Contacts of the helix formed by residues 515 - 529 (chain B) in PDB entry 2CXO
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 VAL 515 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLN 3.8 22.9 - - - +
389A HIS* 5.5 0.9 - - - -
392A TYR* 5.8 1.1 - - + -
393A GLN* 4.5 15.0 - - + +
396A HIS* 5.5 1.6 - - - -
432A GLN* 5.1 3.6 + - - +
358B GLU* 4.0 17.5 - - - +
512B GLN* 3.3 26.7 - - + +
514B GLY* 1.3 79.9 - - - +
516B GLU* 1.3 69.1 + - + +
517B LEU 3.5 0.4 - - - -
518B GLY* 3.7 4.1 + - - -
519B LYS* 3.3 46.0 + - - +
2601B DER 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LYS* 5.2 4.9 + - - +
466A LYS* 2.7 32.9 + - - +
468A PHE* 4.6 3.8 - - + -
513B TRP* 3.2 38.9 + - - +
515B VAL* 1.3 81.4 - - + +
517B LEU* 1.3 66.6 + - - +
519B LYS* 3.1 12.3 + - + +
520B GLN* 3.0 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A HIS* 5.4 0.4 - - - +
435A ALA* 3.6 31.0 - - + +
439A GLY* 3.5 36.6 - - - +
440A LYS* 3.9 21.8 - - + +
468A PHE* 3.8 40.1 - - + -
515B VAL 3.5 0.4 - - - -
516B GLU* 1.3 77.4 - - - +
518B GLY* 1.3 62.6 + - - +
520B GLN* 3.3 11.6 + - - +
521B LEU* 3.1 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A HIS* 5.1 4.2 + - - -
428A ASN* 4.9 1.9 - - - +
431A ALA* 3.8 8.5 - - - +
432A GLN* 3.6 29.5 + - - +
435A ALA* 4.1 15.7 - - - +
514B GLY 5.3 0.4 + - - -
515B VAL 3.7 4.6 + - - -
516B GLU 3.3 0.6 - - - -
517B LEU* 1.3 78.0 - - - +
519B LYS* 1.3 61.2 + - - +
521B LEU* 3.6 0.4 + - - -
522B ALA* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLN* 6.1 0.9 - - - +
389A HIS* 4.6 18.1 - - - -
428A ASN* 5.6 2.2 - - - +
432A GLN* 4.7 0.9 - - - +
215B THR* 5.4 9.4 + - - +
217B GLU* 5.8 0.9 - - - -
515B VAL* 3.3 37.0 + - + +
516B GLU* 3.1 13.5 + - + +
518B GLY* 1.3 74.3 - - - +
520B GLN* 1.3 66.5 + - + +
522B ALA* 3.3 6.4 + - - +
523B LYS* 3.2 27.3 + - - +
2601B DER 4.7 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LYS* 2.7 29.7 + - - +
448A GLU* 3.4 27.1 + - - -
516B GLU* 3.0 23.6 + - + +
517B LEU* 3.6 17.0 + - - +
519B LYS* 1.3 78.6 - - + +
521B LEU* 1.3 69.1 + - + +
523B LYS* 3.4 14.2 + - - +
524B LYS* 3.4 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA* 3.5 13.2 - - + +
434A GLU* 3.4 34.1 - - + +
435A ALA* 3.6 33.4 - - + +
438A LYS* 5.0 13.5 - - + +
517B LEU* 3.1 33.9 + - + +
518B GLY 4.2 0.2 - - - +
520B GLN* 1.3 83.6 - - + +
522B ALA* 1.3 60.9 + - - +
524B LYS* 3.4 20.2 + - + +
525B ILE* 3.2 27.2 + - - +
538B HIS* 5.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ALA* 3.8 12.3 - - + +
428A ASN* 3.8 29.6 - - - +
431A ALA* 3.3 15.0 - - + +
216B GLN* 5.7 3.1 - - - +
518B GLY 3.1 18.8 + - - +
519B LYS* 3.7 6.1 - - - +
520B GLN 3.2 0.2 - - - -
521B LEU* 1.3 74.7 - - - +
523B LYS* 1.3 66.5 + - + +
525B ILE 3.2 0.6 + - - +
526B GLU* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLN* 3.5 22.8 - - + +
519B LYS 3.2 13.7 + - - +
520B GLN* 3.6 11.2 - - - +
522B ALA* 1.3 79.1 - - + +
524B LYS* 1.3 63.3 + - + +
526B GLU* 3.0 30.2 + - - +
527B PRO* 3.2 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLN* 3.4 14.9 + - + +
521B LEU* 3.6 25.6 - - + +
522B ALA 3.2 0.8 - - - -
523B LYS* 1.3 79.0 - - + +
525B ILE* 1.3 62.1 + - + +
527B PRO* 3.5 10.4 - - - +
528B GLU* 3.4 20.4 - - - +
538B HIS* 5.0 9.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ALA* 4.0 13.0 - - + +
430A LEU* 3.8 31.9 - - + -
431A ALA* 3.8 23.3 - - + +
434A GLU* 3.6 23.8 - - - +
521B LEU 3.2 15.0 + - - +
522B ALA 3.2 3.1 + - - +
524B LYS* 1.3 76.7 - - - +
526B GLU* 1.3 69.0 + - - +
528B GLU* 2.9 20.8 + - - +
529B LEU* 3.3 12.4 + - + +
538B HIS* 3.5 25.1 - - + +
542B THR* 4.1 7.6 - - + -
546B ILE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 4.4 7.3 - - - +
423A LYS* 3.4 42.0 + - + +
424A ILE* 3.7 18.7 - - + +
427A ALA* 3.8 14.9 - - + +
216B GLN* 2.8 32.6 + - - +
522B ALA 3.0 16.3 + - - +
523B LYS* 3.0 22.1 + - - +
525B ILE* 1.3 77.5 - - - +
527B PRO* 1.3 70.0 - - + +
528B GLU 3.3 0.2 + - - -
529B LEU* 3.4 11.6 + - - +
530B GLU 4.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LYS* 5.6 0.2 - - - +
523B LYS* 3.2 18.6 - - - +
524B LYS* 3.5 12.3 - - - +
526B GLU* 1.3 94.3 - - + +
528B GLU* 1.3 63.8 + - + +
529B LEU 3.3 0.3 + - - -
530B GLU* 3.4 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LYS* 3.4 19.4 - - - +
525B ILE* 2.9 18.2 + - + +
527B PRO* 1.3 78.9 - - + +
529B LEU* 1.3 57.5 + - - +
530B GLU 3.2 2.6 + - - +
533B SER* 5.5 0.3 + - - -
535B VAL* 3.5 25.8 - - + +
537B SER* 2.7 24.4 + - - -
538B HIS* 2.5 31.7 + - - -
546B ILE* 4.5 2.8 - - + +
550B LYS* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LYS* 3.5 39.7 - - + +
426A LEU* 3.9 12.1 - - + -
427A ALA* 3.8 22.7 - - + +
430A LEU* 4.0 20.0 - - + -
1704A GOL 4.8 3.4 - - - -
525B ILE* 3.3 12.3 + - + +
526B GLU 3.7 5.6 - - - +
527B PRO 3.2 0.6 - - - -
528B GLU* 1.3 75.5 - - - +
530B GLU* 1.3 60.1 - - - +
546B ILE* 4.1 23.3 - - + -
549B ILE* 4.7 17.5 - - + -
550B LYS* 3.6 6.3 - - - +
553B ARG* 2.8 38.9 + - - +
----------------------------------------------------------
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