Contacts of the helix formed by residues 398 - 412 (chain D) in PDB entry 5MKE
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 398 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D SER* 2.9 38.5 + - - +
397D ARG* 1.3 75.5 - - - +
399D ARG* 1.3 60.0 + - - +
400D GLU* 2.2 36.3 + - + +
401D GLU* 4.0 19.5 - - + +
402D THR* 3.1 7.3 - - - +
1001D NAG 2.5 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU* 3.5 37.2 + - + +
289D ASP* 4.5 1.8 - - - +
291D LEU* 2.7 33.3 + - - +
292D TYR* 4.3 4.6 + - - +
293D TRP* 3.2 61.6 - - + +
315D LEU* 5.7 4.9 - - - +
395D LEU* 5.1 6.7 - - - +
396D SER 4.1 6.4 + - - -
397D ARG* 3.3 23.1 + - - +
398D THR* 1.3 71.0 - - - +
400D GLU* 1.3 74.1 + - - +
402D THR* 3.2 26.7 + - - +
403D ALA* 4.1 5.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
398D THR* 2.2 32.8 + - - +
399D ARG* 1.3 83.0 + - - +
401D GLU* 1.3 71.2 + - + +
403D ALA* 3.4 10.6 + - - +
404D ALA* 3.5 7.3 + - - +
1001D NAG 4.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D SER* 5.0 1.3 - - - +
398D THR* 4.0 13.6 - - + +
400D GLU* 1.3 81.8 - - + +
402D THR* 1.3 57.2 + - - +
403D ALA 3.0 2.2 - - - -
404D ALA* 2.6 19.5 + - + -
405D GLN* 2.3 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU* 3.3 30.6 - - + +
395D LEU* 3.1 25.0 - - - +
396D SER* 3.1 27.3 + - - -
398D THR 3.1 15.3 - - - +
399D ARG* 3.2 27.4 + - - +
401D GLU* 1.3 75.9 - - - +
403D ALA* 1.3 61.8 + - - +
405D GLN* 3.5 15.5 - - - +
406D VAL* 3.7 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D GLU* 6.5 0.4 - - + -
288D LEU* 4.3 20.0 - - + -
399D ARG 4.4 5.2 - - - +
400D GLU 3.4 8.9 + - - +
401D GLU 3.0 0.2 - - - -
402D THR* 1.3 81.6 - - - +
404D ALA* 1.3 53.0 + - - +
405D GLN 3.2 0.4 - - - -
406D VAL* 3.1 11.4 + - - +
407D ALA* 2.6 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D GLU 3.5 3.9 + - - +
401D GLU* 2.6 35.1 + - + +
403D ALA* 1.3 72.3 - - - +
405D GLN* 1.3 54.1 + - - +
407D ALA* 3.3 12.0 - - + +
408D SER* 2.2 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ILE* 5.4 0.2 - - - +
393D LEU* 3.9 23.8 - - + +
394D ASP 3.9 19.2 + - - -
395D LEU* 3.2 28.4 + - - +
396D SER* 4.2 15.7 - - - -
401D GLU* 2.3 35.3 + - + +
402D THR* 3.5 16.1 - - - +
404D ALA* 1.3 65.7 - - - +
406D VAL* 1.3 52.6 - - + +
408D SER* 2.8 9.8 + - - -
409D LEU* 2.2 45.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
280D TRP* 4.4 0.7 - - + -
283D THR* 4.3 29.4 - - + +
284D GLU* 5.6 4.7 - - + +
288D LEU* 5.9 3.8 - - + -
402D THR 3.7 13.9 - - - +
403D ALA* 3.1 14.4 + - - +
405D GLN* 1.3 75.4 - - + +
407D ALA* 1.3 50.6 + - - +
409D LEU* 3.0 21.8 + - + +
410D LYS 2.5 29.6 + - - -
414D TRP* 3.2 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D ALA 2.6 12.4 + - - +
404D ALA* 3.0 20.8 + - + +
406D VAL* 1.3 72.2 - - - +
408D SER* 1.3 59.7 + - - +
410D LYS* 3.0 12.4 + - + +
411D LYS* 2.8 23.4 + - - +
414D TRP* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D ASN* 4.0 7.4 + - - -
404D ALA 2.2 30.1 + - - -
405D GLN* 3.3 9.9 - - - -
407D ALA* 1.3 68.6 - - - +
409D LEU* 1.3 51.0 + - - +
411D LYS* 3.1 13.7 - - - +
412D ASN* 2.7 37.4 + - - -
1002D NAG 3.5 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ILE* 5.9 6.1 - - + -
365D ALA* 6.0 2.5 - - + -
393D LEU* 5.8 8.3 - - + -
405D GLN* 2.2 32.1 + - + +
406D VAL* 3.0 29.4 + - + +
408D SER* 1.3 68.1 - - - +
410D LYS* 1.3 52.8 + - - +
412D ASN* 3.4 13.9 - - + +
413D VAL 2.5 8.8 + - - -
414D TRP* 2.2 79.5 + - + -
415D LEU* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D VAL 2.5 13.8 + - - +
407D ALA* 3.0 14.6 + - - +
409D LEU* 1.3 69.2 - - - +
411D LYS* 1.3 59.8 + - - +
412D ASN 3.0 1.1 - - - -
413D VAL* 2.6 33.5 + - + +
414D TRP* 3.4 33.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D PRO* 4.0 12.1 - - - +
407D ALA 2.8 11.1 + - - +
408D SER* 3.1 22.4 - - - +
410D LYS* 1.3 73.2 - - - +
412D ASN* 1.3 61.6 + - - +
413D VAL* 4.8 2.6 - - - +
1002D NAG 2.9 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D PRO* 3.4 36.2 + - + +
362D ASN* 5.0 4.6 - - - +
365D ALA* 3.8 25.2 - - - +
366D TRP* 4.8 5.2 - - + -
408D SER* 2.7 27.5 + - - +
409D LEU* 3.7 16.7 - - + +
410D LYS 3.0 0.4 - - - -
411D LYS* 1.3 78.0 - - - +
413D VAL* 1.3 69.5 + - - +
414D TRP* 2.9 18.4 - - - +
1002D NAG 3.3 22.3 + - - +
----------------------------------------------------------
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