Contacts of the helix formed by residues 1029 - 1038 (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 SER1029 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A TYR* 4.4 0.7 - - - -
1022A THR* 5.4 2.0 - - - -
1024A CYS* 5.7 2.2 - - - +
1025A ASP 3.2 12.7 + - - -
1026A LYS* 3.1 21.7 + - - -
1027A SER 3.6 0.4 - - - -
1028A CYS* 1.3 79.4 - - - +
1030A PRO* 1.3 78.4 - - - +
1031A SER* 3.1 10.4 + - - -
1032A ALA* 3.2 17.0 + - - +
1033A GLU* 2.9 21.0 + - - +
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Residues in contact with PRO1030 (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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992A PHE* 4.0 20.4 - - + +
993A TRP* 4.0 20.2 - - + -
1015A VAL* 3.7 28.0 - - + -
1018A TYR* 4.0 19.4 - - + -
1019A GLU* 4.3 10.8 - - + +
1022A THR* 5.7 0.7 - - - +
1029A SER* 1.3 86.7 - - - +
1031A SER* 1.3 55.2 + - - +
1034A PHE* 3.0 35.5 + - - +
1060A LEU* 4.1 20.6 - - + +
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Residues in contact with SER1031 (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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992A PHE* 3.3 35.5 - - - -
993A TRP* 5.2 5.2 - - - -
1029A SER* 3.2 10.5 + - - -
1030A PRO* 1.3 75.9 - - - +
1032A ALA* 1.3 73.9 + - - +
1035A LEU* 3.0 38.3 + - - +
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Residues in contact with ALA1032 (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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1026A LYS 3.4 25.8 - - - +
1027A SER* 3.7 15.0 - - - +
1029A SER* 3.2 7.4 + - - +
1031A SER* 1.3 81.8 + - - +
1033A GLU* 1.3 59.3 + - - +
1035A LEU* 3.9 6.0 - - - +
1036A ARG* 3.1 29.0 + - - +
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Residues in contact with GLU1033 (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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1018A TYR* 3.9 11.4 - - - +
1027A SER 5.2 2.1 - - - +
1028A CYS* 4.1 13.0 - - - +
1029A SER 2.9 16.8 + - - +
1032A ALA* 1.3 74.7 - - - +
1034A PHE* 1.3 65.3 + - - +
1036A ARG* 2.8 44.5 + - - +
1037A MET* 2.9 37.6 + - - +
1060A LEU* 3.9 8.5 - - + -
1061A PRO* 3.5 39.9 - - + +
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Residues in contact with PHE1034 (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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992A PHE* 3.7 35.0 - + + -
1011A TRP* 5.8 2.5 - + - -
1015A VAL* 5.8 1.3 - - + -
1030A PRO 3.0 24.8 + - - +
1033A GLU* 1.3 76.2 - - - +
1035A LEU* 1.3 51.1 + - - +
1037A MET* 3.1 10.5 + - - +
1038A MET* 2.7 53.9 + - + +
1050A LEU* 3.7 18.4 - - + -
1053A LEU* 3.6 29.2 - - + -
1054A LEU* 4.1 18.4 - - + -
1059A ARG* 4.5 1.6 - - - -
1060A LEU* 3.5 49.8 - - + +
1078A TRP* 6.6 0.2 - + - -
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Residues in contact with LEU1035 (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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992A PHE* 3.8 20.0 - - + -
1031A SER* 3.0 33.6 + - - +
1032A ALA* 3.9 5.2 - - - +
1034A PHE* 1.3 75.5 - - - +
1036A ARG* 1.3 61.8 + - - +
1038A MET* 3.1 38.8 + - + +
1046A ALA* 5.6 8.5 - - + -
1049A ARG* 5.8 4.7 - - - +
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Residues in contact with ARG1036 (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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1032A ALA 3.1 18.7 + - - +
1033A GLU* 2.8 41.2 + - - +
1035A LEU* 1.3 78.3 - - - +
1037A MET* 1.3 67.9 + - - +
1038A MET 3.8 4.7 - - - +
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Residues in contact with MET1037 (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 GLU* 2.9 45.2 + - - +
1034A PHE* 3.5 19.1 - - - +
1036A ARG* 1.3 86.3 - - - +
1038A MET* 1.3 63.3 + - - +
1053A LEU* 3.8 18.4 - - + +
1058A GLN* 3.7 35.7 + - + +
1059A ARG 3.4 29.4 - - - +
1060A LEU* 4.4 1.3 - - - -
1061A PRO* 4.4 4.7 - - - -
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Residues in contact with MET1038 (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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991A ILE* 5.3 0.9 - - - -
992A PHE* 3.5 19.1 - - + -
1034A PHE* 2.7 57.2 + - + +
1035A LEU* 3.1 33.9 + - + +
1036A ARG 3.8 4.7 - - - +
1037A MET* 1.3 76.5 - - - +
1046A ALA* 4.1 11.9 - - - +
1049A ARG* 4.3 31.9 - - + +
1050A LEU* 3.9 34.1 - - + +
1053A LEU* 3.8 17.9 - - + -
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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