Contacts of the helix formed by residues 1020 - 1038 (chain A) in PDB entry 5DSG
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 ALA1020 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 5.5 1.3 - - - -
1019A GLU* 1.3 76.4 - - - +
1021A GLU* 1.3 61.6 + - - +
1022A LYS 3.3 2.2 - - - -
1023A LEU* 3.3 38.8 + - + +
1024A PHE* 3.4 13.4 + - + +
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Residues in contact with GLU1021 (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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135A THR 4.9 1.7 - - - +
136A LYS* 3.3 33.2 - - - +
137A PRO* 3.5 4.1 - - + +
138A LEU* 2.9 51.5 + - + -
139A THR* 3.1 34.7 + - + +
1004A PHE* 5.1 2.5 - - + -
1019A GLU* 3.1 5.7 - - - +
1020A ALA* 1.3 76.9 - - - +
1022A LYS* 1.3 56.5 + - - +
1024A PHE* 3.3 9.3 + - - +
1025A ASN* 2.5 44.7 + - - +
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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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1019A GLU 4.1 6.8 + - - +
1020A ALA 3.3 0.6 - - - -
1021A GLU* 1.3 74.7 - - - +
1023A LEU* 1.3 64.5 + - + +
1025A ASN* 3.2 11.3 + - - +
1026A GLN* 2.9 37.5 + - + +
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Residues in contact with LEU1023 (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 29.4 + - + +
1021A GLU 3.2 0.4 - - - -
1022A LYS* 1.3 81.1 - - + +
1024A PHE* 1.3 59.3 + - + +
1026A GLN* 3.3 7.2 + - + +
1027A ASP* 2.9 45.0 + - - +
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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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138A LEU* 3.6 29.8 - - + -
1004A PHE* 3.5 26.2 - + + -
1007A LEU* 3.7 30.7 - - + -
1008A ARG* 4.1 13.0 - - + -
1011A GLU* 3.4 28.7 - - + -
1020A ALA* 3.4 9.5 + - + +
1021A GLU 3.3 4.6 + - - +
1022A LYS 3.3 0.2 - - - -
1023A LEU* 1.3 81.9 - - + +
1025A ASN* 1.3 57.3 + - - +
1027A ASP* 4.5 2.7 - - - +
1028A VAL* 2.9 38.6 + - + +
1061A PHE* 3.6 24.9 - + - -
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Residues in contact with ASN1025 (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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135A THR 5.3 5.9 + - - -
137A PRO* 6.3 0.6 - - - +
225A ARG* 3.7 12.5 + - - +
1004A PHE* 3.3 27.8 - - - -
1021A GLU* 2.5 35.2 + - - +
1022A LYS* 3.2 12.6 + - - +
1024A PHE* 1.3 77.5 - - - +
1026A GLN* 1.3 64.9 + - + +
1029A ASP* 3.3 27.7 + - - +
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Residues in contact with GLN1026 (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* 2.9 22.4 + - + +
1023A LEU* 3.6 9.4 - - + +
1025A ASN* 1.3 76.8 - - - +
1027A ASP* 1.3 64.0 + - - +
1029A ASP* 3.2 8.0 + - - +
1030A ALA* 2.9 27.7 + - - +
1033A ARG* 5.4 0.3 + - - -
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Residues in contact with ASP1027 (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 LEU* 2.9 34.6 + - - +
1024A PHE* 4.1 1.5 - - - +
1026A GLN* 1.3 74.8 - - - +
1028A VAL* 1.3 60.0 + - - +
1030A ALA* 3.2 8.8 + - - +
1031A ALA* 2.9 29.5 + - - +
1061A PHE* 3.4 29.8 - - + -
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Residues in contact with VAL1028 (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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225A ARG* 4.4 18.2 - - + +
1003A ILE* 4.3 20.4 - - + -
1004A PHE* 4.5 10.3 - - + -
1007A LEU* 3.7 29.8 - - + -
1024A PHE* 2.9 23.1 + - + +
1025A ASN 4.5 0.2 - - - +
1027A ASP* 1.3 75.5 - - - +
1029A ASP* 1.3 72.9 + - - +
1031A ALA* 3.1 6.9 + - - +
1032A VAL* 2.9 33.6 + - + +
1057A ILE* 4.7 9.4 - - + +
1061A PHE* 3.9 6.3 - - + -
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Residues in contact with ASP1029 (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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225A ARG* 3.6 24.1 + - - -
1025A ASN 3.3 15.3 + - - +
1026A GLN* 3.2 10.2 + - - +
1028A VAL* 1.3 77.0 - - - +
1030A ALA* 1.3 58.5 + - - +
1032A VAL* 3.4 7.7 + - - +
1033A ARG* 2.9 45.6 + - - +
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Residues in contact with ALA1030 (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 GLN 2.9 13.9 + - - +
1027A ASP* 3.4 14.8 - - - +
1028A VAL 3.2 0.2 - - - -
1029A ASP* 1.3 77.8 - - - +
1031A ALA* 1.3 56.4 + - - +
1033A ARG* 3.2 24.6 + - - +
1034A GLY* 2.9 25.8 + - - -
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Residues in contact with ALA1031 (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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1027A ASP 2.9 13.6 + - - +
1028A VAL* 3.1 11.6 + - - +
1030A ALA* 1.3 74.7 - - - +
1032A VAL* 1.3 65.3 + - - +
1034A GLY* 3.1 3.2 + - - -
1035A ILE* 2.9 28.4 + - - +
1057A ILE* 4.4 19.7 - - + +
1060A VAL* 3.8 21.9 - - + +
1061A PHE* 4.5 11.0 - - + +
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Residues in contact with VAL1032 (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 VAL* 2.9 27.0 + - + +
1029A ASP* 3.7 8.7 - - - +
1031A ALA* 1.3 74.3 - - - +
1033A ARG* 1.3 58.5 + - - +
1035A ILE* 3.1 11.0 + - + +
1036A LEU* 2.9 46.2 + - + +
1045A TYR* 4.3 18.4 - - + +
1057A ILE* 3.8 29.2 - - + -
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Residues in contact with ARG1033 (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 GLN 5.4 0.2 + - - -
1029A ASP* 2.9 32.0 + - - +
1030A ALA* 3.3 39.2 - - - +
1032A VAL* 1.3 77.8 - - - +
1034A GLY* 1.3 56.5 + - - +
1036A LEU* 3.3 9.5 + - - +
1037A ARG* 2.9 33.0 + - + +
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Residues in contact with GLY1034 (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 ALA 2.9 13.6 + - - -
1031A ALA* 3.1 4.9 + - - -
1033A ARG* 1.3 77.7 - - - +
1035A ILE* 1.3 55.4 + - - +
1037A ARG* 3.2 5.5 + - - -
1038A ASN* 2.9 21.8 + - - +
1060A VAL* 5.5 0.7 - - - -
1065A GLU* 2.9 40.8 - - - +
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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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1031A ALA 2.9 19.7 + - - +
1032A VAL* 3.1 9.6 + - - +
1034A GLY* 1.3 77.0 - - - +
1036A LEU* 1.3 62.0 + - + +
1038A ASN 3.2 18.2 + - - +
1041A LEU* 3.8 23.2 - - + +
1042A LYS* 3.5 8.1 + - - -
1045A TYR* 3.6 42.8 - - + -
1056A LEU* 4.5 5.2 - - + -
1057A ILE* 3.8 33.4 - - + +
1060A VAL* 3.6 31.0 - - + -
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Residues in contact with LEU1036 (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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1032A VAL* 2.9 33.6 + - + +
1033A ARG* 3.8 7.4 - - - +
1035A ILE* 1.3 78.2 - - + +
1037A ARG* 1.3 60.0 + - - +
1038A ASN 4.1 3.5 - - - +
1042A LYS* 4.6 22.3 - - + +
1045A TYR* 4.4 26.9 - - + -
1046A ASP* 5.0 6.5 - - - +
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Residues in contact with ARG1037 (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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1033A ARG* 2.9 20.5 + - + +
1034A GLY* 3.5 7.4 - - - +
1035A ILE 3.2 0.2 - - - -
1036A LEU* 1.3 77.6 - - - +
1038A ASN* 1.3 63.7 + - - +
1039A ALA* 3.6 2.9 + - - +
1065A GLU* 2.8 38.7 + - - +
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Residues in contact with ASN1038 (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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1034A GLY 2.9 16.4 + - - +
1035A ILE 3.2 11.5 + - - +
1036A LEU 3.4 1.5 - - - +
1037A ARG* 1.3 78.0 - - - +
1039A ALA* 1.3 61.8 + - - +
1040A LYS* 2.7 32.7 + - - +
1041A LEU* 2.9 32.6 + - + +
1042A LYS* 3.4 14.9 + - - +
1065A GLU* 4.0 17.5 + - - +
1066A THR* 5.1 1.8 - - - +
1069A ALA* 3.7 18.4 - - - +
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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