Contacts of the strand formed by residues 1099 - 1104 (chain O) in PDB entry 2X4Y
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 TYR1099 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090O TRP* 4.1 2.2 - - - -
1091O ALA* 2.8 32.6 + - - +
1097O PRO* 4.1 5.2 - - + +
1098O SER* 1.3 74.6 - - - +
1100O PRO* 1.4 87.7 - - + +
1101O ALA 3.5 0.2 + - - -
1147O PHE* 3.4 24.7 - + + -
1148O PHE 4.3 0.2 - - - -
1149O ASP* 3.3 43.5 - - + +
1150O ASN 4.8 0.3 + - - -
1187O SER* 3.1 33.2 + - - -
1188O VAL* 3.6 26.0 - - + -
1191O ALA* 3.4 22.2 - - + +
1194O ARG* 4.8 2.1 + - - -
36P M3L 3.7 31.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1100 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089O VAL 3.5 7.4 - - - +
1090O TRP* 3.7 21.8 - - + -
1099O TYR* 1.4 104.4 - - + +
1101O ALA* 1.3 60.0 + - - +
1147O PHE* 3.6 0.2 - - - -
1148O PHE* 3.1 22.2 + - + -
1165O LEU* 3.6 17.0 - - + -
1188O VAL* 3.8 9.4 - - + +
1191O ALA* 3.7 22.4 - - + +
1192O TYR* 3.5 29.6 - - - +
1195O ALA* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1101 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088O LEU* 3.4 6.2 - - - +
1089O VAL* 2.8 33.6 + - + +
1091O ALA* 4.0 12.3 - - + -
1100O PRO* 1.3 76.0 - - - +
1102O LEU* 1.3 60.5 + - - +
1145O VAL* 3.9 17.5 - - + -
1146O LEU 3.3 16.8 - - - +
1147O PHE* 3.9 16.6 - - + -
1148O PHE* 3.6 12.6 - - - -
1165O LEU* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086O LEU* 3.4 39.3 - - + +
1087O ASP 3.5 3.6 - - - +
1088O LEU* 4.0 12.8 - - + -
1101O ALA* 1.3 73.9 - - - +
1103O ILE* 1.3 70.6 + - - +
1104O ILE* 3.5 24.7 + - + +
1120O ILE* 4.4 6.3 - - + -
1121O PRO* 5.6 1.8 - - + -
1145O VAL* 3.2 4.0 - - - -
1146O LEU* 2.7 43.4 + - + +
1148O PHE* 4.1 11.2 - - + -
1152O ARG* 5.2 4.7 - - - +
1198O HIS* 3.9 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083O LEU* 3.7 34.5 - - + -
1084O ASP 3.6 22.4 - - - +
1085O ALA* 4.0 7.9 - - - -
1086O LEU* 2.6 34.3 + - - +
1087O ASP* 3.1 15.8 + - + +
1089O VAL* 3.7 28.7 - - + -
1102O LEU* 1.3 71.0 - - - +
1104O ILE* 1.3 65.7 + - - +
1143O TYR* 4.3 22.0 - - + -
1144O LEU 3.4 10.3 - - - +
1145O VAL* 4.4 6.5 - - + +
1162O LEU* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085O ALA* 4.7 0.2 - - - -
1086O LEU* 3.9 3.4 - - + -
1102O LEU* 3.5 33.0 - - + +
1103O ILE* 1.3 83.8 - - - +
1105O ASP* 1.3 73.6 + - - +
1106O PRO* 3.2 13.5 - - - +
1108O MET* 3.6 20.4 - - - -
1120O ILE* 3.4 28.5 - - + -
1121O PRO 4.4 2.9 - - - +
1123O PRO* 4.1 14.4 - - + -
1144O LEU* 2.8 27.6 + - + +
1146O LEU* 4.0 11.0 - - + -
1154O TRP* 3.9 22.9 - - + -
----------------------------------------------------------
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