Contacts of the helix formed by residues 567 - 588 (chain B) in PDB entry 2C6N
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 ALA 567 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.6 9.8 - - + +
217B GLN* 3.2 31.3 + - + +
218B LEU* 4.4 24.0 - - + -
506B VAL* 4.5 5.2 - - - -
566B ASP* 1.3 75.8 + - - +
568B GLN* 1.3 55.5 + - - +
569B PRO* 3.1 3.8 - - - -
570B LEU* 2.5 33.2 + - - +
571B LEU* 3.1 18.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 568 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLN* 3.8 9.4 - - + +
217B GLN* 4.8 1.0 + - - -
566B ASP* 3.6 18.4 + - - +
567B ALA* 1.3 76.0 - - - +
569B PRO* 1.3 66.1 - - + +
571B LEU* 3.3 16.6 + - - +
572B LYS* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B VAL 5.3 0.2 - - - +
509B PHE* 3.7 23.7 - - + +
510B GLN* 3.8 26.7 - - + +
513B GLU* 4.5 11.4 - - + -
525B LEU* 3.7 6.7 - - + +
566B ASP* 3.7 23.6 - - + +
567B ALA 2.8 2.0 - - - -
568B GLN* 1.3 95.9 - - + +
570B LEU* 1.3 57.3 + - - +
572B LYS* 3.4 14.6 - - + +
573B TYR* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.4 26.9 - - + -
221B LEU* 5.9 1.1 - - + -
432B LYS* 5.7 1.1 - - + -
433B ILE* 4.5 8.7 - - + -
436B LEU* 4.9 7.4 - - + -
505B PHE* 3.6 11.2 - - + +
506B VAL* 4.0 17.7 - - + +
509B PHE* 3.3 41.2 - - + +
566B ASP 5.1 0.4 + - - +
567B ALA* 2.5 18.4 + - - +
569B PRO* 1.3 73.0 - - - +
571B LEU* 1.3 67.3 + - - +
573B TYR* 2.7 15.0 + - - +
574B PHE* 3.0 53.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLN* 3.5 35.0 + - + +
576A PRO* 5.7 2.0 - - + -
579A GLN* 3.1 39.5 - - + +
217B GLN* 4.0 19.1 - - - +
218B LEU* 4.8 7.6 - - + -
221B LEU* 3.8 17.5 - - + -
567B ALA* 3.6 9.6 - - + +
568B GLN* 3.3 28.7 - - - +
570B LEU* 1.3 78.5 - - + +
572B LYS* 1.3 56.8 + - - +
574B PHE* 3.2 4.0 + - - +
575B GLN* 3.0 28.8 + - - +
578B THR* 4.5 4.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A LYS* 4.0 39.2 - - + +
575A GLN* 3.8 15.0 - - - +
513B GLU* 4.9 9.3 - - - +
525B LEU* 4.2 33.4 + - + +
526B HIS* 5.3 2.6 + - - -
568B GLN* 2.9 17.1 + - + +
569B PRO* 3.4 12.0 - - + +
571B LEU* 1.3 77.6 - - - +
573B TYR* 1.3 60.3 + - - +
575B GLN* 4.0 25.6 + - - +
576B PRO* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 4.0 15.5 + - + +
401B THR* 5.5 0.2 - - - +
424B TYR* 3.4 26.2 + - - -
425B LEU* 3.7 14.7 - - + +
428B MET* 3.5 17.8 - - + +
509B PHE* 3.5 29.8 - + + -
512B HIS* 4.1 22.4 - + - -
525B LEU* 4.3 9.6 - - + -
526B HIS* 3.5 54.6 + - + +
569B PRO 3.0 13.6 + - - +
570B LEU 2.7 15.6 + - - +
572B LYS* 1.3 74.5 - - - +
574B PHE* 1.3 89.3 + + + +
575B GLN 3.9 0.2 + - - -
576B PRO* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 4.8 2.0 - - + -
425B LEU* 3.4 16.2 - - + -
428B MET* 3.7 22.7 - - + -
429B ALA* 3.4 27.6 - - + -
432B LYS* 3.9 12.8 - - + -
433B ILE* 3.7 21.5 - - + -
509B PHE* 4.0 9.0 - + - -
570B LEU* 3.0 44.0 + - + +
571B LEU* 4.2 1.6 - - - +
573B TYR* 1.3 103.9 - + - +
575B GLN* 1.3 53.3 + - - +
576B PRO* 3.4 3.1 - - - -
577B VAL* 3.0 18.7 + - + +
578B THR* 2.8 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A GLN* 3.6 31.1 + - - +
571A LEU* 3.5 26.6 - - + +
572A LYS* 3.6 15.2 + - - +
575A GLN* 2.6 37.7 + - - +
571B LEU 3.0 9.6 + - - +
572B LYS* 4.2 15.4 + - - +
573B TYR 3.6 0.4 - - - -
574B PHE* 1.3 73.8 - - - +
576B PRO* 1.3 74.5 - - + +
578B THR* 4.0 6.7 - - + -
579B GLN* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 6.0 3.4 - - + +
568A GLN* 6.5 1.1 - - + -
571A LEU* 5.9 2.5 - - + -
421B ASP* 5.3 3.8 - - - +
422B ILE* 4.1 14.7 - - + +
425B LEU* 3.7 21.8 - - + -
526B HIS* 4.4 16.2 - - + +
572B LYS 5.1 1.3 - - - +
573B TYR 4.5 4.5 - - - +
574B PHE 3.7 3.6 - - - -
575B GLN* 1.3 94.2 - - + +
577B VAL* 1.3 57.5 + - - +
579B GLN* 3.9 4.2 - - + +
580B TRP* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 6.1 0.2 - - + -
422B ILE* 4.2 11.9 - - + +
425B LEU* 3.8 21.2 - - + +
426B LEU* 4.1 23.1 - - + +
429B ALA* 4.7 4.3 - - + -
433B ILE* 5.5 2.2 - - + -
574B PHE* 3.0 34.0 + - + +
576B PRO* 1.3 75.8 - - - +
578B THR* 1.3 70.6 + - - +
579B GLN 3.0 2.0 - - - -
580B TRP* 4.0 18.6 - - + -
581B LEU* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A THR* 5.9 1.1 - - + -
579A GLN* 4.2 21.5 - - - +
582A GLN* 5.3 1.3 - - - +
221B LEU* 3.4 29.4 - - + +
224B ASN* 5.2 2.5 + - - +
571B LEU* 4.5 5.1 + - + +
574B PHE* 2.8 23.4 + - - +
575B GLN* 3.1 14.5 + - + -
577B VAL* 1.3 79.8 - - - +
579B GLN* 1.3 67.9 + - - +
581B LEU* 4.0 5.7 - - - +
582B GLN* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN 5.2 0.7 - - - +
217A GLN* 3.2 35.8 + - + +
220A PRO* 4.0 17.9 - - - +
221A LEU* 3.8 24.0 - - - +
571A LEU* 4.0 29.2 - - + +
578A THR* 4.3 9.0 - - - +
575B GLN* 3.1 20.5 + - - +
576B PRO* 3.9 3.6 - - + +
577B VAL 3.0 0.2 - - - -
578B THR* 1.3 86.0 - - - +
580B TRP* 1.3 64.2 + - - +
581B LEU 3.1 1.8 - - - -
582B GLN* 3.4 12.3 + - - +
583B GLU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 3.6 27.4 - + - -
270B PRO* 3.4 42.4 - - + -
271B PHE* 4.0 23.5 - + - -
422B ILE* 3.9 20.0 - - + -
426B LEU* 5.3 0.4 - - + -
576B PRO 3.0 20.4 + - - +
577B VAL* 3.3 15.5 + - + -
579B GLN* 1.3 76.6 - - - +
581B LEU* 1.3 78.0 + - + +
583B GLU* 3.6 4.5 + - + +
584B GLN* 2.9 70.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 5.4 4.3 - - + +
224B ASN* 4.5 10.1 - - + +
225B LEU* 4.1 33.7 - - + +
228B PHE* 3.2 49.8 - - + -
426B LEU* 4.3 4.7 - - + -
429B ALA* 5.4 2.5 - - + -
433B ILE* 6.4 1.6 - - + -
577B VAL* 2.9 34.1 + - + +
578B THR* 4.0 5.2 - - - +
580B TRP* 1.3 92.1 - - + +
582B GLN* 1.3 66.7 + - - +
584B GLN* 3.0 5.4 + - - +
585B ASN* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PRO* 3.9 19.5 - - + +
221A LEU* 5.9 0.3 - - - +
224A ASN* 3.9 17.0 - - - +
578A THR* 5.1 1.4 - - - +
582A GLN* 3.0 41.9 + - - +
592A LEU* 5.3 5.5 - - + +
224B ASN* 3.7 24.3 + - - +
578B THR* 2.9 28.6 - - - +
579B GLN* 3.9 17.7 + - - +
581B LEU* 1.3 78.3 - - - +
583B GLU* 1.3 63.3 + - - +
585B ASN* 3.9 1.1 - - - +
586B GLN* 3.2 22.2 + - - +
592B LEU* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN* 3.7 32.7 - - + +
219A GLU* 2.6 32.6 - - - +
220A PRO* 3.0 32.6 - - + +
223A LEU* 4.9 2.9 - - - +
579B GLN 3.0 17.4 + - - +
580B TRP* 4.0 5.8 - - + +
582B GLN* 1.3 78.4 - - - +
584B GLN* 1.3 68.8 + - + +
586B GLN* 3.6 4.5 - - - +
587B GLN* 3.1 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN* 5.5 4.0 + - - -
228B PHE* 4.4 15.2 - - + -
580B TRP* 2.9 68.1 + - + +
581B LEU* 3.3 7.4 - - - +
583B GLU* 1.3 81.2 - - - +
585B ASN* 1.3 62.5 + - - +
587B GLN* 3.3 17.2 + - - +
588B ASN* 2.7 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASN* 2.9 51.2 + - - +
227B ALA* 3.9 7.1 - - - -
228B PHE* 3.5 30.0 + - - +
581B LEU 2.9 17.9 + - - +
582B GLN 3.9 4.3 - - - +
583B GLU 3.3 0.2 - - - -
584B GLN* 1.3 75.3 - - - +
586B GLN* 1.3 58.7 + - - +
588B ASN* 3.1 3.7 + - - +
589B GLY 2.8 21.7 + - - -
590B GLU* 2.9 34.3 + - + +
592B LEU* 4.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLU* 4.4 8.1 + - - -
223A LEU* 3.1 35.3 - - + +
592A LEU* 3.6 33.2 - - + +
2434A GOL 3.8 30.2 + - - -
582B GLN 3.2 11.6 + - - +
583B GLU* 3.6 12.1 + - - +
585B ASN* 1.3 74.9 - - - +
587B GLN* 1.3 85.1 + - + +
589B GLY* 2.5 28.3 + - - +
590B GLU 4.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN* 4.7 9.7 + - - +
219A GLU* 4.6 1.6 - - - +
583B GLU* 3.1 45.2 + - + +
584B GLN* 3.7 21.2 + - - +
586B GLN* 1.3 99.8 - - + +
588B ASN* 1.3 62.3 + - - +
589B GLY 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 6.0 2.6 - - - -
231B ARG* 3.8 29.9 + - - +
235B ARG* 5.9 0.9 + - - -
584B GLN* 2.7 44.0 + - - +
585B ASN 3.6 4.0 - - - +
586B GLN 3.0 0.6 - - - -
587B GLN* 1.3 79.8 - - - +
589B GLY* 1.3 64.1 + - - +
590B GLU* 3.4 19.2 + - - +
----------------------------------------------------------
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