Contacts of the strand formed by residues 1131 - 1136 (chain B) in PDB entry 5J67
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 SER1131 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B THR 5.4 0.5 + - - -
1016B GLN* 4.0 12.6 - - - +
1017B PRO 2.9 24.6 + - - -
1018B VAL* 3.9 2.6 - - - +
1019B LEU* 3.1 28.6 + - - +
1116B PHE 4.1 0.2 - - - +
1117B THR* 3.2 3.6 - - - -
1118B LEU* 2.7 40.4 + - - +
1130B LEU* 1.3 76.2 - - - +
1132B THR* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B THR 2.9 20.1 - - - +
790B GLY* 4.1 5.6 - - - +
791B ASP* 5.7 3.1 - - - +
1019B LEU* 4.7 0.4 - - - -
1115B LYS* 3.7 39.4 + - + +
1116B PHE 3.4 10.3 - - - +
1117B THR* 3.6 2.0 - - + +
1130B LEU* 3.2 24.3 - - - +
1131B SER* 1.3 75.4 + - - +
1133B VAL* 1.3 71.5 + - - +
1134B THR* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B LEU 4.6 2.2 - - - +
789B THR* 3.3 10.1 - - - +
790B GLY 3.4 4.3 - - - -
792B ILE* 3.9 15.7 - - + -
1019B LEU* 3.2 50.0 - - + +
1020B ARG* 4.5 2.2 - - - +
1021B LEU* 5.0 3.1 - - + -
1034B LEU* 4.7 7.2 - - + -
1115B LYS* 3.4 1.9 - - - +
1116B PHE* 2.7 45.9 + - + +
1132B THR* 1.3 78.8 - - - +
1134B THR* 1.3 65.2 + - - +
1135B LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B GLY 3.1 4.8 + - - -
791B ASP* 3.1 33.1 + - - +
792B ILE* 2.8 28.9 + - - +
793B ARG* 3.2 11.9 + - - -
1057B VAL* 5.9 2.2 - - + -
1113B LEU* 4.6 6.7 - - + -
1114B TYR 3.2 5.6 - - - +
1115B LYS* 3.5 40.6 - - + +
1132B THR* 4.4 5.8 - - + +
1133B VAL* 1.3 73.3 - - - +
1135B LEU* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ILE* 4.0 21.1 - - + +
793B ARG* 4.5 0.9 - - - +
794B TYR* 6.1 1.8 - - + -
1021B LEU* 3.7 29.8 - - + -
1027B PRO* 4.3 13.5 - - + -
1032B VAL* 4.0 24.9 - - + -
1034B LEU* 4.7 0.4 - - + -
1112B GLY 3.8 0.5 - - - +
1113B LEU* 3.6 10.1 - - - +
1114B TYR* 2.8 31.5 + - + +
1116B PHE* 4.1 20.9 - - + -
1133B VAL* 3.8 22.0 - - + -
1134B THR* 1.3 74.3 - - - +
1136B ARG* 1.3 76.6 + - - +
1137B THR* 4.1 2.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ILE 4.7 3.4 + - - -
793B ARG* 3.5 46.3 - - - +
794B TYR* 5.5 3.8 + - - -
1027B PRO* 5.1 4.2 - - - +
1111B ASP* 5.1 10.8 - - - +
1112B GLY 3.2 7.2 - - - +
1113B LEU* 3.8 32.0 - - + +
1135B LEU* 1.3 84.8 - - - +
1137B THR* 1.3 69.3 + - - +
1225B HIS* 3.7 37.9 + - - -
----------------------------------------------------------
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