Contacts of the helix formed by residues 395 - 413 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D SER* 2.9 17.6 + - - +
393D ILE 3.5 0.2 - - - -
394D ASN* 1.3 76.7 - - - +
396D GLU* 1.3 56.7 + - - +
397D ALA* 2.9 35.5 + - - +
398D VAL* 3.0 45.0 + - + +
399D ILE* 3.1 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ARG* 6.0 4.0 - - - +
394D ASN 3.3 7.5 + - - +
395D ASP* 1.3 72.0 + - - +
397D ALA* 1.3 56.9 + - - +
398D VAL 3.3 0.2 - - - -
399D ILE* 3.9 11.6 - - - +
400D GLU* 3.0 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D ASP* 2.9 13.1 + - - +
396D GLU* 1.3 77.7 - - - +
398D VAL* 1.3 64.7 + - + +
400D GLU* 3.7 5.6 - - - +
401D ARG* 3.1 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 398 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ASP* 3.7 36.1 - - + +
389D VAL* 4.5 6.3 - - - +
392D SER* 3.8 15.9 - - - +
395D ASP* 3.0 39.8 + - + +
397D ALA* 1.3 75.4 - - + +
399D ILE* 1.3 65.5 + - - +
401D ARG* 3.2 22.5 + - - +
402D ILE* 3.0 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ALA* 4.2 13.2 - - + +
339D ARG* 3.7 65.7 - - + +
340D ALA* 3.9 7.9 - - + +
389D VAL* 4.1 19.1 - - + -
392D SER 4.8 3.8 - - - +
393D ILE 3.9 14.6 - - - +
394D ASN 5.6 0.4 - - - -
395D ASP 3.1 16.5 + - - +
396D GLU* 4.0 8.5 - - - +
398D VAL* 1.3 78.1 - - + +
400D GLU* 1.3 57.2 + - + +
402D ILE* 3.4 6.9 + - - +
403D LYS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D GLU* 3.0 22.3 + - + +
397D ALA* 3.7 7.9 - - - +
399D ILE* 1.3 75.2 - - + +
401D ARG* 1.3 64.8 + - - +
403D LYS* 3.3 22.3 + - - +
404D GLY* 3.3 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D ALA* 3.1 21.4 + - - +
398D VAL* 3.2 25.4 + - - +
400D GLU* 1.3 76.0 - - - +
402D ILE* 1.3 68.8 - - - +
404D GLY* 3.3 11.1 + - - -
405D LYS* 3.4 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D ALA* 4.0 14.4 - - + -
342D ILE* 4.0 13.5 - - + -
385D TRP* 3.5 53.8 - - + +
388D ASP* 4.0 14.6 - - + +
389D VAL* 3.9 20.4 - - + -
398D VAL* 3.0 17.7 + - + +
399D ILE 3.8 3.6 - - - +
401D ARG* 1.3 81.4 - - + +
403D LYS* 1.3 67.0 + - - +
405D LYS* 2.9 23.3 + - + +
406D VAL* 3.0 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ARG 3.7 13.3 + - - +
340D ALA* 3.6 16.5 + - - +
341D ASN* 3.4 32.5 - - - +
399D ILE 2.9 17.6 + - - +
400D GLU* 3.5 25.9 + - - +
401D ARG 3.3 0.2 - - - -
402D ILE* 1.3 76.8 - - - +
404D GLY* 1.3 57.0 + - - +
406D VAL* 3.2 3.8 + - - +
407D LEU* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D GLU* 3.3 6.6 + - - -
401D ARG 3.3 7.9 + - - -
402D ILE 3.0 1.0 - - - -
403D LYS* 1.3 80.2 - - - +
405D LYS* 1.3 56.7 + - - +
407D LEU* 3.6 10.0 + - - +
408D ASP* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D TRP* 3.3 53.0 - - + +
401D ARG* 3.4 34.4 + - - +
402D ILE* 2.9 13.3 + - + +
404D GLY* 1.3 73.7 - - - +
406D VAL* 1.3 61.7 + - - +
408D ASP* 3.5 6.5 - - - +
409D ILE* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU 4.1 1.3 - - - +
30D ILE* 3.4 26.5 - - + -
340D ALA 3.3 19.1 - - - +
341D ASN* 3.5 25.1 - - + +
342D ILE* 3.7 21.1 - - + -
385D TRP* 4.3 10.3 - - + -
402D ILE* 3.0 16.9 + - + +
403D LYS 3.5 7.0 - - - +
405D LYS* 1.3 75.3 - - - +
407D LEU* 1.3 61.1 + - - +
408D ASP 3.0 1.1 - - - -
409D ILE* 3.3 6.6 + - - +
410D CYS* 2.8 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU* 3.8 30.7 - - + +
341D ASN* 3.4 27.6 - - - +
403D LYS* 3.0 38.5 + - + +
404D GLY* 3.9 7.4 - - - +
406D VAL* 1.3 76.2 - - - +
408D ASP* 1.3 62.1 + - - +
410D CYS* 3.7 5.2 + - - +
411D ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D GLY 3.1 17.6 + - - +
405D LYS* 3.5 8.7 - - - +
407D LEU* 1.3 74.3 - - - +
409D ILE* 1.3 61.6 + - - +
410D CYS 3.1 1.6 - - - -
411D ALA* 3.0 21.9 + - - +
412D ARG* 3.4 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ILE* 4.1 6.7 - - + -
374D PHE* 3.5 36.9 - - + -
378D GLU* 3.9 26.2 - - + +
381D GLU* 5.0 6.3 - - - +
385D TRP* 3.9 28.5 - - + -
405D LYS 3.0 16.6 + - - +
406D VAL* 3.5 11.0 - - - +
408D ASP* 1.3 75.6 + - - +
410D CYS* 1.3 62.0 + - - +
411D ALA 3.3 0.2 - - - -
412D ARG* 3.5 21.9 + - - +
413D TYR* 3.3 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 3.4 25.1 - - - +
28D GLU* 3.8 19.5 - - - -
29D HIS 4.0 2.2 - - - -
30D ILE* 3.6 26.0 - - - -
372D ARG* 3.4 27.8 + - - +
374D PHE* 5.8 0.4 - - - -
406D VAL* 2.8 26.1 + - - +
407D LEU* 3.9 7.4 - - - +
409D ILE* 1.3 77.5 - - - +
411D ALA* 1.3 62.3 + - - +
412D ARG 3.2 0.4 + - - -
413D TYR 3.6 11.1 + - - +
414D PRO* 3.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D LEU 3.3 12.3 + - - +
408D ASP* 3.0 11.9 + - - +
410D CYS* 1.3 78.3 - - - +
412D ARG* 1.3 62.7 + - + +
413D TYR 3.5 0.4 + - - -
414D PRO* 4.0 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D GLU* 5.5 3.2 + - - +
408D ASP* 3.4 33.6 + - - +
409D ILE* 3.5 25.3 + - - +
410D CYS 3.2 0.6 - - - -
411D ALA* 1.3 81.8 - - + +
413D TYR* 1.3 90.7 + - + +
414D PRO* 3.3 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D ARG* 2.6 63.2 + - + +
373D GLY* 3.7 27.8 - - - -
374D PHE* 3.8 9.2 - + + -
378D GLU* 3.8 26.7 + - + -
409D ILE* 3.3 38.9 + - + +
410D CYS 3.6 3.4 - - - -
412D ARG* 1.3 108.3 + - + +
414D PRO* 1.3 61.5 - - - +
----------------------------------------------------------
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