Contacts of the helix formed by residues 398 - 411 (chain A) in PDB entry 1P0P
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 PHE 398 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A SER* 3.9 3.4 - - - -
224A SER 3.5 20.9 - - - +
225A GLY* 5.0 3.7 + - - +
231A TRP* 3.6 32.8 - + - -
286A LEU* 4.0 6.5 - - + -
321A VAL* 4.4 6.1 - - + -
325A GLU* 3.9 35.4 - - + -
329A PHE* 3.6 40.6 - + - -
393A VAL* 4.3 5.2 - - + -
394A GLY* 2.9 12.1 + - - +
396A TYR 3.6 1.0 - - - -
397A ASN* 1.3 96.9 - - + +
399A ILE* 1.3 65.6 + - - +
401A PRO* 3.2 5.4 - - - +
402A ALA* 3.0 25.6 + - - +
438A HIS* 3.7 20.9 - + - -
601A VXA 4.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 3.9 26.0 - - + -
322A ASN 4.0 13.0 - - - +
323A LYS 4.6 2.2 - - - +
325A GLU* 4.1 10.3 - - + +
394A GLY* 3.1 16.9 + - - +
395A ASP* 3.6 15.5 - - - +
398A PHE* 1.3 70.6 - - - +
400A CYS* 1.3 64.2 + - - +
402A ALA* 3.2 3.6 + - - +
403A LEU* 3.0 36.9 + - + +
420A TYR* 4.7 1.3 - - + -
514A LEU* 4.1 11.2 - - + -
515A ARG* 3.5 52.5 - - + +
519A CYS* 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASP* 3.1 28.4 + - - +
399A ILE* 1.3 77.0 - - - +
401A PRO* 1.3 67.5 - - + +
403A LEU* 3.8 1.1 - - - +
404A GLU* 2.9 26.0 + - - +
515A ARG* 4.9 0.4 - - - -
518A GLN 4.0 1.1 - - - -
519A CYS* 2.0 64.5 - - + +
522A TRP* 3.9 23.3 - - + -
523A THR* 4.4 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 3.7 5.8 - - - +
228A ASN* 2.8 34.3 + - - +
229A ALA* 3.7 21.8 - - + +
230A PRO* 3.9 13.2 - - + -
395A ASP 3.4 10.3 - - - +
396A TYR 3.3 18.6 - - - +
397A ASN 3.9 5.6 - - - +
398A PHE 3.2 16.6 - - - +
400A CYS* 1.3 92.9 - - + +
402A ALA* 1.3 56.0 + - - +
404A GLU* 4.4 1.6 - - + -
405A PHE* 2.9 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY 5.1 8.7 - - - +
226A SER* 3.8 10.7 + - - +
319A VAL* 4.1 19.0 - - + +
320A GLY 4.9 0.9 - - - +
321A VAL* 3.7 21.1 - - + -
398A PHE 3.0 17.9 + - - +
399A ILE 3.5 4.0 - - - +
401A PRO* 1.3 75.6 - - - +
403A LEU* 1.3 63.4 + - - +
405A PHE* 3.4 4.2 + - - +
406A THR* 2.8 30.1 + - - -
418A PHE* 4.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 3.0 28.6 + - + +
400A CYS* 3.8 3.8 - - - +
402A ALA* 1.3 75.7 - - - +
404A GLU* 1.3 57.7 + - - +
406A THR* 3.2 3.6 + - - -
407A LYS* 2.9 30.0 + - - +
418A PHE* 3.6 35.7 - - + -
493A PHE* 4.1 23.3 - - + -
498A GLN* 6.1 0.7 - - - +
500A TYR* 6.0 1.1 - - + -
514A LEU* 3.1 41.1 - - + +
519A CYS* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASN* 4.0 10.5 - - - +
400A CYS 2.9 18.1 + - - +
401A PRO* 3.8 4.9 - - + +
403A LEU* 1.3 74.5 - - - +
405A PHE* 1.3 64.3 + - - +
407A LYS* 3.6 24.3 + - - +
408A LYS* 3.0 65.1 + - + +
519A CYS* 5.9 1.0 - - - +
523A THR* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A SER* 4.1 5.8 - - - -
208A LEU* 4.0 18.4 - - + -
209A LEU* 5.2 2.0 - - + -
222A LEU* 3.9 22.0 - - + -
226A SER* 4.1 10.5 - - - -
227A PHE* 3.5 32.8 - + - -
228A ASN* 3.6 17.0 - - - +
307A LEU* 4.1 23.9 - - + +
317A ILE* 3.6 25.4 - - + -
319A VAL* 4.5 4.3 - - + -
401A PRO 2.9 19.2 + - - +
402A ALA 3.6 4.3 - - - +
404A GLU* 1.3 75.3 - - - +
406A THR* 1.3 67.1 + - - +
408A LYS* 3.9 0.9 - - - +
409A PHE* 2.8 50.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 4.7 2.9 - - + -
319A VAL* 3.5 17.7 - - + +
402A ALA 2.8 22.3 + - - -
403A LEU* 3.2 4.7 + - - -
405A PHE* 1.3 80.0 - - - +
407A LYS* 1.3 65.6 + - - +
409A PHE* 3.9 3.0 - - - +
410A SER* 3.0 26.3 + - - -
416A ALA* 4.1 17.1 - - + +
417A PHE 5.3 0.9 - - - +
418A PHE* 3.4 25.1 - - + -
493A PHE* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU 2.9 16.8 + - - +
404A GLU* 3.6 27.9 + - - +
406A THR* 1.3 75.8 - - - +
408A LYS* 1.3 63.2 + - + +
410A SER* 3.0 16.0 + - - -
411A GLU* 3.1 37.8 + - - +
493A PHE* 3.8 17.0 - - + -
495A SER* 3.3 35.3 + - - +
498A GLN* 4.3 15.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP 5.9 0.2 - - - +
307A LEU* 3.9 35.8 - - + +
308A GLU* 3.0 39.1 + - + +
312A PHE* 4.5 0.3 - - - -
404A GLU* 3.0 46.2 + - + +
405A PHE 4.0 0.9 - - - +
407A LYS* 1.3 76.1 - - + +
409A PHE* 1.3 64.2 + - - +
411A GLU* 3.4 27.6 + - - +
412A TRP* 3.4 19.2 + - - -
523A THR* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.2 16.8 - - + -
209A LEU* 6.2 0.7 - - + -
307A LEU* 4.3 4.2 - - + +
312A PHE* 3.2 44.7 - + + -
313A LYS 3.6 18.4 - - - -
315A THR* 3.2 29.2 - - + -
317A ILE* 3.4 39.5 - - + -
405A PHE* 2.8 38.1 + + + +
406A THR 3.9 3.1 - - - +
408A LYS* 1.3 78.3 - - - +
410A SER* 1.3 64.4 + - - +
411A GLU 3.3 0.7 + - - -
412A TRP* 3.3 17.7 + - - +
414A ASN* 3.7 16.4 + - + +
415A ASN 5.2 0.2 - - - -
416A ALA* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A THR 3.0 14.4 + - - -
407A LYS* 3.0 15.8 + - - -
409A PHE* 1.3 74.8 - - - +
411A GLU* 1.3 61.8 + - - +
412A TRP 2.9 7.0 + - - -
413A GLY* 3.0 15.3 + - - -
414A ASN 3.8 19.7 + - - +
416A ALA* 4.2 7.6 - - - -
493A PHE* 3.7 24.6 + - - -
494A LYS* 4.9 1.6 - - - -
495A SER* 3.9 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 5.7 1.4 - - - +
407A LYS* 3.1 25.9 + - - +
408A LYS* 3.5 26.8 + - - +
409A PHE 3.2 1.0 - - - -
410A SER* 1.3 77.6 - - - +
412A TRP* 1.3 67.3 + - + +
413A GLY 3.3 3.4 + - - -
495A SER* 2.9 33.0 + - - +
----------------------------------------------------------
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