Contacts of the helix formed by residues 1022 - 1035 (chain A) in PDB entry 4G34
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 THR1022 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A PHE* 3.5 9.1 - - - +
1021A SER* 1.3 90.1 - - - +
1023A GLN* 1.3 65.2 + - - +
1024A MET* 3.7 6.2 + - - +
1025A GLU* 3.2 25.6 + - - +
1026A ARG* 3.3 14.9 + - - +
1028A ARG* 5.4 1.0 + - - -
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Residues in contact with GLN1023 (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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896A LYS* 5.0 9.3 - - - +
900A ASN* 3.6 27.1 + - - +
1022A THR* 1.3 71.9 - - - +
1024A MET* 1.3 68.0 + - + +
1026A ARG* 3.1 54.3 + - - +
1027A VAL* 3.2 17.8 + - + +
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Residues in contact with MET1024 (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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1022A THR* 3.3 6.3 + - - +
1023A GLN* 1.3 81.0 - - + +
1025A GLU* 1.3 59.5 + - - +
1027A VAL* 3.4 13.3 + - - +
1028A ARG* 2.9 38.2 + - + +
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Residues in contact with GLU1025 (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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1018A TYR* 4.1 16.3 + - - -
1019A PRO 4.4 1.0 - - - +
1020A PHE* 3.6 21.1 - - + -
1021A SER* 2.7 38.3 + - - -
1022A THR* 3.2 18.8 + - - +
1024A MET* 1.3 75.6 - - - +
1026A ARG* 1.3 58.0 + - - +
1028A ARG* 3.7 29.4 - - - +
1029A THR* 2.8 42.8 + - - +
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Residues in contact with ARG1026 (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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896A LYS* 5.2 16.2 - - - +
900A ASN* 5.6 1.3 - - - -
986A THR* 5.4 4.0 + - - +
988A LEU* 3.6 23.3 - - - +
989A TYR* 2.8 28.5 + - - -
1015A GLU* 2.9 19.0 + - - +
1020A PHE* 3.7 38.0 - - + -
1022A THR 3.3 8.4 + - - +
1023A GLN* 3.1 44.8 + - - +
1024A MET 3.2 0.4 - - - -
1025A GLU* 1.3 77.3 - - - +
1027A VAL* 1.3 73.5 + - - +
1029A THR 3.9 0.2 - - - -
1030A LEU* 2.9 40.6 + - + +
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Residues in contact with VAL1027 (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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988A LEU* 4.7 15.7 - - + -
1023A GLN* 3.2 16.4 + - - +
1024A MET* 4.0 15.7 - - - +
1026A ARG* 1.3 93.4 - - - +
1028A ARG* 1.3 62.6 + - - +
1030A LEU* 4.7 3.4 - - - -
1031A THR* 2.9 47.6 + - + +
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Residues in contact with ARG1028 (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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1022A THR* 5.4 1.2 + - - -
1024A MET* 2.9 21.8 + - + +
1025A GLU* 3.7 38.4 - - - +
1027A VAL* 1.3 78.2 - - - +
1029A THR* 1.3 62.7 + - - +
1031A THR* 3.1 16.4 + - - -
1032A ASP* 3.5 21.5 + - - +
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Residues in contact with THR1029 (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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1014A PHE* 3.8 27.6 - - + -
1018A TYR* 4.3 4.8 + - + +
1020A PHE* 3.5 19.4 - - + -
1025A GLU* 2.8 26.1 + - - +
1028A ARG* 1.3 79.2 + - - +
1030A LEU* 1.3 62.2 + - - +
1032A ASP* 3.1 9.3 + - + +
1033A VAL* 2.9 26.6 + - - +
1039A PRO* 4.0 20.9 - - + -
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Residues in contact with LEU1030 (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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988A LEU* 4.4 14.8 - - + -
989A TYR* 3.9 9.4 - - + +
1011A LEU* 3.8 23.8 - - + +
1014A PHE* 3.6 32.3 - - + -
1015A GLU* 3.8 37.5 - - + +
1020A PHE* 4.3 5.6 - - + -
1026A ARG* 2.9 43.7 + - + +
1027A VAL* 4.3 3.4 - - - +
1029A THR* 1.3 77.5 - - - +
1031A THR* 1.3 58.7 + - - +
1033A VAL* 3.2 3.8 + - - +
1034A ARG* 2.9 33.7 + - - +
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Residues in contact with THR1031 (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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988A LEU* 3.9 23.6 - - + -
1027A VAL* 2.9 30.1 + - + +
1028A ARG* 3.1 11.4 + - - -
1030A LEU* 1.3 76.3 - - - +
1032A ASP* 1.3 62.8 + - - +
1034A ARG* 3.5 14.8 - - - +
1035A ASN* 3.4 19.1 + - - +
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Residues in contact with ASP1032 (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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1028A ARG* 3.5 19.4 + - - +
1029A THR* 3.1 13.6 + - + +
1031A THR* 1.3 79.9 + - - +
1033A VAL* 1.3 59.9 + - - +
1035A ASN* 2.9 20.6 + - - +
1037A LYS* 2.8 65.7 + - + +
1039A PRO* 6.2 0.2 - - + -
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Residues in contact with VAL1033 (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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1011A LEU* 3.7 21.1 - - + -
1014A PHE* 3.7 42.6 - - + -
1029A THR 2.9 18.8 + - - +
1030A LEU* 3.2 6.2 + - - +
1032A ASP* 1.3 71.0 - - - +
1034A ARG* 1.3 60.1 + - - +
1036A LEU* 2.9 20.5 + - - +
1037A LYS 3.7 15.7 - - - +
1038A PHE* 3.7 24.2 - - + -
1039A PRO* 4.2 7.4 - - + -
1053A VAL* 4.5 0.2 - - + -
1057A LEU* 3.4 17.8 - - + +
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Residues in contact with ARG1034 (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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987A LYS 3.2 10.2 + - - -
988A LEU* 2.7 43.2 + - - +
990A MET 2.8 33.5 + - - +
992A PRO* 3.9 13.7 - - - +
995A ILE* 3.5 15.9 - - - +
1007A PHE* 3.8 32.5 - - + -
1011A LEU* 4.0 17.2 - - + +
1030A LEU 2.9 17.3 + - - +
1031A THR* 3.5 18.4 - - - +
1033A VAL* 1.3 75.5 - - - +
1035A ASN* 1.3 56.7 + - + +
1036A LEU* 3.2 8.7 + - - +
1057A LEU* 4.5 10.7 - - - +
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Residues in contact with ASN1035 (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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1031A THR 3.4 8.9 + - - +
1032A ASP* 2.9 14.2 + - - +
1034A ARG* 1.3 76.9 - - + +
1036A LEU* 1.3 69.4 + - - +
1037A LYS* 3.3 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