Contacts of the strand formed by residues 421 - 427 (chain A) in PDB entry 4QDR
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 421 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN 3.6 12.1 - - - +
309A SER 3.3 3.8 - - - -
310A ARG 3.4 22.0 - - - +
311A LEU* 4.1 2.2 - - - -
312A HIS* 3.6 11.9 + - - +
313A GLY* 2.9 31.0 + - - +
314A ASP* 5.2 0.2 - - - +
316A ASN 3.5 17.4 + - - +
317A GLY* 4.1 1.1 - - - -
344A THR* 3.2 7.6 - - - +
345A GLN* 2.8 75.7 + - - +
346A GLY 2.8 26.0 + - - -
347A ALA* 4.2 5.0 - - - +
348A ILE 5.2 1.0 - - - +
390A ALA 3.3 17.6 + - - -
391A THR* 4.5 2.6 - - - +
420A LEU* 1.3 79.1 - - - +
422A LEU* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET* 3.1 20.9 - - + +
309A SER 2.6 15.1 + - - +
311A LEU* 2.9 25.1 + - - +
329A LEU* 3.9 26.5 - - + -
331A VAL* 4.0 20.0 - - + -
342A ILE* 3.6 30.7 - - + -
343A ALA 3.3 8.3 - - - +
344A THR* 3.8 10.5 - - + -
407A VAL* 5.9 0.2 - - + -
409A ILE* 4.1 18.4 - - + -
420A LEU* 5.4 3.4 - - + -
421A ARG* 1.3 77.0 - - - +
423A GLU* 1.3 65.5 + - - +
424A LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PRO* 3.8 16.7 - - + +
281A LEU* 4.4 0.2 - - - -
282A GLY* 3.3 9.6 + - - -
283A MET* 2.9 28.8 + - - +
284A GLU* 3.1 30.3 + - - +
285A SER 4.8 0.2 + - - -
311A LEU* 3.9 19.0 - - + +
342A ILE* 3.5 3.3 - - - -
343A ALA* 2.8 33.2 + - + +
422A LEU* 1.3 75.6 - - - +
424A LEU* 1.3 86.2 + - - +
425A PHE* 3.5 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PRO* 3.5 3.6 - - - +
281A LEU* 2.8 43.1 + - + -
283A MET* 4.2 2.9 - - + +
288A ILE* 4.6 4.0 - - + -
331A VAL* 4.0 36.1 - - + -
333A LEU* 4.0 14.8 - - + -
339A LEU* 4.1 8.1 - - + -
341A ALA 3.6 2.5 - - - -
342A ILE* 4.3 17.0 - - + -
407A VAL* 4.2 27.4 - - + -
409A ILE* 5.0 0.4 - - + -
422A LEU* 4.0 24.2 - - + -
423A GLU* 1.3 86.2 + - - +
425A PHE* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 3.4 26.0 - - + -
279A VAL 3.3 4.0 - - - +
280A PRO* 3.8 26.9 - - + -
281A LEU* 4.0 4.7 - - - -
311A LEU* 5.5 3.4 - - + -
339A LEU* 3.5 7.3 - - - +
340A THR* 2.7 37.5 + - - +
341A ALA* 2.8 37.2 + - + +
343A ALA* 3.5 29.6 - - + -
395A LEU* 3.7 11.4 - - + -
423A GLU* 3.5 25.4 - - + -
424A LEU* 1.3 75.2 - - - +
426A GLY* 1.3 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A CYS* 3.2 21.5 + - - -
279A VAL* 2.9 33.7 + - - +
281A LEU* 3.9 7.9 - - - +
338A MET 3.0 13.2 - - - -
340A THR* 3.4 2.2 + - - -
425A PHE* 1.3 75.1 - - - +
427A CYS* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A MET* 6.1 4.3 - - - -
276A GLN 3.7 15.7 - - - +
277A CYS* 2.0 47.2 - - - -
279A VAL* 4.9 5.4 - - + -
281A LEU* 4.1 5.5 - - - +
337A THR* 3.3 8.6 - - - +
338A MET* 2.7 39.3 + - - +
426A GLY* 1.3 73.2 - - - +
428A ARG* 1.3 71.7 + - - +
429A VAL* 5.5 0.9 - - - -
431A ASP* 4.1 9.9 - - + +
----------------------------------------------------------
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