Contacts of the helix formed by residues 1045 - 1056 (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 PRO1045 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1044A VAL* 1.4 90.4 - - + +
1046A ALA* 1.3 61.0 + - - +
1047A LEU* 4.5 5.4 - - + +
1048A SER* 3.0 23.6 + - - +
1049A ARG* 2.9 25.6 + - - -
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Residues in contact with ALA1046 (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* 4.2 11.9 - - + -
1035A LEU* 5.6 7.9 - - + -
1038A MET* 4.1 7.7 - - - +
1044A VAL 3.9 0.2 + - - -
1045A PRO* 1.3 71.5 - - - +
1047A LEU* 1.3 57.5 + - - +
1049A ARG* 3.3 27.2 + - - +
1050A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU1047 (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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986A PRO* 5.4 13.5 - - + -
991A ILE* 4.0 24.8 - - + +
994A TYR* 6.1 1.1 - - + -
999A LEU* 3.8 51.8 - - + +
1045A PRO* 3.3 4.8 - - + +
1046A ALA* 1.3 77.4 - - - +
1048A SER* 1.3 65.6 + - - +
1050A LEU* 3.4 2.1 + - - +
1051A LEU* 2.9 32.7 + - + +
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Residues in contact with SER1048 (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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1044A VAL* 4.6 6.3 - - - -
1045A PRO* 3.0 32.5 + - - +
1047A LEU* 1.3 84.0 - - - +
1049A ARG* 1.3 58.3 + - - +
1051A LEU* 3.6 6.3 - - - +
1052A GLU* 2.8 38.3 + - - +
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Residues in contact with ARG1049 (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 LEU* 5.8 4.9 - - - +
1038A MET* 4.3 34.6 - - + +
1044A VAL* 3.1 45.4 + - + +
1045A PRO 2.9 17.1 + - - -
1046A ALA* 3.5 24.6 - - - +
1048A SER* 1.3 76.2 - - - +
1050A LEU* 1.3 57.2 + - - +
1052A GLU* 3.4 13.6 - - - +
1053A LEU* 2.9 29.8 + - - +
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Residues in contact with LEU1050 (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* 3.5 47.8 - - + +
992A PHE* 4.1 12.1 - - + -
994A TYR 5.8 0.2 - - - +
999A LEU* 4.2 9.4 - - + -
1034A PHE* 3.7 41.5 - - + -
1038A MET* 3.9 15.6 - - + -
1046A ALA 2.9 19.7 + - - +
1047A LEU 3.8 4.3 - - - +
1049A ARG* 1.3 69.5 - - - +
1051A LEU* 1.3 60.7 + - - +
1053A LEU* 3.3 6.3 + - + +
1054A LEU* 2.8 49.3 + - + +
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Residues in contact with LEU1051 (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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996A PRO* 4.1 26.9 - - + +
999A LEU* 4.1 21.7 - - + +
1000A SER* 3.7 28.9 - - - +
1047A LEU* 2.9 24.1 + - + +
1048A SER* 3.6 7.0 - - - +
1050A LEU* 1.3 76.4 - - - +
1052A GLU* 1.3 52.1 + - - +
1054A LEU* 3.2 4.1 + - + -
1055A GLU* 2.7 72.8 + - + +
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Residues in contact with GLU1052 (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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1044A VAL* 5.1 7.3 - - - +
1048A SER* 2.8 26.9 + - - +
1049A ARG* 3.4 19.8 - - - +
1051A LEU* 1.3 72.6 - - - +
1053A LEU* 1.3 63.3 + - - +
1055A GLU* 3.0 12.8 + - - +
1056A GLU* 3.0 38.8 + - - +
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Residues in contact with LEU1053 (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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1034A PHE* 3.6 31.6 - - + -
1037A MET* 3.8 37.9 - - + +
1038A MET* 3.8 23.1 - - + -
1049A ARG 2.9 20.0 + - - +
1050A LEU* 3.4 6.1 - - + +
1052A GLU* 1.3 73.2 - - - +
1054A LEU* 1.3 67.6 + - + +
1056A GLU* 3.5 10.0 + - - +
1058A GLN* 3.1 65.0 + - + +
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Residues in contact with LEU1054 (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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994A TYR 4.5 5.2 - - - +
996A PRO* 4.5 17.7 - - + -
999A LEU* 4.0 24.7 - - + -
1011A TRP* 3.9 30.7 - - + -
1034A PHE* 4.1 21.8 - - + -
1050A LEU* 2.8 33.8 + - + +
1051A LEU* 3.6 4.5 - - - +
1053A LEU* 1.3 74.5 - - + +
1055A GLU* 1.3 58.7 + - - +
1057A GLY* 3.0 15.4 + - - -
1058A GLN 3.6 15.0 - - - +
1059A ARG* 3.0 28.9 + - - +
1080A PRO* 5.9 1.6 - - - +
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Residues in contact with GLU1055 (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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996A PRO* 5.5 4.0 - - + -
1000A SER* 5.0 3.3 - - - -
1051A LEU* 2.7 57.7 + - + +
1052A GLU* 3.0 10.2 + - - +
1054A LEU* 1.3 73.5 - - + +
1056A GLU* 1.3 59.5 + - + +
1057A GLY* 3.2 0.9 + - - -
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Residues in contact with GLU1056 (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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1052A GLU* 3.0 33.3 + - - +
1053A LEU* 3.8 6.0 + - - +
1054A LEU 3.2 0.4 - - - -
1055A GLU* 1.3 76.5 - - + +
1057A GLY* 1.3 58.9 + - - +
1058A GLN* 3.5 26.6 + - + +
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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