Contacts of the strand formed by residues 1085 - 1093 (chain B) in PDB entry 1Y1V
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 ILE1085 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A GLY* 6.1 0.4 - - - -
662A PHE 4.9 5.4 - - - +
663A SER* 2.9 20.0 - - - +
826B ALA 4.5 0.2 - - - -
827B ILE 3.0 17.7 - - - +
828B ALA* 3.7 18.8 - - + -
1069B PHE* 3.0 8.3 - - - -
1070B GLU* 2.7 38.2 + - - +
1072B MET* 3.3 37.6 - - + +
1081B LEU* 3.6 30.7 - - + -
1083B ALA* 4.5 4.3 - - + +
1084B GLN* 1.3 87.6 - - - +
1086B PHE* 1.3 84.0 + - - +
1087B PHE* 3.3 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A SER* 3.2 5.4 + - - +
664A THR 3.4 20.6 - - - +
665A GLY* 4.1 1.6 - - - -
666A ILE* 3.7 13.9 - - + -
825B VAL 3.6 1.6 - - - +
826B ALA* 3.4 6.9 - - - -
827B ILE* 3.1 48.1 + - + +
1026B LEU* 3.3 35.4 - - + -
1029B CYS* 3.0 40.2 - - + -
1030B LEU* 4.1 11.0 - - + -
1067B ARG 3.2 26.9 - - - -
1068B GLY* 4.1 6.3 - - - -
1069B PHE* 4.0 17.8 - + + +
1085B ILE* 1.3 77.1 - - - +
1087B PHE* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B ILE* 3.3 25.4 - - + -
825B VAL 3.2 16.4 - - - -
826B ALA* 3.9 4.5 - - + -
1002B THR* 3.7 25.4 - - + -
1006B ILE* 4.6 2.0 - - + -
1007B VAL* 3.6 5.6 - - - -
1008B PRO* 3.4 42.4 - - + -
1029B CYS* 4.3 3.5 - - - -
1033B LYS* 2.9 29.1 + - - +
1068B GLY* 3.4 6.5 + - - +
1070B GLU* 3.3 25.1 - - + +
1072B MET* 3.5 35.0 - - + -
1085B ILE 3.3 8.8 + - - +
1086B PHE* 1.3 74.6 - - - +
1088B GLY* 1.3 59.9 + - - +
44J TYR* 4.2 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B ILE* 4.3 3.6 - - - -
825B VAL 2.7 39.5 + - - +
1029B CYS* 3.7 13.9 - - - -
1033B LYS* 4.2 2.5 - - - -
1087B PHE* 1.3 78.6 - - - +
1089B PRO* 1.3 74.4 - - - +
1090B THR* 3.2 6.8 + - - -
44J TYR* 4.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1089 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B LEU* 3.4 23.3 - - + -
822B ASN* 4.9 4.9 - - + -
823B ALA 3.5 9.4 - - - +
824B ILE* 4.2 13.0 - - + -
1029B CYS* 3.6 15.4 - - - -
1032B SER* 3.3 15.4 - - - +
1033B LYS* 3.1 44.6 - - + +
1036B ALA* 4.4 5.2 - - + -
1088B GLY* 1.3 80.4 - - - +
1090B THR* 1.3 69.9 + - - +
44J TYR* 4.2 12.8 - - + -
48J ARG* 5.4 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B ASN* 4.5 1.0 - - - +
823B ALA 2.9 23.6 + - - +
825B VAL* 3.7 12.1 - - - +
982B SER* 5.1 0.4 - - - -
1025B HIS* 4.1 33.6 - - + +
1028B GLU* 3.8 27.1 - - + +
1029B CYS* 4.4 8.9 - - - +
1032B SER* 5.3 0.9 - - - -
1088B GLY 3.2 10.6 + - - -
1089B PRO* 1.3 81.1 + - - +
1091B TYR* 1.3 73.1 + - - +
1092B TYR* 3.0 20.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B ILE* 6.3 0.2 - - + -
800B GLN 2.9 26.4 + - - -
802B PRO* 3.4 34.6 - - + +
803B LEU 5.1 0.4 - - - +
814B PHE* 4.2 13.0 - + - -
818B PRO* 3.4 2.4 - - - +
819B ALA 2.5 19.1 + - - -
820B GLY* 2.3 45.0 + - - -
821B GLN 3.5 5.6 - - - -
822B ASN* 3.4 30.1 + - - +
982B SER* 4.1 7.6 - - - -
983B ARG* 3.7 34.8 - - + +
1028B GLU* 3.7 19.1 + - - +
1032B SER* 5.5 0.8 + - - -
1090B THR* 1.3 76.2 - - - +
1092B TYR* 1.3 64.7 + - - +
1093B GLN* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B GLY* 3.1 4.6 - - - -
821B GLN 3.1 28.8 + - - +
823B ALA* 4.7 4.0 - - + -
825B VAL* 4.0 23.1 - - + -
839B MET* 3.8 23.1 - - + -
851B PHE* 4.0 18.7 - - + -
980B PHE* 4.8 1.3 - - + -
981B ALA* 3.0 32.5 - - - -
982B SER* 3.2 29.1 + - - +
986B GLN* 4.6 8.9 + - - +
1010B LEU* 4.4 6.5 - - + -
1012B ILE* 3.1 29.9 - - + +
1025B HIS* 3.5 20.3 + + - -
1090B THR* 3.0 24.3 + - + +
1091B TYR* 1.3 75.9 - - - +
1093B GLN* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B ILE* 5.8 7.2 - - - +
770B GLN* 3.3 24.1 + - - +
773B MET* 5.2 2.6 - - - +
774B GLY* 3.5 27.0 + - - -
777B ALA* 3.6 20.2 - - + +
814B PHE* 5.7 3.2 - - - -
819B ALA* 3.5 31.2 - - - +
820B GLY* 4.1 0.2 - - - -
851B PHE* 4.2 2.7 - - - -
980B PHE* 3.7 6.4 - - - -
981B ALA* 2.6 32.6 + - + +
982B SER 3.4 11.1 - - - +
983B ARG* 4.0 9.8 - - + +
1091B TYR* 4.4 10.4 - - + -
1092B TYR* 1.3 79.7 - - - +
1094B ARG* 1.3 61.6 + - - +
1095B LEU* 3.8 4.3 + - + +
----------------------------------------------------------
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