Contacts of the strand formed by residues 976 - 980 (chain B) in PDB entry 3SQD
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 LYS 976 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972B LEU 4.4 3.0 + - - +
973B PHE* 3.0 34.1 + - + +
974B LYS 3.9 6.6 + - - +
975B ALA* 1.3 84.3 - - - +
977B TYR* 1.3 65.7 + - - +
978B PHE* 4.1 12.3 - - + -
999B GLY 4.8 0.6 + - - -
1000B GLY* 3.5 4.0 - - - -
1001B LYS* 3.0 26.7 + - - +
1023B GLU* 3.6 30.9 + - + +
1025B ILE* 4.9 9.4 - - + -
1051B PHE* 6.2 0.7 - - + -
1061B LEU* 3.7 21.6 - - + +
1063B TYR* 3.5 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 977 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976B LYS* 1.3 74.6 - - - +
978B PHE* 1.3 64.2 + - - +
1001B LYS* 3.2 39.7 - - + +
1003B LEU* 3.6 30.3 - - + -
1011B LYS* 4.6 13.5 - - - -
1014B GLU* 6.1 1.6 - - - -
1022B SER* 3.3 37.6 + - - -
1023B GLU 2.9 11.5 + - - +
1024B ILE* 3.4 20.1 - - + -
1025B ILE* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 978 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B PHE* 3.5 52.9 - + + -
976B LYS* 4.1 17.5 - - + -
977B TYR* 1.3 81.0 - - - +
979B TYR* 1.3 59.7 + - - +
980B ILE* 4.0 17.3 - - + -
995B VAL* 3.7 19.1 - - + -
1001B LYS 2.9 8.3 + - - +
1002B VAL* 3.4 8.2 - - + +
1003B LEU* 2.8 29.9 + - - +
1025B ILE* 3.1 35.2 - - + +
1027B ILE* 3.9 13.0 - - + -
1051B PHE* 3.9 8.7 - + - -
1052B VAL* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 979 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977B TYR 4.3 0.2 - - - -
978B PHE* 1.3 72.8 - - - +
980B ILE* 1.3 79.9 + - - +
981B THR* 4.2 16.3 - - + +
982B PRO* 4.2 14.6 - - - +
1003B LEU* 3.6 20.0 - - + -
1004B SER 3.6 16.6 + - - -
1005B LYS* 3.5 27.5 - - - -
1006B GLN* 3.7 29.7 + - + +
1007B PRO* 3.9 17.7 - - + -
1024B ILE* 4.6 2.0 - - + +
1025B ILE 2.9 7.3 + - - -
1026B LEU* 3.5 14.3 - - + +
1027B ILE 2.8 27.4 + - - +
1039B TYR* 5.7 2.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 980 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978B PHE* 4.1 15.0 + - + -
979B TYR* 1.3 93.6 - - - +
981B THR* 1.3 72.0 + - - +
982B PRO* 3.6 3.3 - - - +
984B ILE* 3.8 24.9 - - + -
988B LEU* 3.7 28.4 - - + +
991B MET* 4.1 26.5 - - + -
995B VAL* 4.4 8.7 - - + -
1002B VAL* 3.9 30.1 - - + +
1003B LEU 5.0 1.9 + - - +
1027B ILE* 3.3 22.9 - - + +
----------------------------------------------------------
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