Contacts of the strand formed by residues 520 - 523 (chain E) in PDB entry 1R4N
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 TYR 520 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E GLY 3.6 3.4 - - - +
162E MET* 2.8 58.2 + - + +
496E PHE* 3.8 30.4 - + - -
497E LEU* 5.0 2.5 - - + -
500E ALA* 4.9 0.7 - - + -
516E PHE* 4.0 9.9 - + + -
519E THR* 1.3 73.5 - - - +
521E ILE* 1.3 71.5 + - - +
522E TYR* 4.1 10.5 - - + -
529E SER* 2.8 38.1 + - - -
530E ALA* 3.6 10.8 - - - -
531E THR* 3.9 11.0 - - + -
324F PHE* 4.8 1.2 - - - -
330F LEU* 3.2 54.5 - - + +
332F THR* 4.3 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 521 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E VAL* 4.6 4.0 - - + -
160E GLY 3.4 4.5 - - - +
161E TYR* 4.4 8.7 - - + -
422E GLU* 3.7 29.4 - - + +
425E LEU* 4.0 18.2 - - + -
426E TYR* 3.6 37.0 - - + +
429E LEU* 6.1 0.4 - - + -
519E THR* 3.9 15.5 - - + -
520E TYR* 1.3 84.7 - - - +
522E TYR* 1.3 63.5 + - - +
528E THR 3.9 0.2 - - - +
529E SER* 3.0 7.0 - - - -
530E ALA 2.9 39.3 + - - +
532E PHE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 522 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LEU 3.6 0.5 - - - +
159E VAL* 3.2 8.5 - - - +
160E GLY* 2.6 52.7 + - - +
492E THR 5.5 0.3 + - - -
493E ILE* 3.7 29.6 - - + +
496E PHE* 3.3 67.9 - + + +
497E LEU* 5.2 0.9 - - + -
520E TYR* 4.1 7.6 - - + -
521E ILE* 1.3 77.1 - - - +
523E SER* 1.3 77.9 + - - +
524E GLY* 4.2 2.0 - - - -
527E GLN* 2.8 42.9 + - - -
528E THR 3.6 12.6 - - - -
529E SER* 4.1 2.5 - - - -
301F ALA 5.2 0.9 + - - -
302F VAL* 4.3 4.3 - - - +
305F THR* 5.0 1.7 + - - -
322F LEU* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E LEU 3.6 2.5 - - - -
159E VAL* 5.2 0.6 - - - +
422E GLU* 5.0 4.3 - - - -
425E LEU* 3.8 23.0 - - - +
521E ILE 4.2 0.6 + - - -
522E TYR* 1.3 77.7 - - - +
524E GLY* 1.3 55.4 + - - +
525E MET* 3.6 15.1 + - - +
526E SER* 3.0 29.3 + - - -
527E GLN* 2.7 34.0 + - - -
528E THR* 2.8 16.7 + - - -
----------------------------------------------------------
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