Contacts of the helix formed by residues 1021 - 1036 (chain A) in PDB entry 6PUO
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 PRO1021 (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* 1.3 87.3 - - - +
1022A GLU* 1.3 62.0 + - + +
1023A TRP 3.5 0.7 - - - -
1024A LEU* 4.0 8.1 - - + -
1025A THR* 2.9 35.6 + - - -
964B ASP* 5.5 11.7 - - + -
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Residues in contact with GLU1022 (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 PHE 3.3 2.5 - - - -
1021A PRO* 1.3 81.7 - - + +
1023A TRP* 1.3 59.6 + - - +
1025A THR* 4.2 2.1 - - - -
1026A VAL* 2.9 33.4 + - - +
964B ASP* 6.5 0.7 - - + -
968B ARG* 6.0 7.0 - - + -
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Residues in contact with TRP1023 (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 PHE 4.3 6.0 + - - +
1022A GLU* 1.3 78.1 - - - +
1024A LEU* 1.3 58.8 + - - +
1026A VAL* 3.5 4.7 + - - +
1027A LEU* 2.9 30.4 + - - +
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Residues in contact with LEU1024 (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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956A LEU* 6.2 4.5 - - + -
1020A PHE 4.5 4.6 + - - +
1021A PRO* 3.7 12.6 + - + +
1022A GLU 3.4 0.4 - - - -
1023A TRP* 1.3 79.0 - - - +
1025A THR* 1.3 56.9 + - - +
1027A LEU* 3.3 7.0 + - - +
1028A LEU* 3.0 29.3 + - - +
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Residues in contact with THR1025 (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 PRO* 2.9 23.1 + - - -
1022A GLU* 4.2 2.5 - - - -
1024A LEU* 1.3 73.8 - - - +
1026A VAL* 1.3 59.5 + - - +
1028A LEU* 3.5 5.1 + - - +
1029A LEU* 2.9 44.0 + - - +
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Residues in contact with VAL1026 (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 GLU 2.9 20.8 + - - +
1023A TRP* 3.8 5.2 - - - +
1025A THR* 1.3 76.1 - - - +
1027A LEU* 1.3 57.3 + - - +
1029A LEU* 4.1 5.7 - - - +
1030A CYS* 2.9 34.7 + - - +
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Residues in contact with LEU1027 (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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1023A TRP 2.9 18.6 + - - +
1024A LEU* 3.6 8.1 - - - +
1025A THR 3.3 0.2 - - - -
1026A VAL* 1.3 74.3 - - - +
1028A LEU* 1.3 59.1 + - - +
1030A CYS* 3.2 12.1 - - - -
1031A LEU* 2.9 30.3 + - - +
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Residues in contact with LEU1028 (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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948A PHE* 5.5 1.0 - - - -
952A LYS* 6.4 1.6 - - + -
1024A LEU 3.0 17.1 + - - +
1025A THR* 4.0 5.2 - - - +
1027A LEU* 1.3 75.0 - - - +
1029A LEU* 1.3 61.7 + - + +
1031A LEU* 3.3 7.1 + - - +
1032A TYR* 3.0 28.1 + - - +
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Residues in contact with LEU1029 (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 THR* 2.9 27.6 + - - +
1026A VAL* 4.1 4.9 - - - +
1028A LEU* 1.3 77.5 - - + +
1030A CYS* 1.3 58.3 + - - +
1032A TYR* 3.4 6.0 + - + +
1033A LEU* 2.9 44.3 + - + +
975B TYR* 4.6 20.9 - - + -
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Residues in contact with CYS1030 (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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1026A VAL 2.9 18.6 + - - +
1027A LEU* 3.2 25.4 - - - -
1029A LEU* 1.3 75.5 - - - +
1031A LEU* 1.3 61.6 + - - +
1033A LEU* 3.8 6.8 - - - +
1034A LEU* 2.8 32.0 + - - +
938B LEU* 5.2 1.9 - - - +
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Residues in contact with LEU1031 (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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948A PHE* 4.6 16.8 - - + -
1027A LEU 2.9 19.6 + - - +
1028A LEU* 3.6 7.4 - - - +
1029A LEU 3.3 0.2 - - - -
1030A CYS* 1.3 78.1 - - - +
1032A TYR* 1.3 56.5 + - - +
1034A LEU* 3.4 9.1 + - - +
1035A PHE* 3.0 41.7 + - + -
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Residues in contact with TYR1032 (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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948A PHE* 4.7 12.2 - - + -
977A THR* 6.6 0.2 - - - -
1028A LEU 3.0 16.2 + - - +
1029A LEU* 3.7 10.1 - - + +
1030A CYS 3.4 0.2 - - - -
1031A LEU* 1.3 77.3 - - - +
1033A LEU* 1.3 60.0 + - + +
1036A THR* 2.7 52.1 + - + +
1037A ASN* 3.9 0.7 - - - -
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Residues in contact with LEU1033 (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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1029A LEU* 2.9 35.8 + - + +
1030A CYS* 4.0 6.7 - - - +
1031A LEU 3.3 0.2 - - - -
1032A TYR* 1.3 77.5 - - + +
1034A LEU* 1.3 65.0 + - - +
1037A ASN* 3.3 49.1 - - + +
1038A ILE* 3.8 8.5 - - - +
938B LEU* 5.1 2.4 - - - +
941B LEU* 6.4 3.8 - - + -
978B ILE* 4.7 22.4 - - + +
979B PHE* 5.7 4.3 - - + -
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Residues in contact with LEU1034 (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 CYS* 2.8 20.2 + - - +
1031A LEU* 3.5 7.6 - - - +
1033A LEU* 1.3 80.9 - - - +
1035A PHE* 1.3 98.0 + - + +
1038A ILE* 3.4 12.9 - - - +
1039A LEU* 3.3 21.3 - - + +
934B VAL* 5.3 3.8 - - + +
935B PHE* 5.1 12.6 - - + -
938B LEU* 3.7 36.3 - - + +
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Residues in contact with PHE1035 (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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944A TRP* 3.5 42.0 - + + -
948A PHE* 4.4 10.8 - + - -
1031A LEU* 3.0 28.6 + - + +
1034A LEU* 1.3 100.6 - - + +
1036A THR* 1.3 64.8 + - + +
1039A LEU* 3.5 37.2 + - + +
1040A LEU* 4.5 5.4 + - - +
908B LEU* 5.8 11.0 - - + -
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Residues in contact with THR1036 (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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944A TRP* 3.7 35.0 - - + +
945A VAL* 6.2 0.9 - - + -
948A PHE* 5.7 1.6 - - + -
977A THR 5.7 2.4 + - - +
1032A TYR* 2.7 23.1 + - + +
1035A PHE* 1.3 77.6 - - - +
1037A ASN* 1.3 89.3 + - - +
1038A ILE 3.1 2.4 + - - -
1039A LEU 4.4 0.3 + - - -
1040A LEU* 4.8 8.7 + - - +
1041A LEU* 3.3 14.6 - - - +
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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