Contacts of the helix formed by residues 1042 - 1054 (chain A) in PDB entry 4N78
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 ARG1042 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A VAL* 4.4 0.7 - - - -
1040A GLY 5.7 0.9 - - - -
1041A GLU* 1.3 79.4 - - - +
1043A LEU* 1.3 57.8 + - + +
1044A ASP* 4.3 9.4 - - + +
1045A ALA* 2.6 43.6 + - + +
1046A LYS* 2.8 18.8 + - - +
1049A ARG* 5.5 1.2 - - - +
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Residues in contact with LEU1043 (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 ARG* 6.5 1.3 - - + -
1035A VAL* 5.2 5.2 - - + +
1037A VAL* 4.1 24.1 - - + +
1042A ARG* 1.3 73.7 - - + +
1044A ASP* 1.3 96.7 + - - +
1046A LYS* 4.2 8.3 - - - +
1047A MET* 2.6 52.5 + - + +
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Residues in contact with ASP1044 (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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1042A ARG* 3.0 8.7 - - + +
1043A LEU* 1.3 105.0 - - - +
1045A ALA* 1.3 58.3 + - + +
1047A MET* 4.8 1.7 - - - +
1048A LYS* 3.0 36.6 + - - +
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Residues in contact with ALA1045 (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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1042A ARG* 2.6 29.9 + - + +
1044A ASP* 1.3 76.1 - - - +
1046A LYS* 1.3 51.8 + - - -
1048A LYS* 3.6 14.4 - - + +
1049A ARG* 2.5 47.4 + - - +
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Residues in contact with LYS1046 (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 VAL* 3.4 36.8 - - + +
1036A HIS 3.1 15.6 + - - +
1037A VAL* 5.3 2.9 - - + -
1038A LYS* 5.3 2.0 - - - +
1041A GLU* 2.8 38.6 + - - -
1042A ARG 2.8 13.0 + - - +
1043A LEU* 3.9 5.6 - - - +
1045A ALA* 1.3 77.6 - - - +
1047A MET* 1.3 61.2 + - - +
1048A LYS 3.1 1.6 - - - -
1049A ARG* 2.9 33.1 + - + +
1050A LEU* 2.8 29.9 + - + +
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Residues in contact with MET1047 (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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1032A LEU* 4.1 29.1 - - + +
1033A PRO 3.8 18.2 - - - +
1034A ARG* 4.6 4.0 - - - -
1035A VAL* 3.5 33.4 - - + -
1043A LEU* 2.6 45.7 + - + +
1044A ASP* 4.8 2.2 - - - +
1046A LYS* 1.3 73.4 - - - +
1048A LYS* 1.3 55.6 + - - +
1050A LEU* 3.5 9.7 + - - +
1051A GLU* 3.0 29.4 + - - +
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Residues in contact with LYS1048 (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 ASP* 3.0 29.3 + - - +
1045A ALA* 3.6 16.9 - - + +
1047A MET* 1.3 75.9 - - - +
1049A ARG* 1.3 69.1 + - + +
1051A GLU* 3.5 12.3 + - - +
1052A SER* 3.2 23.4 + - - -
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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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1041A GLU* 5.1 9.3 - - - +
1042A ARG 4.9 2.4 + - - +
1045A ALA* 2.5 49.6 + - - +
1046A LYS* 2.9 46.7 + - + +
1048A LYS* 1.3 79.8 - - + +
1050A LEU* 1.3 64.1 + - - +
1052A SER* 3.0 18.3 + - - -
1053A LYS* 3.2 10.2 + - - +
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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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1032A LEU* 3.8 30.7 - - + -
1033A PRO* 4.8 8.1 - - + +
1035A VAL* 4.7 25.4 - - + -
1046A LYS* 2.8 17.7 + - + +
1047A MET* 3.7 9.9 - - - +
1049A ARG* 1.3 76.4 - - - +
1051A GLU* 1.3 58.0 + - - +
1053A LYS* 3.0 36.0 + - + +
1054A TYR* 3.2 31.1 + - + -
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Residues in contact with GLU1051 (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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1030A ASN* 3.2 40.4 + - - +
1032A LEU* 3.7 12.8 - - + +
1047A MET 3.0 19.2 + - - +
1048A LYS* 3.6 12.7 - - - +
1049A ARG 3.2 0.2 - - - -
1050A LEU* 1.3 76.9 - - - +
1052A SER* 1.3 56.4 + - - +
1054A TYR* 3.8 3.9 + - - +
1055A ALA* 3.2 23.9 + - - +
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Residues in contact with SER1052 (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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1048A LYS 3.2 12.8 + - - -
1049A ARG* 3.0 13.9 + - - -
1051A GLU* 1.3 76.9 - - - +
1053A LYS* 1.3 64.1 + - - +
1055A ALA* 3.3 20.0 - - - +
1056A PRO* 3.9 3.1 - - - +
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Residues in contact with LYS1053 (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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1049A ARG 3.2 7.7 + - - +
1050A LEU* 3.0 26.8 + - + +
1052A SER* 1.3 77.4 - - - +
1054A TYR* 1.3 95.2 + - + +
1055A ALA 3.3 0.2 - - - -
1056A PRO* 3.4 15.1 - - - +
1057A LEU* 5.6 0.3 - - - +
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Residues in contact with TYR1054 (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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1027A PRO* 4.8 8.4 - - + +
1030A ASN* 5.8 5.5 - - - +
1032A LEU* 3.5 33.7 - - + -
1050A LEU* 3.2 28.6 + - + +
1051A GLU* 3.8 5.6 - - - +
1053A LYS* 1.3 113.3 + - + +
1055A ALA* 1.3 64.4 + - - +
1056A PRO* 3.3 3.4 - - - -
1057A LEU* 3.1 43.7 + - + +
1058A HIS* 3.5 6.2 + - - +
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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