Contacts of the strand formed by residues 418 - 424 (chain A) in PDB entry 2QQI
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 418 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG 3.5 15.0 - - - +
306A SER* 3.1 6.7 - - - +
307A ARG 3.5 11.0 - - - +
308A LEU* 4.1 2.2 - - - +
309A ASN* 3.4 19.4 + - - +
310A TYR* 2.9 39.0 + - - +
313A ASN 3.7 14.1 + - - -
314A GLY* 4.0 4.9 - - - -
341A THR* 3.3 4.3 - - - -
342A GLN* 2.8 63.9 + - + +
343A GLY 2.8 25.0 + - - +
344A ALA* 4.1 5.2 - - - +
345A ILE 5.4 0.4 - - - +
387A PRO 3.1 16.6 + - - -
388A THR* 4.2 6.7 - - - +
417A MET* 1.3 80.1 - - - +
419A PHE* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET* 3.2 43.9 - - + +
291A ILE* 5.2 0.2 - - + -
306A SER* 2.6 32.8 + - - +
308A LEU* 3.0 24.1 + - - +
326A ILE* 3.8 24.5 - - + -
327A GLN* 4.4 12.1 - - - -
328A VAL* 3.9 18.6 - - + -
339A VAL* 5.5 0.2 - - + -
340A GLY 3.1 13.5 - - - +
341A THR* 4.1 3.8 - - + -
404A VAL* 5.2 2.2 - - + -
406A ILE* 3.6 32.1 - - + -
417A MET* 5.4 3.4 - - + -
418A ARG* 1.3 77.5 - - - +
420A GLU* 1.3 64.9 + - - +
421A VAL* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 3.7 23.8 - - + +
279A LEU 4.1 0.7 - - - -
280A GLY* 3.4 4.5 + - - -
281A MET* 3.0 28.7 + - - +
282A GLU* 3.0 32.3 + - - +
283A SER 4.6 0.5 + - - -
308A LEU* 3.9 15.5 - - + +
339A VAL* 3.3 7.1 - - - +
340A GLY 2.9 29.2 + - - +
419A PHE* 1.3 76.9 - - - +
421A VAL* 1.3 86.8 + - - +
422A TYR* 3.6 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 2.8 51.3 + - + +
281A MET* 4.3 3.5 - - + +
286A ILE* 5.7 0.4 - - + -
328A VAL* 3.7 17.7 - - + -
330A LEU* 4.7 5.4 - - + -
336A VAL* 3.6 28.9 - - + -
338A ALA 3.8 4.0 - - - +
339A VAL* 4.5 3.8 - - + +
404A VAL* 4.1 20.6 - - + -
419A PHE* 3.7 25.4 - - + -
420A GLU* 1.3 86.7 + - - +
422A TYR* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A MET* 3.6 36.8 - - + -
277A GLU 3.2 4.5 - - - +
278A ALA* 3.7 18.8 - - + -
279A LEU* 4.2 3.6 - - - -
308A LEU* 3.9 13.7 - - - +
336A VAL* 3.5 6.9 - - - +
337A THR* 2.8 22.7 + - - -
338A ALA* 2.8 35.3 + - + +
339A VAL 4.0 2.2 - - - -
340A GLY* 3.6 25.3 - - - -
390A VAL* 4.8 5.7 - - - +
392A VAL* 5.0 9.9 - - + +
420A GLU* 3.6 30.5 - - + +
421A VAL* 1.3 72.8 - - - +
423A GLY* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A CYS* 3.5 8.1 - - - -
276A MET 3.5 1.0 + - - -
277A GLU* 2.9 35.0 + - - +
279A LEU* 3.9 7.6 - - - +
335A PHE 3.1 12.3 - - - -
337A THR* 3.6 13.2 - - - -
422A TYR* 1.3 76.1 - - - +
424A CYS* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS 4.3 3.4 - - - +
275A CYS* 2.0 50.5 - - + -
277A GLU* 5.4 4.5 - - + +
279A LEU* 4.0 9.9 - - - +
334A ARG* 3.6 8.7 - - - +
335A PHE* 3.0 35.1 + - - +
423A GLY* 1.3 73.3 - - - +
425A LYS* 1.3 67.1 + - - +
428A ASP* 3.5 16.8 - - + +
429A TYR* 3.8 21.3 - - - -
----------------------------------------------------------
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