Contacts of the helix formed by residues 1063 - 1080 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A ARG* 4.0 16.6 - - - +
1061A ALA* 3.4 1.3 - - - +
1062A LEU* 1.3 91.9 - - + +
1064A SER* 1.3 60.8 - - - +
1065A SER* 3.9 8.4 + - - -
1066A ASP* 2.8 34.7 + - - +
1067A LYS* 2.8 13.2 + - - +
101B PRO* 4.9 7.1 - - - +
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Residues in contact with SER1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A LYS* 3.6 34.5 - - - -
1041A ARG* 4.2 4.9 - - - +
1063A THR* 1.3 74.2 - - - +
1065A SER* 1.3 56.5 + - - +
1067A LYS* 3.4 1.7 + - - +
1068A ASN* 2.6 44.2 + - - -
97B GLU* 4.5 4.4 + - - -
150B ARG* 4.5 14.6 + - - -
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Residues in contact with SER1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A THR* 3.0 7.7 + - - -
1064A SER* 1.3 82.8 + - - +
1066A ASP* 1.3 58.1 + - - +
1068A ASN* 3.7 1.6 - - - +
1069A THR* 3.0 37.3 + - - +
96B PRO 3.7 17.3 - - - -
97B GLU* 2.4 50.6 + - - +
101B PRO* 3.6 14.7 - - - +
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Residues in contact with ASP1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968A HIS* 4.9 3.8 - - - -
971A PRO* 4.5 3.3 - - - +
1061A ALA* 3.5 7.2 - - - +
1062A LEU* 3.3 40.0 + - + +
1063A THR* 2.8 24.8 + - - +
1065A SER* 1.3 77.3 - - - +
1067A LYS* 1.3 63.7 + - - +
1068A ASN 3.1 1.3 - - - -
1069A THR* 3.3 8.2 + - - -
1070A TRP* 2.9 51.8 + - - -
101B PRO* 5.7 5.5 - - + +
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Residues in contact with LYS1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035A SER* 3.9 20.8 + - - -
1036A VAL 4.3 3.4 + - - +
1039A ASP 3.7 11.3 + - - -
1040A LYS* 3.4 31.1 + - - +
1041A ARG 3.6 22.2 - - - +
1042A ALA 3.4 21.6 + - - +
1043A PHE* 4.4 7.1 - - + -
1061A ALA* 3.4 8.7 - - - +
1063A THR 2.8 9.4 + - - +
1064A SER 3.7 2.9 - - - +
1066A ASP* 1.3 77.1 - - - +
1068A ASN* 1.3 71.8 + - - +
1070A TRP* 3.4 5.4 + - - +
1071A MET* 3.0 54.2 + - + +
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Residues in contact with ASN1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A LYS 5.2 0.2 + - - -
1064A SER* 2.6 35.4 + - - +
1065A SER 3.7 5.2 - - - +
1066A ASP 3.1 0.4 - - - -
1067A LYS* 1.3 87.2 - - - +
1069A THR* 1.3 65.7 + - - +
1070A TRP 3.2 0.7 - - - -
1071A MET* 3.3 6.3 + - - +
1072A GLU* 3.2 32.9 + - - +
97B GLU* 3.8 20.8 + - - +
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Residues in contact with THR1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A HIS* 4.5 7.8 + - - -
1065A SER* 3.0 22.0 + - - +
1066A ASP* 3.3 17.8 + - - -
1068A ASN* 1.3 74.8 - - - +
1070A TRP* 1.3 70.2 + - - +
1071A MET 3.2 0.5 + - - -
1072A GLU* 3.2 11.4 + - - +
1073A LEU* 3.1 34.9 + - - +
97B GLU* 4.9 6.1 - - - +
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Residues in contact with TRP1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968A HIS* 3.7 34.4 - + + -
969A GLU* 4.1 3.4 - - - -
970A GLY* 3.9 26.1 - - - -
971A PRO* 4.3 2.4 + - - +
972A LEU* 4.1 24.5 - - + +
986A VAL* 3.3 37.2 - - + -
988A LEU* 4.5 16.6 - - + -
993A LEU* 4.6 6.7 - - + -
1043A PHE* 4.4 16.4 - + + -
1061A ALA* 4.5 2.0 - - + -
1066A ASP* 2.9 50.0 + - - +
1067A LYS 3.5 5.8 - - - +
1069A THR* 1.3 85.6 + - - +
1071A MET* 1.3 57.3 + - - +
1073A LEU* 3.9 4.9 - - + +
1074A LEU* 2.9 53.5 + - + +
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Residues in contact with MET1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A ILE* 3.6 25.1 - - + +
1034A ARG* 5.2 0.9 - - - +
1035A SER* 3.4 38.6 - - - +
1043A PHE* 3.8 25.4 - - + -
1067A LYS* 3.0 31.8 + - + +
1068A ASN* 3.6 9.4 - - - +
1069A THR 3.2 0.2 - - - -
1070A TRP* 1.3 74.5 - - - +
1072A GLU* 1.3 64.1 + - + +
1074A LEU* 3.2 4.7 + - - +
1075A GLU* 2.8 49.1 + - - +
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Residues in contact with GLU1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A ASN* 3.2 22.0 - - - +
1069A THR* 3.2 10.4 + - - +
1071A MET* 1.3 77.2 - - + +
1073A LEU* 1.3 59.2 + - + +
1075A GLU* 3.4 8.1 + - - +
1076A GLU* 2.9 31.0 + - - +
1079A ARG* 5.2 1.2 + - - -
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Residues in contact with LEU1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967A ILE* 4.2 17.2 - - + +
968A HIS* 3.3 47.1 - - + +
988A LEU* 4.1 11.6 - - + +
1069A THR* 3.1 21.9 + - - +
1070A TRP* 3.9 5.2 - - + +
1072A GLU* 1.3 78.1 - - + +
1074A LEU* 1.3 61.7 + - - +
1076A GLU* 3.3 9.4 + - + +
1077A ALA* 2.8 31.9 + - - +
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Residues in contact with LEU1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988A LEU* 3.9 30.9 - - + +
993A LEU* 4.6 7.0 - - + -
1028A LEU* 4.6 12.1 - - + -
1033A ILE* 3.7 25.6 - - + -
1043A PHE* 3.8 29.8 - - + -
1045A ILE* 4.4 9.4 - - + -
1070A TRP* 2.9 39.7 + - + +
1071A MET* 3.3 7.0 - - - +
1073A LEU* 1.3 75.7 - - - +
1075A GLU* 1.3 57.9 - - - +
1077A ALA* 2.9 6.0 + - - +
1078A VAL* 2.8 32.1 + - + +
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Residues in contact with GLU1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A ILE* 4.2 33.6 - - + +
1071A MET* 2.8 37.3 + - - +
1072A GLU* 3.9 6.6 - - - +
1074A LEU* 1.3 73.8 - - - +
1076A GLU* 1.3 57.4 + - - +
1078A VAL* 4.0 7.2 - - - +
1079A ARG* 2.8 48.5 + - - +
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Residues in contact with GLU1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A GLU 2.9 15.3 + - - +
1073A LEU* 3.4 15.3 - - + +
1075A GLU* 1.3 73.7 - - - +
1077A ALA* 1.3 68.7 + - - +
1079A ARG* 3.0 31.3 + - - +
1080A ASN* 2.8 51.1 + - - +
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Residues in contact with ALA1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967A ILE* 3.7 14.1 - - + +
988A LEU* 3.6 21.5 - - + -
990A GLU 4.5 3.8 - - - +
1028A LEU* 3.5 26.1 - - + +
1073A LEU 2.8 16.1 + - - +
1074A LEU* 2.9 9.3 + - + +
1076A GLU* 1.3 73.5 - - - +
1078A VAL* 1.3 61.0 + - - +
1080A ASN* 3.0 18.5 + - - +
1081A ALA* 3.1 12.3 + - - +
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Residues in contact with VAL1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028A LEU* 3.9 21.8 - - + +
1029A ASN* 5.4 1.1 - - - -
1031A VAL* 3.6 42.4 - - + +
1032A LEU* 5.4 5.6 - - + -
1033A ILE* 4.5 14.1 - - + -
1074A LEU* 2.8 21.0 + - + +
1075A GLU* 4.0 6.5 - - - +
1077A ALA* 1.3 73.7 - - - +
1079A ARG* 1.3 61.2 + - - +
1081A ALA* 2.8 30.4 + - - +
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Residues in contact with ARG1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A GLU 5.2 1.0 + - - -
1075A GLU* 2.8 44.9 + - - +
1076A GLU* 3.6 38.4 + - - +
1078A VAL* 1.3 76.8 - - - +
1080A ASN* 1.3 62.4 + - - +
1081A ALA 3.2 1.8 + - - -
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Residues in contact with ASN1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990A GLU 6.0 0.4 - - - -
1076A GLU* 2.8 45.8 + - - +
1077A ALA* 3.0 8.3 + - - +
1079A ARG* 1.3 79.3 - - - +
1081A ALA* 1.3 60.4 + - - +
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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
------------------------------------------------------------
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