Contacts of the helix formed by residues 1067 - 1078 (chain A) in PDB entry 3LXK
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 PRO1067 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923A ALA* 4.5 15.5 - - + -
927A LEU* 5.7 3.4 - - + -
1021A PHE* 3.8 23.8 - - + -
1065A ALA 3.3 6.7 - - - +
1066A CYS* 1.4 93.2 - - - +
1068A ALA* 1.3 66.3 + - - +
1069A GLU* 3.8 16.4 - - - +
1070A VAL* 3.2 26.1 + - + -
1071A HIS* 3.2 10.0 + - - +
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Residues in contact with ALA1068 (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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1066A CYS 3.3 4.3 + - - -
1067A PRO* 1.3 71.0 - - - +
1069A GLU* 1.3 67.5 + - + +
1071A HIS* 3.3 8.8 + - - +
1072A GLU* 2.9 36.0 + - + +
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Residues in contact with GLU1069 (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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1067A PRO* 3.6 13.3 - - - +
1068A ALA* 1.3 91.4 + - + +
1070A VAL* 1.3 57.6 - - + +
1072A GLU* 3.5 9.4 + - - +
1073A LEU* 3.0 30.3 + - - +
1098A LEU* 3.5 37.5 - - + +
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Residues in contact with VAL1070 (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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927A LEU* 3.8 29.2 - - + -
1017A LEU* 4.9 9.4 - - + +
1021A PHE* 3.7 30.5 - - + -
1066A CYS* 3.9 5.6 - - - -
1067A PRO* 3.2 25.0 + - + +
1069A GLU* 1.3 74.1 - - + +
1071A HIS* 1.3 59.5 + - - +
1073A LEU* 3.0 10.6 + - + +
1074A MET* 2.9 46.1 + - + +
1095A LEU* 6.0 1.6 - - + -
1098A LEU* 4.1 11.0 - - + -
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Residues in contact with HIS1071 (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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1060A LEU 4.5 7.3 + - - -
1061A PRO* 4.5 1.9 - - - +
1062A ALA* 3.5 43.9 + - + +
1066A CYS* 3.8 13.2 - - + +
1067A PRO 3.2 8.6 + - - +
1068A ALA* 3.5 10.9 + - - +
1070A VAL* 1.3 79.9 - - - +
1072A GLU* 1.3 65.7 + - - +
1074A MET* 3.2 19.2 + - + +
1075A LYS* 3.0 55.8 + - + +
1078A TRP* 5.4 1.6 - + - -
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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 ALA* 2.9 20.9 + - + +
1069A GLU* 3.6 12.3 - - - +
1071A HIS* 1.3 80.7 + - - +
1073A LEU* 1.3 61.9 + - + +
1075A LYS* 2.8 40.6 + - - +
1076A LEU* 3.2 29.3 + - + +
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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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1017A LEU* 4.6 9.2 - - + -
1069A GLU 3.0 14.1 + - - +
1070A VAL* 3.0 12.1 + - + +
1072A GLU* 1.3 73.3 - - + +
1074A MET* 1.3 64.3 + - - +
1076A LEU* 3.2 17.8 + - + +
1077A CYS* 3.0 27.5 + - - -
1091A LEU* 4.0 21.9 - - + +
1094A GLN* 3.4 40.2 - - + +
1095A LEU* 3.8 24.9 - - + -
1098A LEU* 3.8 27.1 - - + -
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Residues in contact with MET1074 (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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1014A GLY* 3.9 13.2 - - - +
1017A LEU* 3.9 19.0 - - + +
1018A TYR* 3.9 26.0 - - - +
1021A PHE* 4.5 1.1 - - + -
1061A PRO 5.8 0.2 - - - +
1062A ALA* 5.7 0.2 - - - -
1063A PRO* 3.9 19.5 - - + -
1066A CYS* 3.9 18.4 - - - -
1070A VAL* 2.9 35.5 + - + +
1071A HIS* 3.4 14.1 - - + +
1073A LEU* 1.3 74.2 - - - +
1075A LYS* 1.3 64.4 + - - +
1077A CYS* 3.1 9.1 + - - +
1078A TRP* 3.0 57.7 + - + -
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Residues in contact with LYS1075 (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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1059A ARG* 5.4 10.2 + - + -
1071A HIS* 3.0 41.4 + - + +
1072A GLU* 2.8 47.7 + - - +
1073A LEU 3.3 0.2 - - - -
1074A MET* 1.3 78.3 - - - +
1076A LEU* 1.3 61.6 + - + +
1078A TRP* 3.2 33.6 + - + +
1079A ALA* 3.4 2.3 + - - -
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Residues in contact with LEU1076 (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* 3.2 19.8 + - + +
1073A LEU* 3.6 23.8 - - + +
1074A MET 3.2 0.4 - - - -
1075A LYS* 1.3 72.6 - - + +
1077A CYS* 1.3 65.4 + - - +
1078A TRP 3.0 1.8 - - - -
1079A ALA* 3.1 22.1 + - + +
1084A ASP 4.5 4.1 - - - +
1085A ARG* 3.7 0.7 - - - -
1086A PRO* 3.3 33.6 - - + +
1094A GLN* 5.2 6.5 - - - +
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Residues in contact with CYS1077 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A VAL* 3.5 30.1 - - - +
1011A TRP* 3.4 11.3 + - - -
1013A PHE* 4.0 13.2 - - - -
1014A GLY* 3.7 15.5 - - - -
1017A LEU* 4.5 2.9 - - - -
1073A LEU 3.0 19.2 + - - -
1074A MET 3.3 9.0 - - - +
1076A LEU* 1.3 76.0 - - - +
1078A TRP* 1.3 58.5 + - - +
1079A ALA 3.3 0.2 - - - -
1085A ARG* 3.2 24.3 - - - -
1086A PRO* 4.0 1.1 - - - +
1091A LEU* 3.9 33.2 - - - -
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Residues in contact with TRP1078 (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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1011A TRP* 3.2 53.7 + + + -
1014A GLY* 3.3 23.8 - - - -
1015A VAL* 3.4 22.1 - - + +
1018A TYR* 4.3 6.5 - + + -
1034A PHE* 6.6 0.2 - + - -
1059A ARG* 2.9 56.1 + - + +
1060A LEU* 4.0 39.7 - - + -
1071A HIS* 5.4 2.5 - + - -
1074A MET* 3.0 48.6 + - + +
1075A LYS* 3.2 18.5 + - + +
1076A LEU 3.0 1.0 - - - -
1077A CYS* 1.3 77.8 - - - +
1079A ALA* 1.3 64.1 + - - -
1080A PRO* 3.9 0.3 - - - +
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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
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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