Contacts of the strand formed by residues 1023 - 1031 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998B LYS* 5.2 0.8 - - - +
999B TYR* 4.8 3.6 + - - -
1017B VAL* 3.5 3.9 - - - -
1018B ASP* 2.8 63.0 + - + +
1021B LYS* 3.8 19.5 - - + +
1022B ASN* 1.3 78.2 - - - +
1024B GLU* 1.3 64.8 + - - +
1025B VAL* 3.5 19.1 + - + +
1068B LEU* 4.3 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1024 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015B THR* 3.8 17.8 - - + +
1016B ALA 3.4 5.8 - - - +
1017B VAL* 4.5 12.2 - - + +
1022B ASN 4.2 1.0 + - - -
1023B LYS* 1.3 75.8 - - - +
1025B VAL* 1.3 62.1 + - - +
1083B LYS* 3.0 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1025 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B TYR* 3.7 17.3 - - + -
1015B THR* 3.5 9.4 - - - +
1016B ALA* 2.7 52.3 + - + +
1018B ASP 4.6 0.4 - - - +
1023B LYS* 3.9 23.8 - - - +
1024B GLU* 1.3 78.1 - - - +
1026B VAL* 1.3 68.9 + - - +
1068B LEU* 3.5 26.5 - - + -
1080B VAL* 3.7 18.8 - - + -
1081B MET 3.5 9.0 - - - +
1082B GLU* 5.2 0.4 - - - -
1083B LYS* 4.0 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1026 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ADP 3.5 57.2 - - + +
1005B LEU* 3.7 18.4 - - + -
1013B VAL* 3.7 20.6 - - + -
1014B TRP 3.5 5.4 - - - +
1025B VAL* 1.3 80.8 - - - +
1027B VAL* 1.3 60.9 + - - +
1079B LEU 3.5 0.9 - - - +
1080B VAL* 3.3 2.6 - - - +
1081B MET* 2.6 49.0 + - + +
1083B LYS* 3.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1027 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995B TYR* 3.4 42.0 - - + +
1001B THR* 4.5 0.7 - - - +
1012B PHE 3.5 1.6 - - - +
1013B VAL* 3.4 4.0 - - - +
1014B TRP* 3.0 44.6 + - + +
1016B ALA* 4.0 9.6 - - + +
1026B VAL* 1.3 76.8 - - - +
1028B LYS* 1.3 64.5 + - - +
1029B PHE* 3.8 32.5 - - + -
1078B GLN* 4.0 13.7 - - + -
1079B LEU 3.3 7.2 - - - +
1080B VAL* 4.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1028 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ADP 3.3 40.9 + - - +
10B MG 4.0 1.2 - - - -
1012B PHE* 3.5 4.3 - - + +
1013B VAL* 4.1 15.0 - - + +
1027B VAL* 1.3 73.6 - - - +
1029B PHE* 1.3 70.7 + - - +
1030B ILE* 3.7 12.2 + - + +
1052B GLU* 2.7 38.1 + - - +
1078B GLN* 3.7 2.4 - - - -
1079B LEU* 2.8 42.2 + - + +
1081B MET* 3.8 21.5 - - + +
1146B ASP* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1029 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990B ALA* 3.3 40.8 - - + -
991B CYS* 4.2 7.6 - - - -
995B TYR* 4.1 6.5 - + - -
1001B THR* 3.8 24.2 - - + -
1012B PHE* 2.8 66.1 + + + +
1014B TRP* 3.8 22.9 - + - -
1027B VAL* 3.8 27.6 - - + -
1028B LYS* 1.3 75.9 - - - +
1030B ILE* 1.3 62.9 + - - +
1031B LYS 4.2 0.6 + - - -
1076B PHE* 4.0 10.1 - + + -
1077B PHE 3.7 2.2 - - - -
1078B GLN* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1030 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B LYS* 4.0 15.3 - - + +
1029B PHE* 1.3 76.3 - - - +
1031B LYS* 1.3 69.2 + - - +
1032B LYS 4.1 0.5 + - - -
1050B THR* 4.8 12.8 - - + -
1052B GLU* 4.7 12.1 - - - +
1053B ILE* 3.8 27.8 - - + -
1076B PHE* 3.2 7.8 - - - -
1077B PHE* 2.9 59.6 + - + +
1079B LEU* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B PHE* 5.2 8.9 - - + -
1029B PHE 4.2 0.6 + - - -
1030B ILE* 1.3 81.0 - - - +
1032B LYS* 1.3 59.8 + - - +
1033B GLU* 2.8 22.7 + - + +
1075B GLY 3.9 7.6 - - - +
1076B PHE* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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