.0 - - - +
1079E ARG* 1.3 69.6 + - + +
1081E ALA* 2.8 23.1 + - + +
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Residues in contact with ARG1079 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072E GLU* 5.8 1.0 + - - +
1075E GLU* 3.1 48.3 + - - +
1076E GLU* 3.0 41.8 + - - +
1078E VAL* 1.3 79.2 - - - +
1080E ASN* 1.3 55.6 + - - +
1081E ALA* 2.7 16.8 + - - -
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Residues in contact with ASN1080 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076E GLU* 2.9 41.7 + - - +
1077E ALA* 3.6 10.4 + - - +
1078E VAL 3.2 0.4 - - - -
1079E ARG* 1.3 73.6 - - - +
1081E ALA* 1.3 57.2 + - - +
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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