Contacts of the helix formed by residues 395 - 413 (chain B) in PDB entry 1EQB
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 ASP 395 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 2.9 19.9 + - - +
393B ILE 3.5 0.4 - - - -
394B ASN* 1.3 76.6 - - - +
396B GLU* 1.3 62.1 + - - +
397B ALA* 2.9 35.2 + - - +
398B VAL* 3.0 37.0 + - + +
399B ILE* 3.1 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG* 2.8 46.2 + - - +
393B ILE 4.9 0.7 - - - +
394B ASN* 3.3 9.8 + - - +
395B ASP* 1.3 73.7 - - - +
397B ALA* 1.3 57.1 + - - +
399B ILE* 3.6 17.2 - - - +
400B GLU* 2.9 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASP* 2.9 12.9 + - - +
396B GLU* 1.3 76.3 - - - +
398B VAL* 1.3 58.4 + - - +
400B GLU* 3.6 7.3 - - - +
401B ARG* 3.0 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASP* 3.7 36.3 - - + +
389B VAL* 4.4 6.3 - - - -
392B SER* 3.8 15.9 - - - +
395B ASP* 3.0 38.3 + - + +
397B ALA* 1.3 76.0 - - - +
399B ILE* 1.3 65.1 + - - +
401B ARG* 3.2 23.9 + - - +
402B ILE* 3.0 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ALA* 4.1 13.7 - - + +
339B ARG* 3.7 52.9 - - + +
340B ALA* 3.9 7.9 - - + +
389B VAL* 4.2 18.4 - - + -
392B SER 4.9 3.8 - - - +
393B ILE 4.0 13.2 - - - +
395B ASP 3.1 10.2 + - - +
396B GLU* 3.6 34.1 - - - +
398B VAL* 1.3 76.4 - - + +
400B GLU* 1.3 59.0 + - - +
402B ILE* 3.3 6.3 + - - +
403B LYS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG 5.3 2.4 - - - +
396B GLU* 2.9 31.2 + - + +
397B ALA* 3.6 7.9 - - - +
399B ILE* 1.3 79.3 - - + +
401B ARG* 1.3 62.4 + - - +
403B LYS* 3.2 28.3 + - - +
404B GLY* 3.3 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ALA* 3.0 28.8 + - - +
398B VAL* 3.4 29.1 - - - +
400B GLU* 1.3 77.6 - - - +
402B ILE* 1.3 65.4 + - + +
404B GLY* 3.4 3.1 + - - -
405B LYS* 2.9 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA* 3.9 16.2 - - + -
342B ILE* 4.0 8.3 - - + -
385B TRP* 3.5 49.8 - - + +
388B ASP* 4.1 15.3 - - + +
389B VAL* 3.9 19.3 - - + -
398B VAL* 3.0 18.4 + - + +
399B ILE 3.7 3.8 - - - +
401B ARG* 1.3 78.2 - - + +
403B LYS* 1.3 67.8 + - - +
405B LYS* 2.8 23.7 + - + +
406B VAL* 2.9 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG 3.5 21.1 + - - +
340B ALA* 3.6 16.1 + - - -
341B ASN* 3.5 29.0 + - - +
399B ILE 2.9 18.1 + - - +
400B GLU* 3.4 21.3 + - - +
402B ILE* 1.3 75.4 - - - +
404B GLY* 1.3 63.3 + - - +
406B VAL* 3.2 4.3 + - - +
407B LEU* 3.0 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLU 3.3 8.7 + - - -
401B ARG 3.4 4.0 + - - -
402B ILE 3.2 1.0 - - - -
403B LYS* 1.3 81.5 - - - +
405B LYS* 1.3 61.5 + - - +
407B LEU* 3.9 10.5 - - - +
408B ASP* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 5.3 3.8 + - - -
385B TRP* 3.8 51.1 - - + +
401B ARG* 2.9 29.8 - - + +
402B ILE* 2.8 21.8 + - + +
404B GLY* 1.3 76.9 - - - +
406B VAL* 1.3 65.2 + - - +
408B ASP* 3.3 7.0 + - - +
409B ILE* 3.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 4.0 7.6 - - - +
30B ILE* 4.0 13.9 - - + -
340B ALA 3.0 19.1 - - - +
341B ASN* 3.3 35.0 - - + +
342B ILE* 4.1 9.4 - - + -
385B TRP* 4.2 8.9 - - + -
402B ILE* 2.9 26.4 + - + +
403B LYS 3.7 2.7 - - - +
405B LYS* 1.3 70.4 - - - +
407B LEU* 1.3 61.3 + - - +
408B ASP 3.0 1.8 - - - -
409B ILE* 3.0 8.7 + - - +
410B CYS* 2.7 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 3.7 31.9 - - + +
341B ASN* 3.4 27.8 - - - +
403B LYS* 3.0 37.1 + - + +
404B GLY* 3.9 9.6 - - - +
406B VAL* 1.3 80.7 - - - +
408B ASP* 1.3 61.9 + - - +
410B CYS* 3.8 3.9 - - - +
411B ALA* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLY 3.2 18.1 + - - +
405B LYS* 3.4 7.9 - - - +
406B VAL 3.0 0.6 - - - -
407B LEU* 1.3 76.5 - - - +
409B ILE* 1.3 64.6 + - - +
411B ALA* 3.5 13.0 + - - +
412B ARG* 3.6 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.8 11.4 - - + -
374B PHE* 3.5 31.6 - - + -
378B GLU* 3.9 28.5 - - + +
381B GLU* 4.8 7.0 - - - +
385B TRP* 4.3 22.2 - - + -
405B LYS 3.1 9.3 + - - +
406B VAL* 3.0 16.1 + - - +
408B ASP* 1.3 74.6 - - - +
410B CYS* 1.3 70.4 + - - +
412B ARG* 3.1 34.9 + - - +
413B TYR* 3.2 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.3 26.1 - - - +
28B GLU* 3.8 23.6 - - - -
29B HIS 4.0 0.7 - - - -
30B ILE* 3.6 31.0 - - - -
372B ARG* 3.3 27.7 + - - +
374B PHE* 5.7 0.4 - - - -
406B VAL* 2.7 27.6 + - - +
407B LEU* 3.8 5.8 - - - +
409B ILE* 1.3 75.2 - - - +
411B ALA* 1.3 59.1 + - - +
413B TYR* 3.4 13.1 - - - +
414B PRO* 3.7 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU 3.3 15.2 + - - +
408B ASP* 3.7 7.2 - - - +
409B ILE 3.1 0.6 - - - -
410B CYS* 1.3 80.0 - - - +
412B ARG* 1.3 62.3 + - + +
414B PRO* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU* 5.7 1.6 + - - +
408B ASP* 3.6 26.6 + - - +
409B ILE* 3.1 41.9 + - - +
411B ALA* 1.3 80.3 - - + +
413B TYR* 1.3 89.0 + - + +
414B PRO* 3.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ARG* 2.6 61.2 + - + +
373B GLY* 4.0 25.1 - - - -
374B PHE* 3.7 10.5 - + + -
378B GLU* 3.6 26.4 + - + +
409B ILE* 3.2 50.8 + - + +
410B CYS 3.4 4.8 - - - +
411B ALA 3.2 0.2 - - - -
412B ARG* 1.3 105.1 + - + +
414B PRO* 1.3 62.5 - - - +
----------------------------------------------------------
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