Contacts of the strand formed by residues 1169 - 1173 (chain A) in PDB entry 2Y23
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 PHE1169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1158A PHE* 4.0 13.5 - + - -
1160A CYS* 4.2 7.9 - - + -
1163A MET* 3.7 24.5 - - + -
1168A GLU* 1.3 79.2 - - - +
1170A SER* 1.3 62.2 + - - +
1171A TRP* 4.9 2.5 - - + +
1188A SER* 3.9 13.2 + - - +
1190A GLY 4.1 7.2 - - - -
1191A ASN 3.6 22.9 - - - -
1192A LYS* 3.9 19.5 - - - -
1193A THR* 3.3 40.8 - - + +
1210A CYS* 4.0 13.2 - - - -
1211A ASP 3.5 3.1 - - - -
1212A VAL* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168A GLU* 4.9 2.0 - - - -
1169A PHE* 1.3 76.6 - - - +
1171A TRP* 1.3 65.4 + - - +
1172A SER* 6.0 0.2 - - - -
1209A SER 3.9 0.5 - - - +
1210A CYS* 3.7 1.7 - - - -
1211A ASP* 3.0 46.0 + - - +
1213A THR* 5.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144A VAL* 3.9 42.4 - - + -
1156A LEU* 4.0 30.5 - - + -
1158A PHE* 4.2 8.5 - - + -
1169A PHE* 5.0 1.3 - - + -
1170A SER* 1.3 81.0 + - - +
1172A SER* 1.3 60.4 + - - +
1177A SER* 3.9 5.7 + - - -
1178A THR* 3.2 33.5 + - + +
1186A VAL* 3.9 32.1 - - + +
1193A THR* 3.6 33.4 + - + +
1195A MET* 4.2 29.7 - - + +
1208A TYR* 4.6 6.1 - + + -
1209A SER 3.3 25.4 - - - -
1210A CYS* 3.8 19.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170A SER* 5.2 0.7 + - - -
1171A TRP* 1.3 73.1 - - - +
1173A LYS* 1.3 60.3 + - - +
1174A ASP 4.2 0.2 - - - -
1175A TYR* 4.1 10.9 - - - -
1176A VAL 3.1 28.7 - - - -
1177A SER* 4.1 2.0 - - - -
1178A THR* 3.6 6.1 - - - -
1207A ILE 3.6 0.3 - - - +
1208A TYR* 3.3 8.8 - - - +
1209A SER* 3.0 47.1 + - - +
1211A ASP* 4.7 8.1 + - - -
2451A PG0 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172A SER* 1.3 72.8 - - - +
1174A ASP* 1.3 79.9 + - - +
1175A TYR 3.0 4.4 + - - -
1176A VAL* 2.7 26.0 + - - +
1178A THR* 3.4 17.5 - - + +
1183A ARG* 6.2 0.4 - - - +
1184A LEU* 5.9 1.8 - - + -
1203A ASP 3.5 23.2 + - - -
1204A ASP* 4.2 1.6 + - - +
1205A LEU 3.4 24.9 + - - -
1206A GLY* 4.8 1.1 - - - -
1207A ILE 3.4 5.2 - - - +
1208A TYR* 3.4 34.5 - - + +
----------------------------------------------------------
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