Contacts of the helix formed by residues 513 - 532 (chain B) in PDB entry 1XJP
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 ILE 513 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 6.5 1.3 - - + -
204B ARG* 6.1 0.9 - - + -
207B TYR* 3.7 16.4 - - + +
222B LEU* 4.3 8.5 - - + -
226B VAL* 4.1 25.4 - - + -
398B GLU* 3.4 16.8 - - - +
453B THR* 4.6 1.1 - - + -
454B TYR* 4.8 9.2 - - + -
457B GLU* 3.0 30.1 + - + +
461B TRP* 4.0 27.4 - - + -
511B SER* 5.5 2.7 - - - +
512B PHE* 1.3 76.6 - - - +
514B ARG* 1.3 60.4 + - - +
516B TYR* 2.8 39.7 + - + +
517B THR* 3.1 15.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 3.1 62.3 + - + +
399B GLY* 4.5 0.8 - - - -
402B GLU* 6.3 1.6 - - - +
510B TYR* 5.7 7.3 - - - +
511B SER* 3.8 28.3 + - - +
512B PHE 3.0 1.9 + - - +
513B ILE* 1.3 80.1 - - - +
515B TYR* 1.3 89.4 + - + +
517B THR* 3.3 10.6 + - - -
518B ARG* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 3.6 30.1 - - - +
274B PHE* 6.2 0.4 - + - -
402B GLU* 6.2 3.8 - - + -
449B THR* 5.6 4.8 - - + +
450B LEU* 4.6 1.3 - - - +
453B THR* 4.1 14.8 - - + +
505B HIS* 3.3 28.0 + + - -
511B SER 4.5 0.9 - - - -
512B PHE* 3.1 37.4 + + - +
513B ILE 3.1 1.0 - - - -
514B ARG* 1.3 98.4 + - + +
516B TYR* 1.3 59.6 + - - +
518B ARG* 4.1 26.4 - - - +
519B THR* 2.6 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 4.1 24.2 - - + -
229B THR* 2.7 41.4 + - + +
230B PHE* 3.2 33.6 + + - -
233B ILE* 5.4 2.1 - - + +
450B LEU* 3.6 42.0 - - + -
453B THR* 3.9 9.6 - - + +
454B TYR* 4.3 12.1 - - + -
513B ILE* 2.8 25.2 + - + +
515B TYR* 1.3 79.3 - - - +
517B THR* 1.3 67.1 + - + +
519B THR* 3.3 6.6 + - - -
520B LEU* 3.2 42.4 + - + +
579B MET* 4.2 5.6 - - + -
581B VAL* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TYR* 2.9 37.5 + - + +
222B LEU* 4.5 10.8 - - + -
226B VAL* 5.0 0.4 - - + -
399B GLY* 4.3 2.9 - - - -
513B ILE* 3.1 9.3 + - + +
514B ARG* 3.3 8.8 + - - -
516B TYR* 1.3 82.2 - - + +
518B ARG* 1.3 52.1 + - - +
520B LEU* 3.2 2.3 + - - +
521B TYR* 2.7 60.9 + - - +
579B MET* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLY* 3.3 22.9 - - - +
402B GLU* 3.5 23.3 - - + +
403B ALA* 3.4 25.5 - - - +
406B GLU* 4.0 23.1 + - - +
446B ILE* 5.5 6.7 - - - +
514B ARG 2.9 19.8 + - - +
515B TYR* 4.1 26.7 + - - +
517B THR* 1.3 76.7 + - - +
519B THR* 1.3 68.6 + - - +
521B TYR* 3.6 2.9 - - - +
522B GLN* 2.7 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE* 3.9 29.6 - - + +
449B THR* 5.1 5.5 - - - +
450B LEU* 4.1 16.8 - - + +
515B TYR 2.6 20.3 + - - -
516B TYR 3.3 9.1 + - - -
517B THR 3.2 0.4 - - - -
518B ARG* 1.3 90.8 + - - +
520B LEU* 1.3 63.9 + - - +
522B GLN* 3.3 28.4 - - - +
523B PHE* 3.3 12.6 - - + -
584B LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B THR* 2.9 34.1 - - + +
450B LEU* 4.5 9.6 - - + -
516B TYR* 3.2 29.6 + - + +
517B THR 3.2 5.1 + - - +
519B THR* 1.3 81.8 - - - +
521B TYR* 1.3 63.4 + - - +
523B PHE* 3.4 3.5 + - - +
524B GLN* 3.3 27.7 + - - +
579B MET* 3.4 37.7 - - + -
580B ASN 4.2 4.5 - - - +
581B VAL* 4.0 22.0 - - + +
583B PRO* 5.5 0.2 - - - +
584B LEU* 4.4 19.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B TYR* 3.7 13.0 - - - -
397B ASN* 3.1 37.4 + - - -
399B GLY 3.6 20.2 - - - -
400B PHE* 3.8 15.5 - + - -
403B ALA* 3.9 9.4 - - + -
517B THR* 2.7 40.3 + - - +
518B ARG 3.6 3.1 - - - +
520B LEU* 1.3 73.7 - - - +
522B GLN* 1.3 63.1 + - - +
524B GLN* 2.9 20.0 + - - +
525B PHE* 2.9 38.2 + + + -
566B TRP* 3.7 20.3 - + - -
570B LEU* 4.7 10.3 - - + -
579B MET* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA* 3.8 17.9 - - - +
406B GLU* 3.6 23.6 + - + +
407B ILE* 2.8 37.4 - - + +
410B LEU* 4.7 13.7 - - - +
446B ILE* 4.9 7.8 - - - +
518B ARG* 2.7 51.0 + - - +
519B THR* 3.3 17.9 - - - +
521B TYR* 1.3 72.8 - - - +
523B PHE* 1.3 92.2 + - + +
525B PHE* 3.6 1.1 + - - -
526B GLN* 2.9 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 4.0 18.2 - - + -
446B ILE* 3.8 38.1 - - + -
519B THR* 3.3 20.4 + - + -
520B LEU 3.4 5.8 + - - +
521B TYR 3.1 1.0 - - - -
522B GLN* 1.3 99.2 - - + +
524B GLN* 1.3 61.1 + - - +
526B GLN* 3.9 4.2 - - + +
527B GLU* 2.8 31.5 + - - +
539B LEU* 4.8 2.8 - - + +
583B PRO* 3.4 7.3 - - + +
584B LEU* 3.7 41.5 - - + +
587B TYR* 3.5 52.9 - + + -
588B PHE* 4.4 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LEU 3.3 21.6 + - - +
521B TYR* 2.9 16.9 + - - +
523B PHE* 1.3 73.6 - - - +
525B PHE* 1.3 68.7 + - + +
527B GLU* 3.8 1.4 - - - +
528B ALA* 2.9 24.9 + - - +
570B LEU* 3.9 13.4 - - + +
574B VAL* 3.3 23.1 - - + +
576B ALA* 5.6 0.5 - - - +
578B ASN 3.1 18.4 - - - +
579B MET* 3.4 11.3 - - - +
580B ASN* 2.9 44.3 + - + +
583B PRO* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B PHE* 3.9 31.0 - + - -
403B ALA* 3.6 29.6 - - + -
404B VAL* 4.2 10.1 - - + -
407B ILE* 4.1 15.9 - - + -
521B TYR* 2.9 29.7 + - + +
522B GLN 3.7 3.6 - - - +
524B GLN* 1.3 75.7 - - - +
526B GLN* 1.3 52.9 + - - +
528B ALA* 3.1 2.6 + - - +
529B LEU* 2.7 49.0 + - + +
554B LEU* 5.5 3.8 - - + -
557B MET* 4.1 17.3 - - + -
570B LEU* 3.8 24.2 - - + -
573B VAL* 3.9 23.6 - - + -
574B VAL* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ILE* 3.5 31.6 + - + +
410B LEU* 3.9 29.5 - - + +
411B SER* 3.6 16.2 + - - -
522B GLN 2.9 19.6 + - - +
523B PHE* 3.9 8.3 - - + +
525B PHE* 1.3 74.9 - - - +
527B GLU* 1.3 66.0 + - - +
529B LEU* 4.5 2.6 - - - +
530B CYS* 3.0 53.6 + - - -
539B LEU* 4.2 15.0 - - + +
542B CYS* 4.2 8.5 - - - +
544B ILE* 4.4 9.7 - - - +
587B TYR* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B PHE 2.8 22.5 + - - +
524B GLN 3.9 2.7 - - - +
526B GLN* 1.3 72.3 - - - +
528B ALA* 1.3 58.7 + - - +
530B CYS* 3.8 1.0 - - - +
531B GLN* 2.9 56.0 + - + +
539B LEU* 3.8 22.4 - - + +
582B ARG* 5.7 0.5 - - - +
583B PRO* 3.4 26.1 - - + +
586B ASN* 2.6 38.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B GLN 2.9 17.7 + - - +
525B PHE 3.4 3.8 - - - +
527B GLU* 1.3 77.5 - - - +
529B LEU* 1.3 64.0 + - - +
531B GLN* 3.2 9.4 + - - +
532B ALA* 3.0 22.2 + - - +
553B LYS* 4.9 4.5 - - - +
573B VAL* 3.3 29.6 - - + +
574B VAL* 3.7 15.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
407B ILE* 4.7 13.7 - - + -
525B PHE* 2.7 44.5 + - + +
526B GLN* 4.2 4.9 - - - +
528B ALA* 1.3 75.5 - - + +
530B CYS* 1.3 58.2 + - - +
532B ALA* 3.1 6.0 + - - +
533B ALA* 2.9 26.4 + - - +
544B ILE* 4.0 23.1 - - + -
550B ALA* 3.5 34.9 - - + +
553B LYS* 4.1 16.6 - - + -
554B LEU* 4.1 25.4 - - + +
573B VAL* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B GLN* 3.0 44.0 + - - +
527B GLU 3.9 2.9 - - - +
529B LEU* 1.3 73.8 - - - +
531B GLN* 1.3 65.6 + - + +
533B ALA* 3.1 8.0 + - - -
535B HIS* 3.0 33.2 + - + +
539B LEU* 4.1 9.9 - - + -
542B CYS* 2.0 53.8 - - + -
544B ILE* 4.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU* 2.9 42.0 + - + +
528B ALA* 3.7 6.5 - - - +
530B CYS* 1.3 77.6 - - + +
532B ALA* 1.3 59.4 + - - +
534B LYS* 3.1 22.6 + - - +
535B HIS 4.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ALA 3.0 13.1 + - - +
529B LEU* 3.4 10.3 - - - +
530B CYS 3.1 0.2 - - - -
531B GLN* 1.3 76.0 - - - +
533B ALA* 1.3 57.4 + - - +
534B LYS* 3.3 10.0 + - - +
547B SER* 3.4 9.3 + - - -
549B GLU* 3.5 22.4 - - + +
550B ALA* 4.2 13.2 - - - -
553B LYS* 3.9 25.4 - - + -
----------------------------------------------------------
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