Contacts of the helix formed by residues 1003 - 1011 (chain A) in PDB entry 5LUQ
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 SER1003 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995A PHE* 3.2 23.6 - - - -
1000A LYS* 3.1 36.2 + - - +
1001A PHE 3.6 0.7 + - - -
1002A GLU* 1.3 77.3 - - - +
1004A GLN* 1.3 65.7 + - - +
1005A ASP 2.9 2.4 + - - -
1007A VAL* 3.3 24.8 + - - +
1054A VAL* 3.4 31.8 - - - +
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Residues in contact with GLN1004 (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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956A PRO* 6.0 7.9 - - + -
960A GLN* 5.3 10.3 - - + +
1001A PHE* 3.4 19.9 + - - +
1003A SER* 1.3 79.5 + - - +
1005A ASP* 1.3 56.5 + - - +
1007A VAL* 4.6 0.7 - - - +
1008A ALA* 2.6 51.2 + - + +
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Residues in contact with ASP1005 (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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955A ALA 4.4 8.3 - - - +
956A PRO* 4.8 4.2 - - - +
959A TYR* 2.8 45.4 - - + -
960A GLN* 4.4 17.4 + - - +
963A LYS* 4.5 1.1 - - + -
1001A PHE 3.4 14.9 - - - +
1002A GLU* 2.4 30.7 - - - +
1003A SER 2.9 1.6 + - - -
1004A GLN* 1.3 73.6 - - - +
1006A THR* 1.3 69.6 + - - +
1007A VAL 3.2 0.2 - - - -
1008A ALA* 2.7 15.8 + - - +
1009A LEU* 2.9 20.4 + - - +
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Residues in contact with THR1006 (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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963A LYS* 1.9 42.4 + - + +
967A PRO* 6.1 3.6 - - + -
992A ILE* 3.4 26.8 - - + +
995A PHE* 3.0 23.2 - - - -
1005A ASP* 1.3 78.2 - - - +
1007A VAL* 1.3 64.9 + - - +
1009A LEU* 4.1 6.9 - - - +
1010A LEU* 2.8 54.7 + - + +
1031A ARG* 5.8 0.2 - - + -
1035A GLU* 4.1 5.6 - - - +
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Residues in contact with VAL1007 (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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995A PHE* 4.4 2.9 - - + -
1003A SER 3.3 19.1 - - - +
1004A GLN 4.6 0.7 - - - +
1005A ASP 3.2 1.0 - - - -
1006A THR* 1.3 74.1 - - - +
1008A ALA* 1.3 50.5 + - - +
1010A LEU* 3.4 12.4 - - + +
1011A GLU* 2.3 47.4 + - + +
1032A CYS* 6.0 1.8 - - - -
1035A GLU* 2.7 36.3 - - - +
1036A PHE* 6.5 0.7 - - + -
1054A VAL* 4.7 16.8 - - + +
1059A LEU* 5.4 11.9 - - + -
1062A ARG* 5.6 5.8 - - + -
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Residues in contact with ALA1008 (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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960A GLN* 5.4 8.5 - - - +
1004A GLN* 2.6 39.5 + - + +
1005A ASP* 2.7 10.4 + - - +
1007A VAL* 1.3 71.3 - - - +
1009A LEU* 1.3 66.4 + - + +
1011A GLU* 3.0 29.5 + - - +
1012A ALA* 3.0 9.2 + - - +
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Residues in contact with LEU1009 (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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960A GLN* 3.4 39.9 - - + +
961A LEU* 5.3 0.9 - - + -
963A LYS* 3.3 26.0 - - + -
964A ARG* 3.1 56.0 - - + +
1005A ASP 2.9 26.0 + - - +
1006A THR* 4.1 2.2 - - - +
1008A ALA* 1.3 68.7 - - + +
1010A LEU* 1.3 57.7 + - - +
1012A ALA* 2.2 39.8 + - - +
1013A ILE* 2.8 7.5 + - + +
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Residues in contact with LEU1010 (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 PRO* 5.8 7.0 - - + -
1006A THR* 2.8 48.5 + - + +
1007A VAL* 3.4 19.3 - - + +
1009A LEU* 1.3 72.2 - - - +
1011A GLU* 1.3 68.0 + - + +
1013A ILE* 2.4 37.8 + - + +
1014A LEU 3.1 5.7 + - - -
1028A PHE* 3.0 45.9 - - + -
1031A ARG* 3.4 31.9 - - + -
1032A CYS* 3.7 18.2 - - - +
1035A GLU* 4.7 4.0 - - - +
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Residues in contact with GLU1011 (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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1007A VAL* 2.3 49.8 + - + +
1008A ALA* 3.0 23.9 - - - +
1010A LEU* 1.3 78.2 - - + +
1012A ALA* 1.3 53.7 + - - +
1014A LEU* 3.1 24.2 - - - +
1015A ASP 4.5 0.2 + - - -
1028A PHE* 4.6 2.5 - - - -
1062A ARG* 2.7 55.3 + - + +
1066A LEU* 4.1 16.8 - - + +
1075A ARG* 4.2 12.0 + - - +
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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