Contacts of the strand formed by residues 1023 - 1031 (chain A) in PDB entry 3DLS
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 LYS1023 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998A LYS* 5.4 0.2 - - - +
999A TYR* 4.8 2.8 + - - -
1017A VAL* 3.5 3.4 - - - -
1018A ASP* 2.8 60.3 + - + +
1021A LYS* 3.1 35.7 - - + +
1022A ASN* 1.3 78.6 - - - +
1024A GLU* 1.3 63.4 + - - +
1025A VAL* 3.6 19.4 + - + +
1068A LEU* 3.9 22.0 - - - +
1082A GLU* 6.1 0.2 - - - +
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Residues in contact with GLU1024 (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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1002A MET* 6.0 0.3 - - - +
1015A THR* 3.4 26.0 - - + +
1016A ALA 3.3 6.3 - - - +
1017A VAL* 4.8 9.5 - - + +
1022A ASN 4.1 1.4 + - - +
1023A LYS* 1.3 75.3 - - - +
1025A VAL* 1.3 64.2 + - - +
1083A LYS* 3.5 41.4 + - + +
1085A GLY 5.2 1.4 - - - +
1086A SER* 5.9 0.3 - - - -
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Residues in contact with VAL1025 (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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999A TYR* 3.6 24.7 - - + -
1015A THR* 3.5 8.1 - - - +
1016A ALA* 2.8 44.7 + - + +
1018A ASP 4.6 0.2 - - - +
1023A LYS* 3.8 23.3 - - - +
1024A GLU* 1.3 79.7 - - - +
1026A VAL* 1.3 66.8 - - - +
1068A LEU* 3.5 26.0 - - + -
1080A VAL* 3.6 20.2 - - + -
1081A MET 3.4 10.5 - - - +
1082A GLU* 5.0 0.7 - - - -
1083A LYS* 4.0 5.0 - - - +
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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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1A ADP 3.5 55.2 - - + +
1005A LEU* 3.6 20.0 - - + -
1013A VAL* 3.8 18.4 - - + -
1014A TRP 3.4 9.0 - - - +
1025A VAL* 1.3 79.0 - - - +
1027A VAL* 1.3 61.7 + - - +
1079A LEU 3.7 1.0 - - - +
1080A VAL* 3.4 3.1 - - - +
1081A MET* 2.8 45.9 + - + +
1083A LYS* 3.7 15.0 - - + -
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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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995A TYR* 3.4 43.3 - - + +
1001A THR* 4.4 0.7 - - + -
1012A PHE 3.7 1.0 - - - +
1013A VAL* 3.4 4.0 - - - +
1014A TRP* 2.9 47.9 + - + +
1016A ALA* 4.0 9.9 - - + -
1025A VAL 4.2 0.8 - - - -
1026A VAL* 1.3 75.5 - - - +
1028A LYS* 1.3 65.4 + - - +
1029A PHE* 3.6 32.1 - - + -
1078A GLN* 4.1 10.5 - - + -
1079A LEU 3.3 8.7 - - - +
1080A VAL* 4.1 8.5 - - + -
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Residues in contact with LYS1028 (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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1A ADP 3.1 51.4 + - - +
8A MG 4.1 0.6 - - - -
1012A PHE* 3.4 5.2 - - + +
1013A VAL* 4.1 16.8 - - + +
1027A VAL* 1.3 74.1 - - - +
1029A PHE* 1.3 64.9 + - - +
1030A ILE* 3.6 16.3 + - + +
1052A GLU* 2.6 35.9 + - - +
1079A LEU* 2.8 48.3 + - + +
1081A MET* 4.1 13.4 - - + +
1146A ASP* 3.4 14.1 + - - +
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Residues in contact with PHE1029 (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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990A ALA* 3.2 44.2 - - + -
991A CYS* 3.7 22.0 - - - -
995A TYR* 4.0 4.3 - + - -
1001A THR* 3.8 11.9 - - + -
1012A PHE* 2.8 55.6 + + + +
1014A TRP* 4.0 18.6 - + - -
1027A VAL* 3.6 32.3 - - + -
1028A LYS* 1.3 73.9 - - - +
1030A ILE* 1.3 61.5 + - - +
1031A LYS 4.0 1.0 + - - -
1076A PHE* 4.1 11.7 - + + -
1077A PHE 3.6 3.4 - - - -
1078A GLN* 3.7 19.1 - - + -
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Residues in contact with ILE1030 (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 LYS* 3.9 12.6 - - + +
1029A PHE* 1.3 77.1 - - - +
1031A LYS* 1.3 63.8 + - - +
1032A LYS 3.5 0.5 + - - -
1035A VAL* 4.1 23.3 - - + -
1050A THR* 4.3 13.5 - - + +
1052A GLU* 4.1 19.5 - - - +
1053A ILE* 3.8 30.3 - - + -
1076A PHE* 3.5 4.9 - - - -
1077A PHE* 2.9 45.9 + - + +
1079A LEU* 4.0 25.4 - - + -
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Residues in contact with LYS1031 (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 PHE* 4.8 11.8 - - + -
1029A PHE 4.0 1.4 + - - -
1030A ILE* 1.3 71.4 - - - +
1032A LYS* 1.3 64.4 + - - +
1033A GLU* 4.8 2.0 - - + +
1034A LYS* 3.6 23.2 + - + +
1035A VAL* 3.3 18.2 + - - +
1075A GLY 3.9 0.9 - - - +
1076A PHE* 3.6 31.3 - - + -
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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