Contacts of the helix formed by residues 1000 - 1011 (chain A) in PDB entry 6M0X
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 SER1000 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991A GLU* 5.7 2.5 - - - -
998A LYS* 4.5 17.6 - - - +
999A ILE* 1.3 79.2 - - - +
1001A GLN* 1.3 59.8 + - - +
1002A GLU* 3.7 16.5 + - - +
1003A LYS* 3.6 19.0 + - - +
1004A TYR* 2.8 30.5 + - - +
1119A LEU* 5.7 1.6 - - - -
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Residues in contact with GLN1001 (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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1000A SER* 1.3 74.3 - - - +
1002A GLU* 1.3 59.8 + - - +
1004A TYR* 3.4 8.6 - - - -
1005A ASN* 2.5 68.4 + - - +
1116A LYS* 4.2 25.1 - - - +
1117A PRO* 5.7 2.0 + - - +
1119A LEU* 3.5 27.6 - - + +
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Residues in contact with GLU1002 (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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1000A SER* 3.3 12.8 - - - +
1001A GLN* 1.3 85.1 + - + +
1003A LYS* 1.3 58.7 + - - +
1005A ASN* 3.3 8.6 + - - +
1006A ASP* 2.9 37.6 + - - +
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Residues in contact with LYS1003 (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 ALA 4.1 5.7 + - - -
987A ASP* 3.3 51.9 + - - +
989A GLN* 4.3 12.1 - - - +
999A ILE* 4.0 13.0 - - + -
1000A SER* 3.4 17.5 + - - +
1001A GLN 3.3 0.4 - - - -
1002A GLU* 1.3 76.0 - - - +
1004A TYR* 1.3 61.2 + - - +
1006A ASP* 3.1 11.3 + - + +
1007A ILE* 2.8 36.0 + - + +
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Residues in contact with TYR1004 (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 ASP* 2.4 36.5 + - - +
970A TYR* 2.6 29.2 + - - -
981A LEU* 3.5 23.9 - - + +
983A LEU* 4.0 23.1 - - + -
999A ILE* 4.1 12.0 - - + +
1000A SER 2.8 19.0 + - - +
1001A GLN* 3.5 12.3 - - - +
1003A LYS* 1.3 76.4 - - - +
1005A ASN* 1.3 68.7 + - - +
1007A ILE* 3.4 4.4 + - - +
1008A LYS* 2.8 37.0 + - + +
1117A PRO* 3.3 15.7 - - + +
1119A LEU* 4.0 25.8 - - + -
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Residues in contact with ASN1005 (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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1001A GLN* 2.5 52.0 + - - +
1002A GLU* 3.7 8.7 - - - +
1004A TYR* 1.3 80.4 - - - +
1006A ASP* 1.3 61.8 + - - +
1008A LYS* 3.5 18.0 + - + +
1009A LYS* 3.0 32.0 + - + +
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Residues in contact with ASP1006 (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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1002A GLU* 2.9 28.5 + - - +
1003A LYS* 3.1 12.7 + - + +
1005A ASN* 1.3 77.0 - - - +
1007A ILE* 1.3 60.5 + - + +
1009A LYS* 3.2 7.7 + - - +
1010A LYS* 2.9 40.7 + - - +
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Residues in contact with ILE1007 (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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981A LEU* 3.9 15.9 - - + -
982A GLY 3.8 20.9 - - - +
983A LEU* 3.7 13.7 - - + -
987A ASP* 3.5 35.9 - - + +
999A ILE* 4.0 9.9 - - + -
1003A LYS* 2.8 29.2 + - + +
1004A TYR* 3.8 4.3 - - - +
1006A ASP* 1.3 72.9 - - + +
1008A LYS* 1.3 67.8 + - - +
1010A LYS* 3.6 19.2 - - + +
1011A GLU* 3.0 29.9 + - + +
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Residues in contact with LYS1008 (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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970A TYR* 3.7 27.5 + - - +
981A LEU* 3.6 19.9 - - + +
1004A TYR* 2.8 22.0 + - + +
1005A ASN* 3.5 23.8 + - + +
1007A ILE* 1.3 78.8 - - - +
1009A LYS* 1.3 59.8 + - + +
1011A GLU 3.7 0.2 + - - -
1012A GLY 3.6 1.0 + - - -
1013A VAL* 3.0 64.2 + - + +
1014A ASP 3.8 11.4 + - - -
1015A SER* 3.8 22.6 + - - +
1017A SER 4.9 3.6 + - - -
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Residues in contact with LYS1009 (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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1005A ASN* 3.0 18.4 + - - +
1006A ASP* 3.6 9.0 - - - +
1007A ILE 3.1 0.2 - - - -
1008A LYS* 1.3 73.9 - - + +
1010A LYS* 1.3 58.9 + - - +
1011A GLU 3.0 3.8 - - - -
1012A GLY* 2.8 22.7 + - - -
1013A VAL 4.3 7.6 - - - +
1015A SER* 4.5 24.0 + - - +
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Residues in contact with LYS1010 (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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1006A ASP* 2.9 29.7 + - - +
1007A ILE* 3.6 23.9 - - + +
1009A LYS* 1.3 72.5 - - - +
1011A GLU* 1.3 57.3 + - + +
1012A GLY 3.3 0.4 - - - -
1053A LYS* 2.6 33.3 + - - +
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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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980A ILE 3.5 20.9 - - - +
981A LEU* 4.1 8.3 - - + -
982A GLY* 3.0 31.0 + - - +
1007A ILE* 3.0 22.1 + - + +
1008A LYS 4.3 2.9 - - - +
1009A LYS 3.0 0.2 + - - -
1010A LYS* 1.3 80.3 - - + +
1012A GLY* 1.3 61.5 + - - +
1013A VAL* 3.4 3.5 + - + +
1047A ARG* 2.8 36.1 + - - +
1050A PRO* 3.7 13.2 - - - +
1053A LYS* 3.5 24.7 + - - +
1054A HIS* 4.1 6.3 + - - +
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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