Contacts of the strand formed by residues 965 - 972 (chain B) in PDB entry 1ATZ
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 THR 965 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B CYS* 4.6 12.6 + - - +
925B GLN 4.8 0.2 + - - -
927B LEU* 3.3 27.0 - - + +
929B VAL* 4.0 12.3 - - + -
954B PHE* 5.2 1.8 - - + -
958B ALA* 4.3 11.4 - - + -
959B ASN* 3.0 25.3 + - - +
960B ILE* 3.4 9.6 - - - +
961B GLY 3.0 22.0 + - - +
964B LEU* 1.3 81.3 - - - +
966B GLN* 1.3 63.8 + - - +
967B VAL* 4.0 21.8 - - + -
986B PRO* 5.7 0.3 - - - +
1105B LEU* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 966 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927B LEU 2.9 6.7 + - - +
928B ASP* 3.1 22.9 + - - +
929B VAL* 3.0 27.9 + - - +
960B ILE* 4.9 0.9 - - - -
961B GLY 3.9 8.3 - - - +
962B PRO* 4.0 16.5 - - + +
965B THR* 1.3 76.3 - - - +
967B VAL* 1.3 61.7 + - - +
982B TRP* 3.6 27.3 + - + +
986B PRO* 5.9 6.0 - - + +
1024B GLY 2.9 29.6 + - - +
1026B ARG* 3.4 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 967 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B VAL* 3.4 20.2 - - + +
931B LEU* 3.7 37.9 - - + -
954B PHE* 4.0 11.2 - - + -
955B ILE* 3.9 23.2 - - + +
958B ALA* 4.5 0.7 - - + -
960B ILE* 3.6 28.6 - - + +
965B THR* 4.0 5.8 + - + -
966B GLN* 1.3 73.9 - - - +
968B SER* 1.3 65.2 + - - +
969B VAL* 4.3 1.8 - - + +
980B VAL* 4.3 13.2 - - - +
981B PRO 4.9 2.6 - - - +
982B TRP* 4.3 3.0 - - - -
984B VAL* 5.4 0.9 - - - +
991B LEU* 4.4 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 968 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B VAL 2.9 5.7 + - - +
930B ILE* 3.4 8.7 - - - -
931B LEU 2.9 25.6 + - - -
967B VAL* 1.3 75.0 - - - +
969B VAL* 1.3 63.3 + - - +
970B LEU* 3.3 8.8 - - - +
980B VAL 2.9 19.2 + - - -
981B PRO* 4.1 1.1 - - - +
982B TRP* 3.4 37.1 - - - -
1017B TYR* 3.3 20.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 969 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B LEU* 3.5 18.4 - - + +
933B LEU* 4.1 12.1 - - + -
951B ALA* 4.9 4.7 - - + -
955B ILE* 4.4 8.1 - - + -
967B VAL* 4.3 14.4 - - + -
968B SER* 1.3 79.6 + - - +
970B LEU* 1.3 69.0 + - - +
979B ASP* 2.8 25.0 + - - +
980B VAL* 3.0 37.2 + - + -
995B VAL* 4.3 13.7 - - + -
998B MET* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 970 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B ILE* 4.1 18.6 - - + -
931B LEU 3.0 9.3 + - - +
932B LEU* 3.9 11.4 - - + -
933B LEU* 2.9 27.6 + - - +
968B SER* 3.3 26.0 - - - +
969B VAL* 1.3 78.2 - - - +
971B GLN* 1.3 63.1 + - - +
976B THR* 4.0 5.8 - - + -
977B THR 3.1 15.3 - - - +
978B ILE* 3.8 18.8 - - + -
979B ASP 4.3 0.2 - - - +
998B MET* 4.7 1.1 - - - -
1013B PHE* 3.6 32.8 - - + -
1014B ALA* 4.2 17.7 - - + -
1017B TYR* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 971 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B LEU* 4.2 3.6 - - - -
933B LEU* 3.2 21.8 - - + +
935B GLY* 3.7 4.6 - - - +
944B PHE* 3.5 25.1 - - + -
970B LEU* 1.3 76.7 - - - +
972B TYR* 1.3 59.3 + - - +
975B ILE 3.9 0.7 - - - +
976B THR* 3.3 2.8 - - - +
977B THR* 2.9 41.4 + - - +
979B ASP* 2.9 28.4 + - - +
998B MET* 4.0 4.3 - - + +
999B GLN 2.9 24.0 + - - +
1001B GLU* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 972 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B LEU* 3.8 22.7 - - + -
933B LEU 3.0 30.7 + - - -
934B ASP* 3.5 26.6 + - - -
935B GLY* 2.8 33.1 + - - -
936B SER* 3.2 2.0 + - - -
971B GLN* 1.3 74.3 - - - +
973B GLY* 1.3 61.9 + - - +
975B ILE 3.6 3.8 - - - -
976B THR* 3.4 20.2 - - - +
1001B GLU* 4.8 3.1 - - - -
1005B SER* 4.1 11.6 + - - -
1006B GLN* 4.5 13.9 - - + +
1007B ILE* 3.9 28.7 - - + +
1010B ALA* 3.4 16.6 - - + -
1035B ILE* 4.2 9.0 - - + -
1036B LEU 2.6 29.7 + - - -
1037B VAL* 3.6 8.3 - - - +
----------------------------------------------------------
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