Contacts of the strand formed by residues 308 - 315 (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 PHE 308 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 4.1 17.3 - - + -
298A GLU 3.4 7.0 - - - +
299A TRP* 3.4 52.7 - + + -
300A LEU* 4.0 0.2 - - - -
306A TYR* 3.5 25.1 - - + -
307A LYS* 1.3 79.4 - - - +
309A MET* 1.3 70.1 + - - +
567A VAL* 4.9 0.4 - - + -
569A PRO* 3.4 19.3 - - + -
570A LEU* 3.6 37.2 - - + -
573A TYR* 3.6 32.3 - + + -
1099A LEU* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.4 4.1 - - - -
298A GLU* 2.9 36.0 + - + +
300A LEU* 3.4 35.0 - - + -
307A LYS* 5.8 2.7 - - - -
308A PHE* 1.3 78.7 - - - +
310A TYR* 1.3 64.8 + - - +
311A MET* 3.5 6.8 + - + +
1099A LEU* 4.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 5.0 1.3 - - + -
296A ASN 4.8 0.2 - - - -
297A LEU* 3.8 22.0 - - + -
309A MET* 1.3 72.8 - - - +
311A MET* 1.3 61.2 - - - +
312A GLY* 3.1 44.8 - - - -
313A VAL* 3.7 0.9 - - - +
1070A SER 3.6 24.7 - - - -
1071A VAL* 3.9 20.6 - - + -
1072A ASP* 3.2 28.6 + - - +
1075A LEU* 3.7 18.3 - - + +
1077A LEU* 6.4 0.9 - - + -
1097A PRO* 5.9 1.1 - - + -
1099A LEU* 3.5 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASN* 2.8 45.0 + - - +
297A LEU 4.0 1.3 - - - +
298A GLU* 3.3 47.3 - - + +
309A MET* 3.7 12.8 - - + +
310A TYR* 1.3 78.9 - - - +
312A GLY* 1.3 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 3.8 0.9 - - - +
296A ASN* 2.9 26.2 + - - -
310A TYR* 3.1 37.2 - - - -
311A MET* 1.3 80.4 - - - +
313A VAL* 1.3 60.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR* 3.8 33.2 - - + -
294A CYS 3.4 6.7 - - - +
296A ASN* 4.4 6.7 + - - +
310A TYR* 3.7 2.9 - - - +
312A GLY* 1.3 79.1 - - - +
314A MET* 1.3 59.3 + - - +
315A PRO* 3.7 9.2 - - + +
1072A ASP* 3.3 45.1 - - + +
1074A ARG* 4.5 4.7 - - - +
1075A LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A TYR* 3.6 3.1 - - - -
294A CYS* 2.7 43.3 + - - +
295A PRO 4.3 5.4 - - - +
296A ASN* 4.6 9.4 - - + -
313A VAL* 1.3 72.0 - - - +
315A PRO* 1.3 107.2 - - + +
316A LEU* 3.3 5.5 + - + +
320A TYR* 3.8 30.5 - - + +
577A PRO 3.7 16.6 - - - +
578A PRO* 4.1 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLY 3.8 0.2 - - - +
293A TYR* 3.8 27.1 - - + -
313A VAL* 3.7 11.2 - - + +
314A MET* 1.3 113.7 - - + +
316A LEU* 1.3 63.8 + - - +
317A SER* 5.0 1.6 + - - -
320A TYR* 4.0 6.2 - - - -
----------------------------------------------------------
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