Contacts of the strand formed by residues 1023 - 1031 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017D VAL* 3.5 6.7 - - - -
1018D ASP* 3.1 40.7 + - + +
1021D LYS* 4.8 12.0 - - + +
1022D ASN* 1.3 78.7 - - - +
1024D GLU* 1.3 73.3 + - - +
1025D VAL* 3.7 13.3 + - + +
1068D LEU* 4.4 18.8 - - - +
1082D GLU* 6.1 2.9 - - - +
1244E LYS* 6.6 0.2 - - + -
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Residues in contact with GLU1024 (chain D).
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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1002D MET* 6.1 1.4 - - - +
1015D THR* 3.4 19.4 - - + +
1016D ALA 3.4 4.7 - - - +
1017D VAL* 4.4 11.4 - - + -
1023D LYS* 1.3 86.8 - - - +
1025D VAL* 1.3 63.5 + - - +
1083D LYS* 2.7 51.6 + - + +
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Residues in contact with VAL1025 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999D TYR* 3.6 29.6 - - + -
1015D THR* 3.6 8.5 - - - +
1016D ALA* 2.7 51.1 + - + +
1017D VAL 4.3 0.2 - - - +
1018D ASP* 4.5 4.5 - - + -
1023D LYS* 4.2 15.9 - - - +
1024D GLU* 1.3 78.9 - - - +
1026D VAL* 1.3 66.5 + - - +
1068D LEU* 3.5 24.2 - - + -
1080D VAL* 3.7 12.8 - - + -
1081D MET 3.6 10.8 - - - +
1083D LYS* 4.1 6.5 - - - +
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Residues in contact with VAL1026 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ADP 3.8 32.3 - - + +
1005D LEU* 3.2 25.6 - - + -
1013D VAL* 4.0 13.5 - - + -
1014D TRP 3.5 6.7 - - - +
1025D VAL* 1.3 75.6 - - - +
1027D VAL* 1.3 62.9 + - - +
1079D LEU 3.6 1.0 - - - +
1080D VAL* 3.3 4.0 - - - -
1081D MET* 2.7 62.2 + - + +
1083D LYS* 3.6 26.2 - - + +
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Residues in contact with VAL1027 (chain D).
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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995D TYR* 3.5 45.1 - - + +
1001D THR* 4.4 1.1 - - + -
1012D PHE 3.4 1.0 - - - +
1013D VAL* 3.4 5.9 - - - +
1014D TRP* 3.0 50.1 + - + +
1016D ALA* 4.0 8.9 - - + +
1025D VAL 4.3 0.6 - - - -
1026D VAL* 1.3 75.2 - - - +
1028D LYS* 1.3 63.8 + - - +
1029D PHE* 3.7 33.0 - - + -
1078D GLN* 4.2 8.7 - - + -
1079D LEU 3.4 6.7 - - - +
1080D VAL* 4.1 7.9 - - + -
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Residues in contact with LYS1028 (chain D).
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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4D ADP 3.2 42.1 + - - +
14D MG 4.2 0.2 - - - -
1012D PHE* 3.4 6.1 - - + +
1013D VAL* 4.2 12.1 - - + +
1027D VAL* 1.3 74.1 - - - +
1029D PHE* 1.3 70.2 + - - +
1030D ILE* 3.8 11.4 + - + +
1052D GLU* 2.7 35.1 + - - +
1077D PHE 3.7 0.5 - - - +
1078D GLN* 3.6 1.2 - - - -
1079D LEU* 2.8 56.6 + - + +
1081D MET* 3.8 15.0 - - + -
1146D ASP* 3.1 23.4 + - - +
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Residues in contact with PHE1029 (chain D).
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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990D ALA* 3.3 42.0 - - + -
991D CYS* 4.0 12.3 - - - -
995D TYR* 4.2 3.8 - + - -
1001D THR* 3.9 17.5 - - + -
1011D GLY 5.3 0.2 - - - -
1012D PHE* 2.9 61.6 + + + +
1014D TRP* 4.0 21.1 - + - -
1027D VAL* 3.7 33.4 - - + -
1028D LYS* 1.3 74.2 - - - +
1030D ILE* 1.3 63.1 + - - +
1031D LYS 4.0 0.7 - - - -
1076D PHE* 4.1 12.6 - - + -
1077D PHE 3.3 3.8 - - - +
1078D GLN* 3.7 19.5 - - + -
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Residues in contact with ILE1030 (chain D).
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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1028D LYS* 4.4 17.7 - - + +
1029D PHE* 1.3 76.1 - - - +
1031D LYS* 1.3 63.0 + - - +
1032D LYS 3.3 2.1 + - - -
1035D VAL* 3.7 26.7 - - + -
1050D THR* 4.4 8.5 - - + -
1052D GLU* 3.7 28.3 - - - +
1053D ILE* 3.9 26.5 - - + -
1076D PHE* 3.9 2.0 - - - -
1077D PHE* 2.7 53.8 + - + +
1079D LEU* 4.6 9.9 - - + -
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Residues in contact with LYS1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984D GLU* 4.1 15.2 + - - -
986D GLU* 3.9 27.2 + - - -
1012D PHE* 5.1 16.1 - - + -
1029D PHE 4.0 1.6 + - - -
1030D ILE* 1.3 69.6 - - - +
1032D LYS* 1.3 66.2 + - - +
1033D GLU* 3.9 18.9 - - + +
1034D LYS* 3.2 49.5 + - + +
1035D VAL* 3.3 13.8 + - - +
1075D GLY 4.2 3.9 + - - +
1076D PHE* 3.7 41.2 - - + -
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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