Contacts of the helix formed by residues 1020 - 1039 (chain A) in PDB entry 4B87
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 THR1020 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A VAL 3.3 0.4 - - - -
1019A GLY* 1.3 84.0 - - - +
1021A TRP* 1.3 66.4 + - - +
1022A LYS* 3.6 9.4 + - - +
1023A SER* 3.1 26.3 + - - -
1024A ARG* 3.0 30.9 + - - +
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Residues in contact with TRP1021 (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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1020A THR* 1.3 74.2 - - - +
1022A LYS* 1.3 76.1 + - + +
1024A ARG* 3.2 29.6 + - + +
1025A SER* 2.9 57.8 + - - -
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Residues in contact with LYS1022 (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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1020A THR* 3.1 8.3 + - - +
1021A TRP* 1.3 92.4 - - + +
1023A SER* 1.3 54.7 + - - +
1025A SER* 3.4 3.0 + - - -
1026A THR* 2.6 50.7 + - - +
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Residues in contact with SER1023 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A ASN* 2.7 33.7 + - - +
1020A THR* 3.1 24.8 + - - -
1022A LYS* 1.3 79.7 - - - +
1024A ARG* 1.3 62.9 + - - +
1026A THR* 3.1 8.5 + - - -
1027A MET* 3.0 30.9 + - - +
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Residues in contact with ARG1024 (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 PRO* 5.0 9.7 - - + +
1017A ASN 4.5 0.2 + - - -
1018A VAL* 2.7 46.6 + - + +
1019A GLY* 3.4 5.9 + - - -
1020A THR* 3.0 31.5 + - - +
1021A TRP* 3.5 40.3 - - + +
1023A SER* 1.3 78.3 + - - +
1025A SER* 1.3 61.5 + - - +
1027A MET* 3.4 11.5 + - + +
1028A GLU* 3.2 21.0 + - - +
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Residues in contact with SER1025 (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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1021A TRP* 2.9 58.4 + - - -
1022A LYS* 3.7 5.8 - - - -
1024A ARG* 1.3 70.2 - - - +
1026A THR* 1.3 61.6 - - - +
1028A GLU* 3.3 7.4 + - - +
1029A LYS* 3.0 28.6 + - - +
1032A ARG* 4.9 1.7 + - - -
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Residues in contact with THR1026 (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 LYS* 2.6 41.8 + - - +
1023A SER* 3.1 8.2 + - - -
1025A SER* 1.3 77.0 - - - +
1027A MET* 1.3 64.3 + - - +
1029A LYS* 3.3 10.1 + - + +
1030A TYR* 3.0 47.3 + - + +
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Residues in contact with MET1027 (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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839A THR* 3.4 34.3 - - - +
842A CYS* 3.9 22.4 - - + +
1014A PRO* 3.6 23.1 - - + -
1016A VAL 3.7 7.4 - - - +
1017A ASN* 3.4 29.6 - - - +
1018A VAL* 4.0 4.3 - - + -
1023A SER* 3.0 23.0 + - - +
1024A ARG* 3.9 7.6 - - - +
1026A THR* 1.3 77.0 - - - +
1028A GLU* 1.3 53.8 + - - +
1030A TYR* 2.9 29.4 + - + +
1031A PHE* 2.9 34.3 + - + -
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Residues in contact with GLU1028 (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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1012A ILE* 4.5 10.9 + - - +
1024A ARG 3.2 13.9 + - - +
1025A SER* 3.6 11.0 - - - +
1027A MET* 1.3 73.6 - - - +
1029A LYS* 1.3 58.7 + - - +
1031A PHE* 3.1 23.3 + - - +
1032A ARG* 2.9 67.7 + - - +
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Residues in contact with LYS1029 (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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1025A SER 3.0 13.2 + - - +
1026A THR* 3.5 12.6 - - + +
1027A MET 3.2 0.2 - - - -
1028A GLU* 1.3 77.1 - - - +
1030A TYR* 1.3 65.2 + - + +
1032A ARG* 3.2 28.3 + - - +
1033A GLU* 3.1 45.9 + - + +
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Residues in contact with TYR1030 (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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842A CYS* 3.7 29.6 - - - -
843A SER* 4.1 5.0 + - - -
844A PRO* 3.5 34.2 - - + +
997A TYR* 4.1 14.4 - + - -
1026A THR* 3.0 42.4 + - + +
1027A MET* 2.9 17.6 + - + +
1029A LYS* 1.3 73.0 - - + +
1031A PHE* 1.3 57.7 + - + +
1033A GLU* 3.3 24.7 + - - +
1034A TRP* 2.9 52.2 + - + -
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Residues in contact with PHE1031 (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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837A LEU* 3.9 9.4 - - + -
839A THR* 3.9 16.8 - - + -
842A CYS* 3.9 13.2 - - - -
1004A VAL* 6.1 0.2 - - - -
1012A ILE* 3.4 48.9 - - + -
1014A PRO* 4.1 13.0 - - + -
1027A MET* 2.9 39.2 + - + -
1028A GLU* 3.5 25.4 - - - +
1030A TYR* 1.3 77.2 - - - +
1032A ARG* 1.3 63.2 + - + +
1034A TRP* 3.3 37.7 + + - +
1035A LYS* 3.1 21.7 + - - +
1040A TYR* 4.6 2.8 + - - -
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Residues in contact with ARG1032 (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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1025A SER 4.9 1.2 + - - -
1028A GLU* 2.9 49.7 + - - +
1029A LYS* 3.8 31.4 - - - +
1031A PHE* 1.3 77.6 - - - +
1033A GLU* 1.3 56.6 + - - +
1035A LYS* 3.1 16.4 + - + +
1036A LEU* 2.9 28.4 + - - +
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Residues in contact with GLU1033 (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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997A TYR* 5.4 1.7 + - - -
1029A LYS* 3.1 34.9 + - + +
1030A TYR* 3.4 26.6 - - - +
1032A ARG* 1.3 76.1 - - + +
1034A TRP* 1.3 61.7 + - + +
1036A LEU* 3.3 8.0 + - - +
1037A GLU* 3.0 31.3 + - - +
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Residues in contact with TRP1034 (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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842A CYS* 4.2 1.8 - - - -
997A TYR* 3.0 45.8 + + - -
1000A MET* 4.1 16.6 - - + -
1001A LYS* 3.5 51.5 - - + +
1004A VAL* 3.8 39.5 - - + -
1005A GLN* 2.9 35.7 + - + +
1030A TYR* 2.9 32.6 + - + +
1031A PHE* 3.3 39.7 + + - +
1033A GLU* 1.3 78.3 - - + +
1035A LYS* 1.3 57.6 + - - +
1037A GLU* 4.7 0.9 - - - -
1038A ALA* 3.1 18.0 + - - +
1040A TYR* 3.9 6.3 - - - +
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Residues in contact with LYS1035 (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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1009A PRO 4.7 3.6 - - - -
1010A GLN* 4.4 18.6 - - - +
1031A PHE 3.1 12.0 + - - +
1032A ARG* 3.2 18.8 - - + +
1034A TRP* 1.3 72.6 - - - +
1036A LEU* 1.3 60.8 + - - +
1037A GLU 3.1 0.3 + - - -
1038A ALA 3.3 0.2 + - - -
1039A GLY* 2.6 35.3 + - - -
1040A TYR* 3.1 61.3 + - + +
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Residues in contact with LEU1036 (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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1032A ARG 2.9 16.5 + - - +
1033A GLU* 3.3 11.8 + - - +
1035A LYS* 1.3 74.6 - - - +
1037A GLU* 1.3 63.3 + - - +
1039A GLY* 3.7 7.2 + - - -
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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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1001A LYS* 3.0 35.7 + - - -
1005A GLN* 3.3 10.4 + - - +
1033A GLU 3.0 17.7 + - - +
1034A TRP* 4.0 2.6 - - - +
1036A LEU* 1.3 79.4 - - - +
1038A ALA* 1.3 59.8 + - - +
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Residues in contact with ALA1038 (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 GLN* 3.8 21.3 - - + +
1008A LYS* 5.2 6.1 - - - +
1034A TRP 3.1 17.2 + - - +
1037A GLU* 1.3 78.3 - - - +
1039A GLY* 1.3 62.2 + - - +
1040A TYR* 3.6 20.2 - - + -
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Residues in contact with GLY1039 (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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1008A LYS* 4.5 5.9 - - - -
1035A LYS 2.6 19.8 + - - -
1036A LEU 3.7 5.6 + - - -
1037A GLU 3.6 1.0 - - - -
1038A ALA* 1.3 74.2 - - - +
1040A TYR* 1.3 64.2 + - - +
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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