Contacts of the helix formed by residues 389 - 401 (chain B) in PDB entry 4I5L
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 389 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 3.8 14.3 - - + +
386B ASP* 4.1 19.7 + - - +
387B LYS 3.4 0.8 - - - -
388B LYS* 1.3 78.4 - - - +
390B PRO* 1.3 72.3 - - + +
391B THR* 3.3 15.3 - - - +
392B SER* 3.1 31.1 + - - +
393B ILE* 2.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ARG* 3.5 27.1 - - - +
388B LYS 3.9 3.8 - - - +
389B THR* 1.3 87.9 - - + +
391B THR* 1.3 61.7 + - - +
393B ILE* 3.6 9.0 + - + +
394B GLU* 3.2 28.9 + - - +
459B LYS* 4.1 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 3.0 58.5 + - + +
272B ALA* 5.0 0.7 - - - -
275B ARG* 3.1 26.2 + - - +
277B TRP* 3.9 10.3 - - + +
379B TRP* 3.9 18.2 - - + -
383B SER* 5.4 0.2 - - - +
389B THR* 3.1 3.6 - - - +
390B PRO* 1.3 78.1 - - - +
392B SER* 1.3 58.3 + - - +
394B GLU* 3.3 6.0 + - - +
395B TYR* 2.9 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 3.5 17.2 + - - -
383B SER* 2.9 23.5 + - - -
386B ASP 3.0 21.5 + - - -
387B LYS* 3.2 12.4 - - - -
389B THR* 3.1 14.6 + - - +
391B THR* 1.3 73.1 - - - +
393B ILE* 1.3 68.0 + - - +
395B TYR* 3.1 6.2 + - - -
396B TRP* 2.9 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LYS 3.5 16.6 - - - +
388B LYS* 3.7 19.3 - - - +
389B THR 2.8 22.0 + - - +
390B PRO* 4.0 4.7 - - + +
392B SER* 1.3 70.7 - - - +
394B GLU* 1.3 57.5 + - - +
397B PHE* 2.9 32.6 + - - +
455B LEU* 4.2 7.2 - - + -
458B LEU* 3.9 35.7 - - + +
459B LYS* 4.0 29.4 - - + +
462B LYS* 6.4 1.1 - - - -
464B ALA* 3.8 19.5 - - + -
468B PHE* 3.8 14.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.8 30.5 - - - +
275B ARG* 2.9 32.4 + - - +
277B TRP* 2.8 34.0 + - + -
390B PRO 3.2 9.2 + - - +
391B THR* 3.5 6.7 - - - +
393B ILE* 1.3 74.7 - - - +
395B TYR* 1.3 65.5 + - - +
397B PHE* 3.9 0.7 - - - +
398B ARG* 3.1 31.5 + - - +
455B LEU* 4.2 14.4 - - + -
459B LYS* 2.7 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 5.7 0.2 - + - -
277B TRP* 4.0 19.9 - + + -
355B ILE* 4.0 15.4 - - + +
360B VAL* 3.5 43.4 - - + +
376B ASP 4.7 2.3 + - - -
379B TRP* 4.0 26.5 - + + -
380B PHE* 3.4 26.7 + - - +
383B SER* 3.5 27.1 - - - +
391B THR* 2.9 13.9 + - + +
392B SER 3.1 9.2 + - - +
394B GLU* 1.3 77.3 - - - +
396B TRP* 1.3 95.8 + + - +
398B ARG* 3.4 4.5 + - - +
399B CYS* 3.1 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 4.0 8.1 - - + -
351B MET* 3.7 34.1 - - + -
355B ILE* 3.8 11.9 - - + -
380B PHE* 3.9 25.1 - + - -
383B SER* 3.0 24.5 + - - -
384B GLU* 3.8 29.6 - - + -
387B LYS* 3.9 17.0 - - + +
392B SER* 2.9 35.1 + - - +
395B TYR* 1.3 91.6 - + - +
397B PHE* 1.3 60.3 + - - +
399B CYS* 3.2 5.5 + - + +
400B MET* 2.9 32.4 + - - +
468B PHE* 3.7 28.5 - + + -
472B PHE* 3.6 21.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 5.6 1.3 - - - -
393B ILE 2.9 19.2 + - - +
394B GLU 3.9 2.5 - - - +
396B TRP* 1.3 73.5 - - - +
398B ARG* 1.3 64.6 + - + +
400B MET* 3.1 4.0 + - - +
401B ASP* 2.9 48.2 + - + +
406B GLY* 3.4 32.8 - - - -
407B ALA 4.1 0.7 - - - -
408B LEU* 3.7 29.6 - - + -
453B ILE 3.9 0.9 - - - -
454B THR* 3.5 8.3 - - - -
455B LEU* 3.3 47.8 - - + -
458B LEU* 3.6 20.4 - - + -
468B PHE* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 2.4 41.6 + - - +
140A TRP* 3.2 41.0 - - - -
141A PHE* 4.1 22.1 - - + -
142A THR* 4.9 12.2 + - - +
180A MET* 5.2 0.9 - - - +
277B TRP* 3.9 33.0 - - - +
354B ARG* 3.2 17.5 + - - -
359B ALA* 2.8 46.2 + - + +
360B VAL* 4.1 3.6 - - + -
394B GLU 3.1 22.2 + - - +
395B TYR 3.4 4.5 - - - +
397B PHE* 1.3 82.0 - - + +
399B CYS* 1.3 62.3 + - - +
401B ASP* 3.7 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B MET* 3.4 22.9 - - + -
354B ARG* 2.7 48.9 + - + +
355B ILE* 4.1 25.8 - - - -
359B ALA* 4.2 2.9 - - - -
360B VAL* 3.8 18.2 - - - -
395B TYR* 3.1 16.0 + - - +
396B TRP* 3.5 15.7 - - + +
397B PHE 3.2 0.2 - - - -
398B ARG* 1.3 80.0 - - - +
400B MET* 1.3 59.5 + - - +
416B PHE* 3.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B MET* 3.7 18.2 - - + -
396B TRP 2.9 16.8 + - - +
397B PHE* 3.1 3.5 + - - +
399B CYS* 1.3 74.5 - - - +
401B ASP* 1.3 60.4 + - - +
402B LEU* 2.9 12.9 + - - +
408B LEU* 3.8 17.3 - - + +
412B GLU* 3.9 7.4 - - - +
413B LEU* 3.7 31.0 - - + -
416B PHE* 3.6 31.7 - - + -
467B PHE* 4.0 11.0 - - + -
468B PHE* 3.7 29.8 - - - -
471B PHE* 3.7 26.2 - - + -
472B PHE* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 4.9 1.2 + - - -
180A MET* 4.2 1.2 - - - +
354B ARG* 3.5 10.6 + - - -
397B PHE* 2.9 27.8 + - + +
398B ARG* 3.7 5.1 + - - +
399B CYS 3.5 1.0 - - - -
400B MET* 1.3 72.7 - - - +
402B LEU* 1.3 66.4 + - - +
403B ASP* 3.1 22.5 - - - +
404B GLY* 3.0 19.8 + - - -
405B ASP* 3.1 13.4 + - - +
406B GLY* 2.8 28.0 + - - -
407B ALA 3.2 10.0 - - - +
408B LEU* 3.8 11.9 - - + -
412B GLU* 3.4 2.0 - - - +
----------------------------------------------------------
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