Contacts of the helix formed by residues 399 - 417 (chain A) in PDB entry 4IKV
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 PRO 399 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 3.6 23.1 - - + -
325A GLN* 3.4 22.7 - - + +
328A VAL* 3.9 23.1 - - + -
333A LEU* 4.3 7.9 - - + -
338A PHE* 3.8 17.2 - - + -
397A VAL 3.5 0.6 - - - +
398A HIS* 1.3 99.7 - - + +
400A ILE* 1.3 64.5 + - - +
401A TRP 3.1 0.4 - - - -
402A LEU* 3.1 16.3 + - + +
403A VAL* 3.1 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 3.1 31.3 + - + +
399A PRO* 1.3 78.8 - - - +
401A TRP* 1.3 79.0 + - + +
403A VAL* 3.3 20.0 + - + +
404A LEU* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 3.7 32.3 - - + +
385A ILE* 4.0 9.3 - - + +
387A VAL* 4.1 21.1 - - + -
388A PRO* 3.5 50.7 - - + +
391A LEU* 5.7 4.7 - - + -
397A VAL* 5.1 1.3 - - + -
398A HIS* 3.4 26.2 + - + +
399A PRO 3.1 0.8 - - - -
400A ILE* 1.3 91.7 - - + +
402A LEU* 1.3 58.3 + - - +
404A LEU* 3.5 14.9 + - + +
405A SER* 3.1 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.0 28.9 - - + +
319A TYR* 3.9 19.3 - - + -
320A ALA* 3.7 37.7 - - + +
324A THR* 3.8 12.8 - - - +
338A PHE* 3.8 18.2 - - + -
385A ILE* 4.0 11.5 - - + +
398A HIS 4.5 0.6 + - - +
399A PRO* 3.1 12.8 + - + +
401A TRP* 1.3 77.5 - - - +
403A VAL* 1.3 65.3 + - - +
405A SER* 3.1 4.4 + - - -
406A TYR* 3.0 49.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 4.2 8.7 - - + -
341A LEU* 4.0 26.9 - - + -
345A PHE* 4.0 23.1 - - + -
399A PRO* 3.1 18.8 + - + +
400A ILE* 3.6 21.3 - - + +
402A LEU* 1.3 76.7 - - - +
404A LEU* 1.3 62.6 + - - +
406A TYR* 3.3 2.8 + - - +
407A PHE* 2.9 22.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 3.8 21.8 - - + -
400A ILE* 2.9 20.8 + - + +
401A TRP* 3.7 16.2 - - + +
403A VAL* 1.3 77.5 - - - +
405A SER* 1.3 57.7 + - - +
407A PHE* 3.3 16.0 + - + +
408A ILE* 2.9 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.9 19.2 - - - +
381A SER* 3.0 37.8 + - - +
382A PHE* 5.0 1.0 - - - -
384A VAL* 4.6 4.5 - - - +
385A ILE* 4.1 14.1 - - - +
401A TRP 3.1 14.4 + - - -
402A LEU* 3.1 11.3 + - - -
404A LEU* 1.3 77.2 - - - +
406A TYR* 1.3 62.8 + - - +
408A ILE* 3.3 1.6 + - - -
409A VAL* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLY* 2.7 41.8 + - - -
316A LEU* 3.4 24.9 + - + +
338A PHE* 3.9 30.0 - - + +
339A GLN* 3.4 12.3 + - - -
341A LEU* 3.7 32.8 - - + -
342A ASN* 4.8 15.1 + - + +
345A PHE* 4.2 2.9 - - + -
402A LEU* 3.0 47.9 + - + -
403A VAL 3.7 5.6 - - - +
405A SER* 1.3 75.1 - - - +
407A PHE* 1.3 62.3 + - - +
409A VAL* 3.4 10.6 + - + +
410A VAL* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 3.7 38.3 - + + -
349A LEU* 3.5 28.7 - - + -
403A VAL* 2.9 19.0 + - + +
404A LEU* 3.5 16.6 - - + +
405A SER 3.2 0.2 - - - -
406A TYR* 1.3 75.6 - - - +
408A ILE* 1.3 74.2 + - + +
410A VAL* 3.2 5.9 + - - +
411A LEU* 3.1 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PHE* 3.2 35.0 - - + +
380A LEU* 4.0 22.0 - - + -
381A SER* 3.8 9.9 - - - +
384A VAL* 3.7 31.2 - - + -
404A LEU* 2.9 39.4 + - + +
405A SER 3.8 4.0 - - - +
407A PHE* 1.3 78.5 - - + +
409A VAL* 1.3 66.2 + - - +
411A LEU* 3.2 22.2 + - + +
412A GLY 3.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 4.0 7.5 - - + -
308A ILE* 4.4 13.0 - - + +
309A GLN* 3.5 40.4 - - + +
316A LEU* 5.9 4.5 - - + -
342A ASN* 4.8 4.3 - - - +
377A PHE 4.9 2.0 - - - -
378A ALA* 5.0 4.9 - - - +
381A SER* 3.1 26.9 - - - +
382A PHE* 6.2 0.2 - - + -
405A SER* 3.1 17.4 + - - +
406A TYR* 3.6 12.8 - - + +
408A ILE* 1.3 76.9 - - - +
410A VAL* 1.3 58.0 + - - +
412A GLY* 3.0 4.0 + - - +
413A GLU* 2.8 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASN* 3.6 42.2 - - - +
345A PHE* 3.9 26.7 - - + +
346A ILE* 3.9 16.8 - - + -
349A LEU* 4.2 5.2 - - + -
406A TYR 3.2 14.3 + - - +
407A PHE 3.2 7.8 + - - +
409A VAL* 1.3 74.0 - - - +
411A LEU* 1.3 66.1 + - - +
413A GLU* 3.6 5.8 - - - +
414A LEU* 2.9 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 4.0 18.6 - - + -
353A PHE* 3.7 33.8 - - + -
377A PHE* 3.8 36.6 - - + -
407A PHE* 3.1 38.0 + - + +
408A ILE* 3.4 17.0 - - + +
410A VAL* 1.3 76.2 - - - +
412A GLY* 1.3 63.3 + - - +
414A LEU 3.5 0.5 + - - -
415A CYS* 3.4 23.7 + - - -
609A OLA 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.7 7.2 - - - -
374A GLY* 3.4 21.0 - - - -
377A PHE* 3.5 23.0 - - - +
408A ILE 3.2 4.4 + - - -
409A VAL 3.0 7.3 + - - -
411A LEU* 1.3 78.0 - - - +
413A GLU* 1.3 63.7 + - - +
415A CYS 3.0 10.8 + - - -
416A LEU* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.4 14.4 - - + -
306A TRP* 3.8 36.2 - - + -
309A GLN* 3.6 11.5 - - - +
342A ASN* 2.9 28.6 + - - +
346A ILE* 3.7 21.3 - - + +
409A VAL 2.8 16.0 + - - +
410A VAL* 3.1 11.7 + - + +
412A GLY* 1.3 71.6 - - - +
414A LEU* 1.3 62.9 + - + +
417A SER* 2.9 35.1 + - - +
418A PRO* 3.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 4.6 16.2 - - + +
349A LEU* 3.6 30.7 - - + -
350A ALA* 3.7 27.4 - - + +
353A PHE* 3.7 42.4 - - + +
357A TRP* 4.2 9.4 + - - -
410A VAL* 2.9 30.7 + - + +
411A LEU 4.0 0.4 - - - -
412A GLY 3.2 0.2 - - - -
413A GLU* 1.3 79.4 - - + +
415A CYS* 1.3 58.7 + - - +
418A PRO* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PHE* 4.1 13.2 - - - -
357A TRP* 4.4 19.1 - - + -
370A LYS* 3.4 41.5 - - + +
373A LEU* 3.9 19.1 - - + -
374A GLY 3.9 4.7 - - - +
377A PHE* 4.2 13.9 - - - -
411A LEU 3.4 14.5 + - - -
412A GLY 3.0 8.5 + - - +
414A LEU* 1.3 80.7 - - - +
416A LEU* 1.3 63.2 + - - +
418A PRO* 4.2 3.0 - - - +
419A VAL* 3.6 7.8 - - - +
609A OLA 4.4 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ALA 4.3 3.6 - - - +
302A SER* 4.2 9.0 - - - +
305A PHE* 3.7 35.7 - - + -
306A TRP* 4.2 11.9 - - + +
370A LYS 3.9 10.3 - - - +
371A PHE* 3.7 44.3 - - + +
374A GLY* 4.1 3.6 - - - -
375A LEU 4.7 0.2 - - - +
412A GLY 3.0 13.9 + - - +
413A GLU 5.1 0.2 - - - -
415A CYS* 1.3 77.1 - - - +
417A SER* 1.3 69.8 - - - +
419A VAL* 3.1 21.9 + - - +
420A GLY* 3.3 6.8 + - - -
440A TRP* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TRP* 3.7 32.7 - - - -
413A GLU* 2.9 29.6 + - - +
416A LEU* 1.3 81.4 - - - +
418A PRO* 1.3 63.6 - - - +
419A VAL 3.1 1.2 + - - -
420A GLY* 3.2 10.9 + - - -
421A LEU 4.6 1.4 + - - -
440A TRP* 4.0 12.5 + - - -
----------------------------------------------------------
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