Contacts of the helix formed by residues 1015 - 1026 (chain A) in PDB entry 5JQE
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 ASP1015 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013A GLN 3.6 4.5 + - - +
1014A LEU* 1.3 78.7 - - - +
1016A SER* 1.3 64.5 + - - +
1017A GLU* 3.1 20.6 + - - +
1018A ASP* 2.9 38.1 + - - +
1019A LEU* 3.3 8.4 + - - +
1071A ARG* 4.2 5.5 + - - -
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Residues in contact with SER1016 (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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1015A ASP* 1.3 75.8 - - - +
1017A GLU* 1.3 61.8 + - - +
1019A LEU* 3.5 13.7 + - - +
1020A ALA* 3.4 17.2 + - - +
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Residues in contact with GLU1017 (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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1015A ASP* 3.2 9.7 + - - +
1016A SER* 1.3 76.0 - - - +
1018A ASP* 1.3 75.0 + - - +
1019A LEU 3.1 1.3 - - - -
1020A ALA* 2.9 19.6 + - + +
1021A SER* 3.0 17.9 + - - +
1110A GLU* 5.3 6.7 - - - +
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Residues in contact with ASP1018 (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 LEU* 4.3 11.2 - - + -
1015A ASP* 2.9 37.3 + - - +
1017A GLU* 1.3 81.9 - - - +
1019A LEU* 1.3 57.3 + - - +
1021A SER* 3.3 8.3 + - - -
1022A LEU* 2.8 36.4 + - + +
1069A ILE* 4.0 24.2 - - + +
1071A ARG* 2.9 28.4 + - - -
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Residues in contact with LEU1019 (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 LEU* 5.3 1.7 - - - +
1015A ASP 3.3 8.6 + - - +
1016A SER* 3.6 15.0 - - - +
1017A GLU 3.1 0.6 - - - -
1018A ASP* 1.3 77.3 - - - +
1020A ALA* 1.3 59.1 + - - +
1022A LEU* 3.3 4.9 + - + +
1023A LYS* 2.8 49.5 + - + +
1038A ILE* 4.7 7.6 - - + +
1039A LYS 3.7 26.0 - - - +
1040A ASP* 3.7 14.8 - - - +
1041A ALA* 3.6 32.3 - - + +
1044A LEU* 4.1 20.9 - - + -
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Residues in contact with ALA1020 (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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1016A SER 3.4 8.9 + - - +
1017A GLU* 2.9 13.8 + - + +
1019A LEU* 1.3 77.9 - - - +
1021A SER* 1.3 61.6 + - - +
1023A LYS* 3.6 10.5 + - - +
1024A PHE* 3.3 21.7 + - - +
1138A ASN* 4.7 17.0 - - - +
1140A LEU* 4.4 7.4 - - + +
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Residues in contact with SER1021 (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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1017A GLU* 3.0 19.6 + - - +
1018A ASP* 3.6 9.9 - - - -
1020A ALA* 1.3 75.4 - - - +
1022A LEU* 1.3 65.1 + - - +
1024A PHE* 3.2 4.0 + - - +
1025A LEU* 3.1 28.7 + - - +
1069A ILE* 3.9 11.7 - - - -
1106A TYR* 3.3 35.0 + - - -
1110A GLU* 5.0 2.8 + - - -
1140A LEU* 4.6 10.4 - - - +
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Residues in contact with LEU1022 (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 LEU* 3.5 32.1 - - + -
1018A ASP 2.8 27.9 + - - +
1019A LEU* 3.8 7.4 - - + +
1021A SER* 1.3 72.6 - - - +
1023A LYS* 1.3 55.2 + - - +
1025A LEU* 3.5 3.9 + - - +
1026A SER* 2.5 37.7 + - - +
1041A ALA* 5.3 0.4 - - + -
1044A LEU* 3.6 20.9 - - + -
1045A PHE* 5.0 5.8 - - + -
1065A LEU* 3.6 50.0 - - + +
1066A LEU* 4.5 4.0 - - + +
1069A ILE* 4.0 21.3 - - + -
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Residues in contact with LYS1023 (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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1019A LEU* 2.8 39.8 + - + +
1020A ALA* 3.9 8.3 - - - +
1022A LEU* 1.3 75.8 - - - +
1024A PHE* 1.3 65.3 + - - +
1026A SER* 3.4 2.5 + - - -
1027A LEU* 3.3 23.9 + - - +
1035A GLN* 3.4 60.1 + - - +
1038A ILE* 3.6 33.9 + - + +
1044A LEU* 4.3 7.9 - - + -
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Residues in contact with PHE1024 (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 ALA 3.3 10.3 + - - +
1021A SER 3.2 8.3 + - - +
1023A LYS* 1.3 80.5 - - - +
1025A LEU* 1.3 73.3 + - + +
1027A LEU* 3.2 33.3 + - + +
1102A ARG* 3.7 54.0 - - - -
1105A LEU* 3.8 27.6 - - + -
1106A TYR* 4.3 5.2 - + + -
1140A LEU* 3.8 42.4 - - + -
1143A PHE* 4.3 7.4 - - + -
1144A ILE* 4.0 23.3 - - + -
1147A GLU* 5.5 0.2 - - - -
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Residues in contact with LEU1025 (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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1021A SER 3.1 14.3 + - - +
1022A LEU 3.5 0.6 + - - +
1024A PHE* 1.3 79.4 - - + +
1026A SER* 1.3 59.1 + - - +
1027A LEU 3.2 0.7 + - - -
1028A ASP* 4.3 6.9 + - - +
1029A TYR* 5.0 0.7 - - - -
1061A PHE* 4.7 1.9 - - - -
1065A LEU* 3.7 23.8 - - + -
1068A ARG* 3.6 24.5 - - + -
1069A ILE* 3.6 30.5 - - + -
1098A ILE* 4.0 38.9 - - + +
1102A ARG* 4.3 15.8 - - - +
1103A VAL* 4.8 3.4 - - + -
1106A TYR* 3.9 33.2 - - + -
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Residues in contact with SER1026 (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 LEU 2.5 23.2 + - - -
1023A LYS* 3.4 4.5 + - - -
1024A PHE 3.2 0.4 - - - -
1025A LEU* 1.3 74.5 - - - +
1027A LEU* 1.3 60.0 + - - +
1028A ASP 3.2 2.9 - - - -
1029A TYR* 3.1 4.4 + - - +
1030A ILE* 2.8 51.2 + - - +
1035A GLN* 4.8 1.1 - - - -
1044A LEU* 4.2 10.7 - - - +
1048A LEU* 4.8 0.6 - - - +
1061A PHE* 4.4 14.8 - - - -
1065A LEU* 3.8 20.6 - - - +
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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