Contacts of the strand formed by residues 423 - 431 (chain A) in PDB entry 3CPE
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 TRP 423 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 3.8 13.2 - - + -
417A ASP 3.3 7.4 - - - +
418A VAL* 3.5 34.0 + - + +
420A ASP 3.5 16.5 + - - -
421A ASP* 4.2 3.5 + - - +
422A VAL* 1.3 73.8 - - - +
424A GLU* 1.3 59.8 + - - +
506A LEU* 3.5 28.9 - - + -
511A LYS* 2.6 47.3 + - + +
512A LEU* 3.3 6.0 - - + -
513A ILE* 2.8 27.4 + - - +
550A PHE* 3.6 23.8 - + - -
554A SER* 3.7 15.7 - - - -
559A PHE* 3.4 31.6 - + - -
560A ILE* 5.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS* 3.2 38.2 - - - +
416A ILE* 3.3 4.4 - - - +
417A ASP* 2.5 50.8 + - + +
422A VAL* 4.7 4.5 - - + +
423A TRP* 1.3 76.2 - - - +
425A GLN* 1.3 64.6 + - - +
426A VAL* 3.2 11.6 + - + +
513A ILE* 3.8 11.7 - - + +
515A HIS* 2.6 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.8 5.0 - - + -
414A HIS* 3.0 34.2 + - - +
415A ILE 3.5 10.3 - - - +
416A ILE* 3.9 14.6 - - + -
424A GLU* 1.3 68.2 - - - +
426A VAL* 1.3 61.8 + - - +
427A GLY 4.5 0.4 - - - +
428A VAL* 3.2 26.0 - - + +
512A LEU* 4.4 1.8 - - - +
513A ILE 3.0 19.4 + - - +
514A ILE* 3.5 16.5 - - + +
515A HIS* 2.7 56.9 + - - +
516A HIS* 2.8 12.2 + - - +
519A THR* 3.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 2.8 32.4 + - - -
388A LYS* 3.3 28.5 + - + +
389A LYS 5.6 0.7 - - - +
396A TYR* 3.8 13.0 - - + -
415A ILE* 2.8 30.0 + - + +
417A ASP* 3.6 21.3 - - + +
424A GLU* 3.6 27.8 - - - +
425A GLN* 1.3 74.4 - - - +
427A GLY* 1.3 57.1 - - - +
450A TYR* 3.6 26.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PHE* 3.7 21.3 - - - -
385A HIS 3.2 11.7 - - - -
387A PHE* 3.8 2.2 - - - -
413A LEU 3.8 0.2 - - - +
415A ILE* 2.7 37.3 + - - +
425A GLN* 3.6 1.7 - - - +
426A VAL* 1.3 81.7 - - - +
428A VAL* 1.3 65.5 + - - +
450A TYR* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLY 3.2 3.3 - - - +
384A PHE* 3.7 5.7 - - - -
385A HIS* 2.7 44.1 + - + -
387A PHE* 3.5 18.4 - - + -
413A LEU 3.1 11.2 - - - +
414A HIS* 3.7 8.3 - - + +
425A GLN* 3.2 31.2 - - - +
427A GLY* 1.3 79.8 - - - +
429A LEU* 1.3 66.2 + - - +
430A HIS* 4.5 0.9 - - + -
516A HIS* 4.0 15.7 - - + +
543A LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A HIS* 4.0 5.8 - - + -
383A GLY* 3.4 14.6 - - - +
384A PHE* 3.4 32.5 - - + +
400A LEU* 5.6 0.9 - - + -
411A HIS* 3.3 12.0 - - + +
412A ALA* 3.4 2.1 - - - -
413A LEU* 2.8 53.1 + - + +
428A VAL* 1.3 73.3 - - - +
430A HIS* 1.3 62.7 + - - +
431A SER* 5.0 2.5 - - - -
434A ILE* 4.7 5.4 - - + -
439A LEU* 3.9 26.9 - - + -
442A ILE* 4.5 7.2 - - + -
443A VAL* 4.1 15.0 - - + -
446A TYR* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLY* 3.0 26.7 + - - +
385A HIS* 4.4 7.9 - - + -
410A TYR* 3.4 53.4 - + + +
411A HIS 3.3 5.4 - - - -
412A ALA* 4.7 2.2 - - + -
428A VAL* 4.5 2.9 - - + -
429A LEU* 1.3 74.8 - - - +
431A SER* 1.3 60.8 + - - +
516A HIS* 4.7 0.2 - - + -
518A ALA* 5.3 1.3 - - + -
522A GLU* 4.2 8.6 + - - -
540A HIS* 5.8 1.8 - + - +
542A ASP* 4.8 1.9 + - + -
543A LEU* 3.5 43.5 - - + +
568A PO4 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLY* 4.5 7.5 + - - -
410A TYR* 3.4 10.0 - - - -
411A HIS* 2.7 48.6 + - - +
429A LEU* 4.3 3.8 - - - -
430A HIS* 1.3 76.4 - - - +
432A ASN* 1.3 56.7 + - - +
433A THR* 3.1 28.3 + - - -
434A ILE* 3.3 31.6 + - - +
----------------------------------------------------------
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