Contacts of the strand formed by residues 1148 - 1155 (chain A) in PDB entry 1YO8
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 GLY1148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A ASP 5.1 1.6 - - - -
882A ALA* 3.6 8.4 - - - +
1004A GLU* 4.4 2.5 - - - -
1005A PHE* 2.9 38.4 + - - +
1030A GLY* 3.7 8.7 + - - -
1031A TYR 3.5 11.7 - - - -
1032A GLN* 4.6 2.0 - - - -
1147A GLY* 1.3 74.2 - - - -
1149A ARG* 1.3 67.3 + - - -
1150A LEU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A ASN 4.3 1.8 + - - -
852A ASP* 5.2 2.0 - - - +
853A LEU* 3.6 20.2 - - - +
963A GLN* 2.4 30.7 + - - +
1000A VAL* 3.2 22.6 + - + +
1001A GLY 2.6 40.6 + - - +
1002A PHE* 3.8 28.9 - - - +
1003A ASP 3.6 11.4 - - - +
1004A GLU* 3.9 20.6 + - + +
1005A PHE* 4.7 0.2 - - - -
1029A PHE 3.4 1.6 - - - -
1030A GLY 3.2 8.5 + - - -
1031A TYR* 2.7 63.9 + - + +
1032A GLN 5.5 1.6 + - - -
1148A GLY* 1.3 76.8 - - - -
1150A LEU* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A PHE* 3.9 10.2 - - + -
1000A VAL* 3.3 5.9 - - - +
1001A GLY* 2.9 25.9 + - - +
1003A ASP 4.4 2.6 + - - -
1005A PHE* 3.4 25.4 - - + -
1008A VAL* 4.3 13.0 - - + -
1010A PHE* 3.7 33.7 - - + -
1028A VAL* 3.4 6.1 - - - -
1029A PHE* 3.5 28.7 - - + -
1030A GLY 4.7 1.3 - - - +
1148A GLY 5.4 0.7 - - - +
1149A ARG* 1.3 76.2 - - - +
1151A GLY* 1.3 59.5 + - - +
1167A TYR* 3.4 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A PHE* 4.1 7.5 - - - -
999A ALA 2.9 13.9 - - - -
1000A VAL* 3.7 4.5 - - - -
1010A PHE* 4.2 2.2 - - - -
1027A PHE* 3.3 9.0 - - - +
1028A VAL* 2.8 36.3 + - - +
1150A LEU* 1.3 77.8 - - - +
1152A LEU* 1.3 67.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A PHE* 5.2 6.3 - - + -
979A TRP* 3.7 17.9 - - + -
988A LEU* 3.7 28.5 - - + -
998A ILE* 3.2 6.4 - - - +
999A ALA* 2.8 34.0 + - + +
1010A PHE* 4.3 6.5 - - + -
1026A GLY 3.8 1.1 - - - -
1027A PHE* 4.0 4.0 - - + -
1112A TRP* 3.7 24.0 - - + -
1151A GLY* 1.3 80.8 - - - +
1153A PHE* 1.3 60.8 + - - +
1162A PHE* 3.2 48.7 - - + -
1165A LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A LEU* 3.6 26.0 - - + -
979A TRP* 4.2 0.4 - - - -
996A PRO* 4.8 0.4 - - + -
997A GLY 3.7 10.5 - - - -
998A ILE* 3.9 12.3 - - + -
1024A TYR* 4.5 2.0 - - + -
1025A ALA* 3.2 4.9 - - - -
1026A GLY 2.9 49.2 + - - +
1027A PHE* 3.8 11.2 - - - +
1028A VAL* 4.2 9.4 - - + -
1037A PHE* 5.2 1.6 - + - -
1039A VAL* 4.0 13.9 - - + -
1040A VAL 4.8 0.2 - - - -
1041A MSE 3.7 42.6 - - + -
1082A LEU* 4.8 7.9 - - + -
1152A LEU* 1.3 75.3 - - - +
1154A VAL* 1.3 71.4 + - - +
1155A PHE* 3.9 36.1 - + + -
1162A PHE* 3.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977A PRO* 4.1 12.1 - - + -
979A TRP* 3.5 20.8 - - + -
990A GLN* 3.6 35.7 - - + +
994A SER* 3.5 22.7 - - - +
995A ASP 4.3 0.2 - - - +
996A PRO* 3.3 2.1 - - - +
997A GLY 3.0 36.1 + - - +
1024A TYR 3.9 4.5 - - - +
1025A ALA* 4.8 4.3 - - + -
1153A PHE* 1.3 85.2 - - - +
1155A PHE* 1.3 62.5 + - - +
1156A SER 5.1 0.7 - - - +
1157A GLN 4.4 9.9 - - - +
1160A VAL* 4.8 1.1 - - + -
1162A PHE* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A SER 4.5 0.9 - - - -
996A PRO* 3.4 37.7 - - + -
1023A ASP* 3.4 1.7 - - - +
1024A TYR* 3.1 50.6 + + + +
1041A MSE 5.5 0.2 - - - -
1049A TYR* 4.0 14.8 - + - -
1050A TRP* 5.5 1.1 - + - -
1079A ARG* 3.7 41.7 - - + -
1082A LEU* 4.3 8.5 - - + -
1083A TRP* 3.5 42.9 - + + -
1153A PHE* 3.9 15.7 - + + -
1154A VAL* 1.3 74.5 - - - +
1156A SER* 1.3 76.3 + - - +
1157A GLN 3.4 0.7 - - - -
----------------------------------------------------------
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