Contacts of the strand formed by residues 1059 - 1069 (chain B) in PDB entry 6ZGI
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 GLY1059 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B LEU 3.2 13.0 - - - -
729B VAL* 4.0 11.6 - - - +
782B PHE* 3.9 12.4 - - - -
948B LEU* 4.1 8.1 - - - -
1056B ALA* 2.8 30.1 + - - +
1057B PRO 3.3 1.0 - - - -
1058B HIS* 1.3 81.3 - - - +
1060B VAL* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1060 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B GLU 3.7 0.9 - - - +
726B ILE* 3.6 3.3 - - - +
727B LEU* 2.9 47.3 + - + +
729B VAL* 4.4 4.9 - - + -
781B VAL* 4.9 2.7 - - + -
782B PHE* 4.0 24.7 - - + -
948B LEU* 5.2 0.4 - - - +
1025B ALA* 4.2 11.4 - - + -
1029B MET* 4.5 8.7 - - + -
1053B PRO* 4.6 0.4 - - + -
1054B GLN 3.4 17.5 - - - +
1056B ALA* 4.4 0.8 - - - +
1059B GLY* 1.3 73.3 - - - +
1061B VAL* 1.3 75.4 + - - +
1062B PHE* 3.7 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1061 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B THR* 4.4 11.9 - - + -
725B GLU 3.2 4.5 - - - +
726B ILE* 3.5 35.0 - - + -
818B ILE* 6.4 0.4 - - + -
822B LEU* 3.7 33.9 - - + -
938B LEU* 6.5 0.4 - - + -
945B LEU* 4.9 0.7 - - + -
1052B PHE 3.9 0.3 - - - +
1053B PRO* 3.5 3.6 - - - +
1054B GLN* 2.9 41.9 + - + +
1056B ALA* 4.1 12.1 - - + -
1060B VAL* 1.3 79.9 - - - +
1062B PHE* 1.3 71.2 + - - +
1063B LEU* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1062 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B THR 3.5 1.4 - - - +
724B THR* 3.2 8.0 - - - -
725B GLU* 2.9 42.4 + - - +
727B LEU* 4.3 15.9 - - + -
1025B ALA 3.9 18.2 - - - -
1028B LYS* 4.0 17.3 - - + -
1029B MET* 3.9 31.2 - - + -
1032B CYS* 5.7 0.7 - - + -
1033B VAL* 4.0 30.1 - - + -
1051B SER* 5.0 2.0 - - - -
1052B PHE 3.6 1.8 - - - -
1053B PRO* 4.3 8.5 - - + -
1060B VAL* 3.7 28.0 - - + -
1061B VAL* 1.3 76.9 - - - +
1063B LEU* 1.3 61.9 + - - +
1064B HIS* 3.6 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1063 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B VAL* 4.3 13.2 - - + -
723B THR 3.4 3.6 - - - +
724B THR* 3.6 29.2 - - + -
805B ILE* 4.0 27.4 - - + -
818B ILE* 4.7 10.1 - - + -
931B ILE* 4.7 15.5 - - + -
934B ILE* 4.4 12.3 - - + -
1051B SER* 3.1 5.8 - - - -
1052B PHE* 2.9 58.1 + - + +
1054B GLN* 4.6 14.1 - - + -
1061B VAL* 4.6 7.6 - - + -
1062B PHE* 1.3 73.2 - - - +
1064B HIS* 1.3 61.4 + - - +
1065B VAL 3.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1064 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B SER 3.4 2.6 - - - +
722B VAL* 3.2 4.0 - - - -
723B THR* 2.9 51.8 + - + +
724B THR 5.1 0.2 - - - -
725B GLU* 3.2 33.8 + - + +
1028B LYS* 4.8 1.4 - - - +
1032B CYS* 4.3 7.7 - - - -
1042B PHE 4.8 0.6 + - - -
1043B CYS* 3.4 44.7 - - + +
1044B GLY* 4.2 4.9 + - - -
1048B HIS* 4.9 0.4 - - + -
1050B MET 3.7 3.1 - - - +
1051B SER* 3.0 28.9 + - - +
1062B PHE* 3.6 30.1 + + + +
1063B LEU* 1.3 70.8 - - - +
1065B VAL* 1.3 60.4 + - - +
1066B THR* 3.9 2.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1065 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B ILE* 3.7 28.5 - - + -
721B SER 3.4 5.6 - - - +
722B VAL* 4.0 20.2 - - + -
927B PHE* 4.2 11.7 - - + -
1048B HIS* 4.2 0.5 - - - -
1049B LEU* 2.8 39.4 + - + +
1050B MET* 2.8 32.8 + - + +
1052B PHE* 3.8 29.4 - - + -
1063B LEU 4.5 1.1 - - - +
1064B HIS* 1.3 72.8 - - - +
1066B THR* 1.3 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B ILE* 3.6 6.6 - - - +
721B SER* 2.9 49.1 + - - -
723B THR* 5.4 3.4 - - + +
1043B CYS 3.7 22.9 - - - +
1044B GLY* 4.5 1.8 - - - -
1045B LYS 3.0 29.6 + - - +
1046B GLY* 4.1 5.4 - - - +
1047B TYR 3.3 11.4 - - - -
1048B HIS* 3.8 13.2 - - - +
1049B LEU* 4.1 6.3 - - - +
1064B HIS* 4.6 5.3 + - + +
1065B VAL* 1.3 78.9 - - - +
1067B TYR* 1.3 59.5 + - - +
1068B VAL* 4.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B ASN 4.9 1.6 + - - -
718B PHE* 3.5 46.1 - + + +
719B THR 3.7 2.9 - - - -
720B ILE* 4.3 9.4 - - + -
906B PHE* 4.1 27.4 - + - -
909B ILE* 3.7 25.8 - - + -
911B VAL* 4.3 17.9 - - + +
1046B GLY* 3.8 1.9 - - - -
1047B TYR* 2.9 51.3 + + + +
1049B LEU* 4.3 7.6 - - + -
1066B THR* 1.3 71.7 - - - +
1068B VAL* 1.3 66.4 + - - +
1069B PRO* 4.1 19.5 - - + +
1108B ASN* 4.1 17.6 + - + -
1109B PHE* 4.2 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1068 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B PHE* 3.4 2.4 - - - +
719B THR* 2.8 51.3 + - + +
721B SER* 3.7 26.7 - - - +
1045B LYS 4.5 11.9 - - - +
1046B GLY* 4.9 0.2 - - - -
1066B THR* 4.5 0.2 - - - +
1067B TYR* 1.3 82.1 - - - +
1069B PRO* 1.3 79.1 - - + +
1070B ALA* 5.7 0.4 - - - -
890C ALA 4.3 14.1 - - - +
891C GLY* 4.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1069 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B PRO* 3.7 28.7 - - + -
717B ASN 4.0 5.6 - - - +
718B PHE* 4.6 0.9 - - - -
1047B TYR* 4.1 25.1 - - + +
1067B TYR* 4.1 16.8 - - + +
1068B VAL* 1.3 96.4 - - + +
1070B ALA* 1.3 61.3 + - - +
1108B ASN* 5.2 5.6 - - - +
890C ALA* 4.7 11.4 - - + +
891C GLY* 5.5 2.4 - - - -
892C ALA* 5.3 9.5 + - - +
894C LEU* 5.4 7.6 - - + -
----------------------------------------------------------
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