Contacts of the strand formed by residues 1050 - 1054 (chain D) in PDB entry 2O8J
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 TRP1050 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937D CYS* 3.6 11.7 - - - -
938D VAL 3.6 22.0 - - - -
939D ASN* 3.8 11.9 - - + -
944D GLU* 3.8 28.4 - - + +
945D PRO 3.1 24.7 + - - -
946D CYS* 4.0 10.5 - - - -
947D PRO* 3.6 29.5 - - + +
1042D LEU* 3.9 12.1 - - + -
1043D TYR 3.5 20.4 - - - -
1044D ARG* 3.2 34.4 - - + +
1049D GLY* 1.3 73.7 - - - -
1051D GLY* 1.3 58.0 + - - +
1110D PHE* 3.5 24.9 - + + +
1112D ASN* 3.0 7.6 - - - +
1517D SAH 2.7 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1051 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042D LEU* 3.4 9.2 - - - +
1043D TYR* 2.9 36.3 + - - -
1045D THR* 3.7 12.2 - - - +
1050D TRP* 1.3 74.3 - - - +
1052D VAL* 1.3 65.0 + - - -
1110D PHE 3.4 9.0 - - - -
1112D ASN* 3.5 10.5 - - - -
1149D GLU* 3.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1052 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040D LEU* 4.1 15.3 - - + -
1041D GLN 3.4 9.6 - - - +
1042D LEU* 4.6 0.2 - - + -
1043D TYR* 3.7 1.7 - - - -
1051D GLY* 1.3 79.9 - - - +
1053D ARG* 1.3 57.7 + - - +
1107D ILE* 3.6 49.8 - - + +
1110D PHE* 3.6 18.2 + - + -
1111D ILE* 3.9 17.5 - - + +
1149D GLU* 3.4 8.9 + - - +
1150D LEU* 2.7 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1053 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938D VAL* 3.6 18.6 - - - +
1040D LEU* 3.4 5.2 - - - +
1041D GLN* 2.8 65.0 + - + +
1043D TYR* 3.4 45.3 - - + +
1052D VAL* 1.3 75.5 - - - +
1054D ALA* 1.3 66.0 + - - +
1055D LEU* 5.0 3.2 - - + +
1147D GLY* 3.4 25.3 + - - +
1148D GLU 3.3 16.4 - - - +
1149D GLU* 3.9 0.4 - - - -
1150D LEU* 3.8 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1054 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039D ARG 3.9 5.4 - - - +
1040D LEU* 4.4 2.7 - - - -
1053D ARG* 1.3 72.5 - - - +
1055D LEU* 1.3 61.2 + - - +
1056D GLN 3.3 21.1 - - - +
1058D ILE* 3.7 21.8 - - + -
1144D ILE* 4.0 18.4 - - + -
1145D ARG 4.0 6.3 - - - +
1147D GLY* 2.8 31.4 + - - -
1148D GLU 3.0 8.4 + - - +
1150D LEU* 3.5 5.1 - - + +
----------------------------------------------------------
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