Contacts of the helix formed by residues 422 - 434 (chain C) in PDB entry 3IFS
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 422 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLU* 4.3 14.4 - - - +
419C GLN* 3.3 28.0 + - + +
421C GLY* 1.3 76.1 - - - +
423C GLU* 1.3 77.0 + - - +
424C ALA 3.3 0.2 - - - -
425C TYR* 3.3 22.4 - - + -
426C LYS* 3.3 35.1 - - - +
311D LEU 3.9 20.9 - - - +
312D HIS* 5.6 0.7 - - - -
315D GLY 4.5 1.6 - - - -
316D GLN* 3.9 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C GLN 5.0 0.7 - - - +
420C PRO* 3.6 20.0 - - + +
421C GLY 3.2 1.6 - - - -
422C VAL* 1.3 94.4 - - + +
424C ALA* 1.3 63.5 + - - +
426C LYS* 3.2 20.7 + - - +
427C LYS* 2.9 38.4 + - + +
430C PHE* 5.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C PRO 4.6 1.0 + - - -
421C GLY 3.8 4.3 + - - +
422C VAL 3.3 0.6 - - - -
423C GLU* 1.3 79.1 - - - +
425C TYR* 1.3 64.2 + - - +
427C LYS* 3.5 13.0 + - - +
428C ASN* 3.2 26.4 + - - +
319D GLN* 3.7 33.2 - - + +
373D ALA* 3.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 425 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 4.3 5.4 + - - -
421C GLY 4.8 1.1 + - - -
422C VAL* 3.3 39.0 - - + -
423C GLU 3.4 0.2 - - - -
424C ALA* 1.3 79.6 - - - +
426C LYS* 1.3 77.7 + - + +
428C ASN* 3.3 2.4 + - - +
429C MSE 2.9 51.8 + - + +
308D SER* 5.6 0.9 - - - -
311D LEU* 3.8 38.5 + - + -
312D HIS* 3.2 34.7 + - - -
315D GLY* 5.9 2.0 - - - -
319D GLN* 4.7 1.5 + - - +
366D ALA* 5.8 0.7 - - + -
369D GLY 4.3 4.6 - - - -
370D THR* 3.5 38.4 - - + +
373D ALA* 3.7 11.8 - - + +
374D HIS* 5.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C THR* 5.3 8.9 + - - +
422C VAL* 3.3 34.7 - - - +
423C GLU* 3.2 27.5 + - - +
425C TYR* 1.3 112.8 - - + +
427C LYS* 1.3 57.6 + - - +
429C MSE 3.2 10.9 + - + +
430C PHE* 2.9 54.4 + - + -
312D HIS* 4.7 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLU* 2.9 29.5 + - + +
424C ALA* 3.7 13.5 - - - +
426C LYS* 1.3 78.2 - - - +
428C ASN* 1.3 62.2 + - - +
430C PHE* 3.4 10.8 + - + +
431C ALA* 3.0 29.8 + - - +
438C PHE* 3.9 18.8 - - + -
441C LEU* 3.6 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ALA* 3.2 15.2 + - - +
425C TYR 3.7 1.1 - - - +
426C LYS 3.3 0.2 - - - -
427C LYS* 1.3 77.8 - - - +
429C MSE 1.3 58.5 + - - +
431C ALA* 3.4 2.1 + - - +
432C LEU* 3.0 34.5 + - - +
441C LEU* 3.9 12.8 - - - +
445C LEU* 3.5 28.5 - - + +
369D GLY* 3.0 35.6 + - - +
372D LEU* 3.9 10.1 - - - +
373D ALA* 3.3 22.6 - - - +
376D ASP* 5.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.8 7.0 - - - -
150C THR* 3.4 36.3 - - + +
151C GLU* 5.5 3.8 - - - +
425C TYR* 2.9 34.5 + - + +
426C LYS* 3.5 13.7 - - + +
428C ASN* 1.3 74.7 - - - +
430C PHE* 1.3 84.0 + - + +
432C LEU* 3.3 2.1 + - - +
433C LEU* 2.9 44.9 + - + +
308D SER* 6.4 0.4 - - - -
362D VAL* 5.0 2.0 - - - +
365D LYS 4.1 12.8 - - - +
366D ALA* 3.6 39.7 - - - +
369D GLY* 4.3 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C THR 5.4 5.6 - - - -
150C THR* 3.5 24.2 - - - -
423C GLU* 5.9 1.1 - - - -
426C LYS* 2.9 43.5 + - + +
427C LYS* 3.7 7.4 - - + +
429C MSE 1.3 86.9 - - + +
431C ALA* 1.3 64.1 + - - +
433C LEU* 3.3 11.3 + - + +
434C GLY 3.2 3.8 + - - -
435C LYS* 2.9 63.1 + - + +
438C PHE* 3.8 27.6 - + + -
353D TYR* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C LYS 3.0 17.5 + - - +
428C ASN 3.5 5.4 - - - +
430C PHE* 1.3 75.7 - - - +
432C LEU* 1.3 58.2 + - - +
434C GLY* 3.0 17.0 + - - -
435C LYS 5.2 0.2 - - - +
438C PHE* 3.5 21.7 - - + +
441C LEU* 3.8 14.4 - - + -
442C LYS* 3.3 46.7 - - - +
445C LEU* 3.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ASN 3.0 19.3 + - - +
429C MSE 3.9 3.1 - - - +
431C ALA* 1.3 71.5 - - - +
433C LEU* 1.3 60.9 + - - +
434C GLY 3.0 5.7 + - - -
442C LYS* 4.4 15.5 + - + +
445C LEU* 3.9 22.4 - - + -
446C GLU* 3.7 31.9 - - + +
449C LEU* 3.9 17.7 - - + -
361D PHE* 4.5 2.4 - - - -
365D LYS* 3.9 35.4 - - + +
368D GLU* 3.9 17.5 - - + +
369D GLY* 3.6 31.6 - - - +
372D LEU* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C THR* 5.0 5.6 - - + -
429C MSE 2.9 44.4 + - + +
430C PHE* 3.7 11.4 - - + +
431C ALA 3.3 0.2 - - - -
432C LEU* 1.3 76.9 - - - +
434C GLY* 1.3 59.6 + - - +
442C LYS* 5.2 0.4 - - - -
353D TYR* 3.5 35.3 - - + +
354D LEU* 4.0 13.6 - - + +
361D PHE* 3.8 29.1 - - + -
362D VAL* 3.8 31.0 - - + -
365D LYS* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ALA 3.0 14.9 + - - -
432C LEU 3.0 1.2 - - - -
433C LEU* 1.3 80.4 - - - +
435C LYS* 1.3 66.7 + - - +
436C PRO* 3.4 6.1 - - - +
439C GLU* 5.6 0.2 - - - +
442C LYS* 4.2 18.4 - - - -
353D TYR* 3.8 8.9 - - - +
----------------------------------------------------------
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