Contacts of the strand formed by residues 996 - 1008 (chain B) in PDB entry 3PT6
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 ARG 996 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943B VAL 3.8 0.3 - - - +
945B LEU* 2.6 37.2 + - + +
946B PRO 3.3 19.9 + - - +
947B PRO* 3.3 22.7 + - + +
950B PHE* 2.9 57.5 + - + +
951B THR* 4.8 7.5 - - - +
952B PHE* 3.8 31.8 - - - -
993B GLU* 3.1 41.2 + - - +
994B PRO* 4.5 5.9 + - - +
995B TYR* 1.3 75.0 + - - +
997B ILE* 1.3 70.5 + - - +
1026B ARG* 5.4 0.6 - - - +
1029B ASN* 4.3 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 997 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B SER* 4.5 0.2 - - - +
943B VAL 3.6 10.3 - - - +
944B TYR* 4.1 16.8 - - + -
945B LEU* 5.7 0.2 - - - -
950B PHE* 3.9 10.9 - - - -
952B PHE* 6.1 0.2 - - - -
995B TYR 4.1 0.2 + - - -
996B ARG* 1.3 83.3 - - - +
998B GLY* 1.3 65.6 + - - +
1024B PHE* 3.0 53.3 + - + +
1026B ARG* 3.6 25.8 - - + +
1045B LEU* 4.3 10.3 - - + -
1063B CYS* 3.9 16.6 - - - -
1065B VAL* 4.2 7.4 - - + -
1086B PHE* 3.8 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 998 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B SER* 3.2 7.2 + - - -
943B VAL* 3.0 32.8 + - - +
945B LEU* 5.3 0.6 - - - +
950B PHE* 5.3 1.1 - - - -
997B ILE* 1.3 77.3 - - - +
999B ARG* 1.3 62.6 + - - -
1000B ILE 3.8 0.7 + - - -
1021B LEU* 4.4 17.9 - - - +
1022B TYR 3.0 15.5 - - - -
1023B LYS* 4.6 0.7 - - - -
1024B PHE* 3.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 999 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940B GLY* 2.7 32.7 + - - +
941B ASP 3.7 0.2 - - - -
942B SER* 3.4 16.3 + - - +
998B GLY* 1.3 71.9 - - - -
1000B ILE* 1.3 70.9 + - - +
1001B LYS 3.3 0.2 + - - -
1021B LEU* 3.0 4.6 - - - -
1022B TYR* 2.7 54.9 + - + -
1024B PHE* 4.0 8.8 - - + -
1047B TRP* 3.3 31.2 - - + -
1065B VAL* 4.3 17.4 + - - +
1066B GLU* 5.7 2.0 + - - -
1088B PHE* 4.1 13.5 - - - -
1105B HIS 5.7 1.3 + - - -
1106B ALA 3.9 11.4 + - - -
1107B ARG* 4.0 24.9 + - - +
1108B SER* 4.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1000 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B TYR* 4.5 11.0 - - + -
938B ARG 3.0 39.7 - - - +
939B LEU* 3.7 4.7 - - + +
940B GLY* 3.2 21.0 + - - +
941B ASP* 3.1 23.4 + - + +
942B SER 5.1 0.2 - - - -
943B VAL* 4.5 13.2 - - + -
998B GLY 4.8 0.2 - - - +
999B ARG* 1.3 75.1 - - - +
1001B LYS* 1.3 59.4 + - - +
1002B GLU 4.7 7.9 - - - +
1003B ILE* 3.8 18.4 - - + -
1019B LEU* 4.2 18.4 - - + -
1020B ARG 3.6 1.3 - - - +
1021B LEU* 3.3 25.1 - - + -
1022B TYR* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1001 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B LEU* 3.2 16.6 - - - +
999B ARG 3.3 0.4 + - - -
1000B ILE* 1.3 73.0 - - - +
1002B GLU* 1.3 79.6 + - + +
1020B ARG* 2.5 25.9 + - + +
1021B LEU 5.6 0.4 - - - +
1022B TYR* 2.6 54.5 + - + +
1051B GLU* 3.5 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1002 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926B TYR* 3.5 35.6 + - + -
939B LEU* 3.6 4.7 - - - -
1000B ILE* 4.7 0.9 - - - +
1001B LYS* 1.3 99.8 + - + +
1003B ILE* 1.3 71.1 + - - +
1004B HIS* 4.2 5.7 + - - +
1019B LEU* 3.7 4.3 - - - +
1020B ARG* 3.0 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1003 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926B TYR* 3.3 7.5 - - - +
927B CYS* 2.6 57.7 + - + +
928B SER 3.8 25.4 - - - +
929B SER 4.7 0.4 - - - +
930B ILE* 4.0 25.8 - - + -
937B TYR 4.9 1.8 - - - +
938B ARG* 4.5 2.5 - - - -
939B LEU* 3.8 16.2 - - + +
1000B ILE* 3.8 24.5 - - + -
1002B GLU* 1.3 81.5 - - - +
1004B HIS* 1.3 57.3 + - - +
1017B ILE* 4.0 17.5 - - + -
1018B LYS 3.8 3.4 - - - -
1019B LEU* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1004 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924B ARG* 3.7 28.9 + - + -
925B VAL 3.6 4.0 - - - +
926B TYR* 3.4 43.5 + + + -
1002B GLU* 4.5 7.3 + - - +
1003B ILE* 1.3 74.4 - - - +
1005B CYS* 1.3 59.6 + - - +
1017B ILE* 4.8 1.3 - - - -
1018B LYS* 3.1 52.2 + - + +
1020B ARG* 4.8 27.1 - - + -
1053B VAL* 5.0 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1005 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914B VAL* 4.7 6.1 - - - -
924B ARG* 2.8 13.2 - - - +
925B VAL* 2.6 63.7 + - - -
927B CYS* 3.7 17.2 - - - -
1004B HIS* 1.3 73.4 - - - +
1006B GLY* 1.3 58.0 + - - +
1012B VAL* 3.9 20.4 - - - -
1013B ASN 3.5 9.2 - - - +
1016B ASP 3.3 13.5 - - - +
1017B ILE* 3.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1006 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B GLY 4.8 1.3 - - - -
924B ARG* 2.5 23.2 - - - +
925B VAL* 5.0 0.4 - - - -
1005B CYS* 1.3 75.7 - - - +
1007B LYS* 1.3 58.7 + - - -
1012B VAL* 3.9 1.1 - - - -
1013B ASN* 2.5 43.5 + - - +
1016B ASP* 3.3 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1007 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B GLY* 4.3 16.5 + - - +
924B ARG 5.8 0.9 - - - -
925B VAL* 4.8 9.2 - - + +
1005B CYS 3.9 2.8 + - - -
1006B GLY* 1.3 77.2 - - - -
1008B LYS* 1.3 65.6 + - - +
1010B GLY 5.6 4.3 - - - +
1011B LYS 3.6 11.2 - - - +
1012B VAL* 4.3 3.1 - - - +
1013B ASN* 4.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1008 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B LYS* 1.3 79.3 - - - +
1009B LYS* 1.3 75.5 + - + +
1010B GLY 3.3 0.6 - - - +
1011B LYS* 2.6 25.8 + - - +
1012B VAL 4.5 2.6 - - - +
1013B ASN* 3.4 42.4 + - + +
----------------------------------------------------------
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