Contacts of the strand formed by residues 1238 - 1245 (chain A) in PDB entry 1MUK
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 VAL1238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A MET* 3.9 20.6 - - + -
1064A CYS 3.5 26.9 - - - +
1065A GLU 3.9 1.8 - - - -
1066A ALA* 3.6 21.5 - - + +
1067A ARG* 4.2 9.4 - - - +
1196A HIS* 4.2 4.0 - - - +
1230A VAL* 3.4 31.3 + - + +
1236A VAL* 3.3 11.6 + - + +
1237A ALA* 1.3 75.5 - - - +
1239A ASP* 1.3 78.0 + - - +
1240A ILE 3.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064A CYS* 2.9 26.7 + - - +
1065A GLU* 3.0 32.7 + - - +
1066A ALA 5.3 0.3 - - - +
1067A ARG* 3.8 9.4 - - - +
1196A HIS* 2.8 43.8 + - - +
1198A LYS* 3.9 14.7 - - - -
1238A VAL* 1.3 78.4 - - - +
1240A ILE* 1.3 59.9 + - - +
1241A TYR* 4.0 17.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A TRP* 3.3 37.4 - - + -
1062A ARG 3.6 9.9 - - - +
1063A MET* 3.9 14.6 - - + -
1196A HIS 3.2 11.8 + - - +
1197A VAL* 3.6 16.1 - - + -
1198A LYS* 2.9 28.4 + - - +
1226A GLY* 3.7 25.4 - - - +
1229A MET* 4.0 18.8 - - + -
1230A VAL* 3.5 22.9 - - + -
1238A VAL 3.7 0.2 + - - -
1239A ASP* 1.3 75.6 - - - +
1241A TYR* 1.3 64.9 + - - +
1242A LEU 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A TRP* 3.5 4.7 - - - -
1062A ARG* 2.7 42.7 + - + +
1064A CYS* 3.6 28.5 - - + -
1065A GLU* 3.6 11.1 + - - -
1198A LYS* 3.4 48.6 - - + +
1200A LEU 3.9 13.5 - - - -
1201A PRO 4.7 0.4 - - - -
1202A LYS* 3.4 59.6 + - + +
1239A ASP* 4.0 13.2 + - + -
1240A ILE* 1.3 77.2 - - - +
1242A LEU* 1.3 66.3 + - - +
1243A GLU 3.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A VAL* 3.6 24.2 - - + -
1060A LYS 3.6 16.6 - - - +
1061A TRP* 3.3 22.6 - - + -
1198A LYS 2.8 17.6 + - - +
1199A LEU* 3.7 26.0 - - + +
1201A PRO* 3.1 28.5 - - - +
1202A LYS 4.2 1.0 + - - -
1209A THR* 4.0 29.4 - - + +
1211A ILE* 5.4 0.7 - - + -
1222A LEU* 4.2 21.8 - - + -
1241A TYR* 1.3 70.7 - - - +
1243A GLU* 1.3 59.7 + - - +
1244A ASP 4.0 10.3 - - - +
1245A ILE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A LYS* 3.0 16.1 + - + +
1061A TRP 3.9 7.4 - - - +
1062A ARG* 3.0 52.4 + - + -
1202A LYS 4.7 4.9 + - - -
1203A ASP* 4.6 3.1 - - - +
1206A HIS* 3.2 45.4 + - - -
1209A THR* 3.7 4.0 - - - +
1241A TYR 3.1 0.8 + - - -
1242A LEU* 1.3 77.9 - - - +
1244A ASP* 1.3 70.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A LEU 4.2 0.4 - - - -
1059A VAL* 3.4 4.3 - - - +
1060A LYS* 2.8 61.0 + - + +
1206A HIS* 5.2 2.1 + - - +
1208A ASN* 3.1 29.4 + - - +
1209A THR* 4.2 6.4 - - - +
1242A LEU* 3.8 2.2 - - - +
1243A GLU* 1.3 87.6 - - + +
1245A ILE* 1.3 78.4 + - - +
1246A HIS* 3.9 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A LEU* 3.4 10.8 - - + +
1059A VAL* 4.6 5.8 - - + -
1208A ASN* 3.2 34.5 - - - +
1209A THR* 4.4 10.8 - - - +
1210A ASP 5.3 0.4 - - - +
1211A ILE* 5.3 1.6 - - + -
1218A LEU* 5.5 0.7 - - + -
1222A LEU* 4.5 13.0 - - + -
1242A LEU* 4.4 20.2 - - + -
1244A ASP* 1.3 84.5 + - - +
1246A HIS* 1.3 69.7 + - - +
1247A GLY 4.6 1.8 - - - +
1248A GLY 2.9 29.5 + - - +
1249A GLY* 4.1 12.6 - - - -
1252A LEU* 3.8 32.1 - - + -
----------------------------------------------------------
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