Contacts of the helix formed by residues 1030 - 1037 (chain A) in PDB entry 3H0G
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 ALA1030 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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903A TYR* 3.9 28.3 - - + -
936A THR* 4.7 11.7 - - + +
940A ALA* 5.2 4.9 - - + -
993A LEU* 5.7 1.6 - - - -
1026A ARG* 3.1 28.0 + - - +
1027A SER 4.4 0.2 - - - -
1028A LYS 3.8 0.2 - - - -
1029A PHE* 1.3 82.1 - - - +
1031A VAL* 1.3 69.5 + - - +
1032A LYS 3.7 1.3 - - - +
1033A ARG* 3.1 16.6 + - + +
1034A VAL* 3.5 3.1 - - - +
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Residues in contact with VAL1031 (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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903A TYR 5.8 0.2 - - - +
905A ILE* 5.7 1.3 - - + -
913A LEU* 5.6 4.5 - - + -
933A GLU* 3.8 35.4 - - - +
936A THR* 4.2 16.3 + - + +
986A PRO* 4.1 13.2 - - + -
989A ILE* 3.7 35.9 - - + +
990A ILE* 3.7 17.0 - - + -
1029A PHE 3.7 0.6 + - - -
1030A ALA* 1.3 67.1 - - - +
1032A LYS* 1.3 55.3 + - - +
1033A ARG 2.7 15.7 + - - -
1034A VAL* 2.8 18.9 + - - +
1035A ILE* 3.6 20.9 + - + +
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Residues in contact with LYS1032 (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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900A GLU 3.7 3.2 + - - -
901A LYS* 3.5 13.5 - - - +
902A LYS* 3.3 47.7 - - - +
903A TYR* 3.5 16.3 + - - +
904A ARG 3.5 24.1 + - - +
905A ILE* 3.9 16.0 - - + +
913A LEU* 4.9 16.4 - - + -
1030A ALA* 3.7 0.6 - - - +
1031A VAL* 1.3 78.2 - - - +
1033A ARG* 1.3 56.3 + - - +
1034A VAL 3.3 0.2 - - - -
1035A ILE* 4.1 1.6 - - - +
1036A MET* 3.1 45.3 + - + +
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Residues in contact with ARG1033 (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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890A ASP* 2.9 32.3 + - - +
902A LYS* 3.6 35.0 + - - +
903A TYR* 3.6 16.0 + - + -
1027A SER 2.6 34.3 + - - +
1028A LYS* 4.0 12.4 - - - +
1030A ALA* 3.1 23.3 - - + +
1031A VAL 2.7 6.1 + - - -
1032A LYS* 1.3 77.0 - - - +
1034A VAL* 1.3 48.8 + - + -
1035A ILE 3.2 0.9 - - - -
1036A MET* 5.2 0.4 - - - -
1037A GLU* 2.6 68.9 + - - +
1038A TYR* 3.4 27.5 + - - +
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Residues in contact with VAL1034 (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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982A THR* 5.1 1.6 - - - -
984A LEU* 4.4 13.4 - - + +
989A ILE* 4.9 9.2 - - + -
1028A LYS 4.6 3.1 - - - +
1029A PHE* 3.7 30.7 - - + +
1030A ALA 3.5 15.9 - - - +
1031A VAL* 2.8 7.7 + - - +
1033A ARG* 1.3 79.1 - - + +
1035A ILE* 1.3 64.8 + - + +
1037A GLU 3.7 5.8 - - - -
1038A TYR* 3.5 13.7 - - + +
1039A ARG* 3.6 1.2 - - - -
1040A LEU* 3.5 48.9 + - + +
1045A PHE* 4.7 8.3 - - + -
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Residues in contact with ILE1035 (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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913A LEU* 4.2 26.0 - - + +
916A TYR* 3.4 39.6 - - + -
917A MET* 4.5 17.0 - - - +
982A THR* 3.8 22.4 - - + +
984A LEU* 5.9 5.4 - - + -
985A LEU 6.1 0.2 - - - -
986A PRO* 4.5 10.8 - - + -
989A ILE* 6.2 3.4 - - + -
1031A VAL* 3.6 28.6 + - + +
1032A LYS 4.6 0.9 - - - +
1034A VAL* 1.3 89.2 - - + +
1036A MET* 1.3 66.1 + - - +
1037A GLU 4.4 0.2 - - - -
1039A ARG* 3.6 20.2 + - - +
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Residues in contact with MET1036 (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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913A LEU* 4.8 6.8 - - + +
916A TYR* 4.8 21.8 - - - -
1032A LYS* 3.1 36.8 + - + +
1035A ILE* 1.3 76.3 - - - +
1037A GLU* 1.3 72.1 + - + +
1038A TYR 3.9 0.3 + - - -
1039A ARG* 3.3 25.9 + - - -
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Residues in contact with GLU1037 (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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902A LYS* 3.5 25.0 + - - +
1033A ARG* 2.6 63.7 + - - +
1034A VAL 3.7 2.4 - - - -
1036A MET* 1.3 92.9 - - + +
1038A TYR* 1.3 89.3 + - + +
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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