Contacts of the helix formed by residues 358 - 377 (chain D) 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 THR 358 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D GLU* 4.1 21.3 + - + +
339D LEU 3.2 14.8 - - - +
340D THR* 4.2 12.6 - - - +
341D ILE* 4.1 2.7 - - - -
356D GLY 5.1 2.0 - - - +
357D GLU* 1.3 81.1 + - - +
359D VAL* 1.3 63.7 + - - +
360D ASP* 3.6 7.1 + - - +
361D PHE* 3.1 38.9 + - - +
362D VAL* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 3.6 32.6 - - + +
123C SER* 3.9 23.6 - - - +
126C MSE 4.4 7.4 - - + -
154C LEU* 4.3 8.7 - - + -
158C ILE* 4.0 22.0 - - + -
339D LEU* 2.9 33.4 + - + +
340D THR 5.5 0.4 - - - -
341D ILE* 4.2 16.8 - - + -
357D GLU 4.3 0.2 + - - -
358D THR* 1.3 73.6 - - - +
360D ASP* 1.3 62.3 + - - +
362D VAL* 3.0 8.3 + - - +
363D ASN* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE 5.1 0.7 - - - -
123C SER* 4.4 7.8 + - - +
275D GLU* 4.6 4.7 - - - +
331D LYS* 5.6 2.1 + - - -
332D VAL 5.4 4.0 - - - +
333D GLY 4.6 8.7 - - - +
335D SER* 3.9 30.3 + - - -
338D GLU* 3.7 22.7 + - - +
358D THR* 3.2 3.4 + - - +
359D VAL* 1.3 77.6 - - - +
361D PHE* 1.3 60.1 + - - +
363D ASN* 3.3 18.0 + - - +
364D THR* 2.8 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LEU 4.5 1.6 - - - -
433C LEU* 3.8 39.7 - - + -
354D LEU* 4.2 3.1 - - + -
357D GLU* 3.8 45.1 - - + +
358D THR* 3.1 28.0 + - - +
360D ASP* 1.3 75.5 - - - +
362D VAL* 1.3 68.0 + - + +
364D THR* 3.3 7.4 + - - -
365D LYS* 3.0 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 3.8 23.6 - - + -
150C THR* 4.3 20.6 - - + -
154C LEU* 4.4 7.2 - - + -
429C MSE 5.0 2.4 - - - +
433C LEU* 3.8 27.9 - - + +
341D ILE* 3.8 20.9 - - + -
354D LEU* 4.3 9.9 - - + -
358D THR 3.7 12.8 - - - +
359D VAL 3.0 8.2 + - - +
361D PHE* 1.3 78.6 - - + +
363D ASN* 1.3 60.3 + - - +
365D LYS* 3.1 3.1 + - - +
366D ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 3.3 47.9 + - - +
122C SER* 4.8 0.2 - - - +
274D TYR* 3.0 49.2 + - - +
275D GLU* 4.1 11.7 + - - +
307D PHE 5.1 0.2 - - - +
308D SER 5.0 2.4 + - - -
331D LYS* 5.8 0.4 - - - -
359D VAL 3.0 7.1 + - - +
360D ASP* 3.3 18.3 + - - +
362D VAL* 1.3 76.0 - - - +
364D THR* 1.3 57.2 + - - +
366D ALA* 3.4 2.9 + - - +
367D TYR* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D LYS* 3.9 26.8 + - - +
360D ASP* 2.8 30.5 + - - -
361D PHE* 3.5 8.2 - - - -
362D VAL 3.2 0.2 - - - -
363D ASN* 1.3 77.2 - - - +
365D LYS* 1.3 63.5 + - + +
367D TYR* 3.2 8.3 + - + +
368D GLU* 3.0 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C MSE 4.1 8.3 - - - +
432C LEU* 3.9 33.1 + - + +
433C LEU* 3.7 33.9 - - + -
446C GLU* 5.4 6.1 + - - +
449C LEU* 5.8 0.4 - - - +
361D PHE* 3.0 47.4 + - + +
362D VAL 3.1 0.4 + - - +
364D THR* 1.3 78.3 - - - +
366D ALA* 1.3 61.6 + - - +
368D GLU* 3.3 28.6 + - - +
369D GLY* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 3.9 17.0 - - + -
425C TYR* 5.8 1.1 - - + -
429C MSE 3.6 29.9 - - - +
274D TYR* 4.2 10.5 - - + -
308D SER* 5.1 4.7 - - - -
311D LEU* 5.8 1.6 - - + -
362D VAL 2.9 12.7 + - - +
363D ASN 3.5 9.2 - - - +
365D LYS* 1.3 77.7 - - - +
367D TYR* 1.3 55.0 + - - +
370D THR* 2.7 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 367 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D TYR* 3.5 38.2 + + + -
329D VAL* 3.7 22.9 - - + -
331D LYS* 3.3 43.2 - - + +
363D ASN 3.0 14.4 + - - +
364D THR* 3.4 11.7 - - + +
366D ALA* 1.3 76.4 - - - +
368D GLU* 1.3 80.5 + - + +
370D THR* 3.9 1.6 - - - -
371D LEU* 3.0 45.2 + - + +
383D ILE* 3.2 36.0 - - - +
385D ASN* 5.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LEU* 3.9 12.2 - - + +
449C LEU* 3.5 35.3 - - + +
364D THR* 3.0 29.8 + - - +
365D LYS* 3.3 33.2 + - - +
367D TYR* 1.3 94.2 - - + +
369D GLY* 1.3 64.2 + - - +
371D LEU* 3.4 5.5 + - - +
372D LEU* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 369 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C TYR 4.6 2.9 - - - -
428C ASN* 3.0 36.5 + - - +
429C MSE 4.3 1.6 - - - -
432C LEU* 3.6 10.2 - - - +
365D LYS 2.9 17.6 + - - -
366D ALA 4.0 0.4 - - - -
368D GLU* 1.3 76.6 - - - +
370D THR* 1.3 56.4 + - - +
372D LEU* 3.5 2.0 + - - -
373D ALA* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 370 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C TYR* 3.5 24.9 + - + +
274D TYR* 3.4 17.9 - - - +
307D PHE* 4.5 2.5 - - + -
311D LEU* 3.6 23.6 - - + +
366D ALA 2.7 22.7 + - - -
369D GLY* 1.3 74.5 - - - +
371D LEU* 1.3 60.8 + - - +
373D ALA* 4.4 0.2 - - - -
374D HIS* 2.8 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C LEU* 5.6 2.0 - - + -
11D LYS* 4.0 28.3 - - + -
329D VAL* 5.1 2.9 - - + -
367D TYR* 3.0 34.1 + - + +
368D GLU* 3.8 6.3 - - - +
370D THR* 1.3 75.8 - - - +
372D LEU* 1.3 76.1 + - + +
374D HIS* 4.0 1.7 - - - +
375D SER* 2.8 40.2 + - - +
381D ASN* 3.8 31.9 - - + +
383D ILE* 3.7 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ASN* 3.9 7.6 - - - +
432C LEU* 4.9 2.2 - - + -
445C LEU* 3.9 33.7 - - + +
448C ARG* 3.7 41.5 + - + +
449C LEU* 3.9 30.7 - - + -
11D LYS* 5.3 4.9 - - + -
368D GLU 3.2 18.7 + - - +
369D GLY 3.9 3.6 - - - +
371D LEU* 1.3 89.0 - - + +
373D ALA* 1.3 64.7 + - - +
375D SER* 3.4 4.9 + - - +
376D ASP* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ALA* 3.8 7.4 - - + -
425C TYR* 3.7 24.7 - - + +
428C ASN* 3.3 12.9 - - - +
319D GLN* 2.9 32.7 + - - +
369D GLY 3.0 18.6 + - - +
370D THR 3.7 3.1 - - - +
372D LEU* 1.3 76.3 - - - +
374D HIS* 1.3 63.0 + - + +
376D ASP* 3.1 8.4 + - - +
377D GLY 2.9 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C TYR* 5.2 3.8 - - + +
307D PHE* 3.9 3.5 - + - -
311D LEU* 3.8 19.3 - - + +
315D GLY 4.6 5.1 + - - -
318D VAL* 3.4 29.3 - - + +
319D GLN* 3.3 22.4 + - - +
327D GLU* 2.8 33.7 + - - +
370D THR* 2.8 47.1 + - + +
371D LEU 4.0 0.7 - - - +
373D ALA* 1.3 74.6 - - + +
375D SER* 1.3 62.0 + - - +
377D GLY* 3.1 9.6 + - - +
378D GLY 3.3 0.3 + - - -
379D VAL* 3.0 30.0 + - + +
381D ASN* 3.9 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ARG* 4.8 5.8 - - - -
11D LYS 4.2 11.5 + - - -
14D SER* 5.7 0.7 - - - -
15D PHE* 3.4 23.1 - - - -
371D LEU* 2.8 33.6 + - - +
372D LEU* 3.6 8.1 - - - -
374D HIS* 1.3 76.9 - - - +
376D ASP* 1.3 65.9 + - - +
378D GLY* 3.2 10.6 + - - -
379D VAL 3.5 16.1 + - - -
381D ASN* 4.1 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C ASN* 5.3 2.4 + - - -
445C LEU* 5.7 0.2 - - - +
448C ARG* 2.8 41.9 + - - -
319D GLN* 4.6 1.6 - - - +
372D LEU 2.9 19.2 + - - +
373D ALA* 3.1 8.4 + - - +
375D SER* 1.3 76.1 - - - +
377D GLY* 1.3 57.9 + - - +
378D GLY 3.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C GLN* 5.9 0.7 + - - -
319D GLN* 3.6 26.4 - - - +
323D ARG* 2.9 29.6 + - - -
373D ALA 2.9 9.7 + - - -
374D HIS 3.1 6.5 + - - -
376D ASP* 1.3 77.2 - - - +
378D GLY* 1.3 55.6 + - - +
379D VAL 3.6 0.4 - - - -
----------------------------------------------------------
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