Contacts of the strand formed by residues 523 - 528 (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 ARG 523 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 4.4 5.4 - - - -
274A LYS* 4.6 4.5 - - - +
377A LEU* 3.4 28.4 - - - +
520A GLN* 3.5 30.0 + - + +
521A VAL 2.9 9.1 + - - +
522A GLN* 1.3 80.7 - - - +
524A ARG* 1.3 136.6 + - - +
525A PRO* 4.1 1.8 + - - +
526A ARG* 3.9 50.0 - - - +
783A LYS* 5.7 9.0 - - - +
797A ARG* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 3.3 23.1 - - - +
271A LEU* 4.5 7.5 - - + +
377A LEU* 4.3 1.0 - - - +
379A ARG* 3.7 4.7 - - - +
387A GLN* 4.7 3.1 - - - +
388A GLU* 2.6 41.5 + - - -
520A GLN* 3.7 4.6 - - - +
523A ARG* 1.3 143.0 + - - +
525A PRO* 1.3 74.0 + - + +
526A ARG 3.7 0.2 + - - -
588A ALA* 5.4 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 4.1 5.8 - - + +
377A LEU 4.0 11.0 - - - +
379A ARG* 3.5 37.8 + - + +
384A THR* 3.6 26.8 - - + +
388A GLU* 4.8 3.3 - - - +
517A LEU* 4.3 13.2 - - + -
518A ARG 3.6 7.6 - - - +
519A ASN* 3.7 26.9 - - - +
523A ARG* 4.1 2.1 + - - +
524A ARG* 1.3 94.5 + - + +
526A ARG* 1.3 60.1 + - - +
527A SER* 3.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LEU* 3.6 4.5 - - - +
518A ARG* 2.9 44.7 + - + +
520A GLN* 3.8 27.0 + - - +
523A ARG* 3.9 33.5 - - - +
524A ARG 3.7 1.0 + - - -
525A PRO* 1.3 72.3 - - - +
527A SER* 1.3 70.5 + - - +
528A ILE* 4.1 2.7 - - + +
734A ASP* 5.0 11.3 + - - -
783A LYS* 6.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR* 3.4 24.6 - - - +
388A GLU* 4.6 5.0 - - - +
389A TYR* 2.7 35.5 + - - -
515A MET* 3.6 13.4 - - - +
516A GLY 3.7 5.2 - - - -
517A LEU* 4.5 2.2 - - - -
525A PRO 3.8 0.9 + - - -
526A ARG* 1.3 80.5 - - - +
528A ILE* 1.3 62.2 + - - +
529A MET* 4.0 0.4 - - - -
682A SER* 3.1 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ARG* 6.2 1.6 - - - +
514A SER 3.5 0.5 - - - +
515A MET* 3.5 0.7 - - - +
516A GLY* 2.6 46.8 + - - -
517A LEU 3.9 24.5 - - - +
518A ARG* 4.0 33.4 - - + +
526A ARG* 4.1 7.6 - - + +
527A SER* 1.3 77.6 - - - +
529A MET* 1.3 60.8 + - - +
530A PRO* 2.9 27.1 - - + +
682A SER* 3.6 3.8 - - - +
683A GLY* 5.7 3.8 - - - -
----------------------------------------------------------
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