Contacts of the helix formed by residues 291 - 300 (chain D) in PDB entry 3ER8
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 GLN 291 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D MET 2.9 12.7 + - - +
289D PHE 4.1 2.6 - - - +
290D SER* 1.3 75.4 - - - +
292D ILE* 1.3 96.6 + - - +
293D ASP* 2.7 41.6 + - + +
294D ARG* 2.9 20.1 + - + +
295D LEU 3.6 4.3 + - - -
402D ASN* 3.8 19.6 - - + +
403D THR* 3.4 22.5 + - - +
460D ARG* 3.1 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D VAL 5.2 0.2 - - - +
290D SER 3.5 4.0 + - - -
291D GLN* 1.3 82.1 - - - +
293D ASP* 1.3 78.8 + - - +
295D LEU* 2.9 21.9 + - - +
296D GLU* 3.0 38.1 + - + +
403D THR* 3.2 4.9 + - - -
405D LEU* 3.7 19.7 - - + +
454D ILE* 3.9 28.7 - - + -
457D HIS* 3.0 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D GLN* 2.7 33.6 + - + +
292D ILE* 1.3 79.6 - - - +
294D ARG* 1.3 56.2 + - + +
296D GLU* 2.5 39.9 + - - +
297D ASP* 2.8 19.5 + - - +
460D ARG* 5.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D MET* 2.9 69.2 - - + +
289D PHE* 4.1 8.7 - - - -
291D GLN* 2.9 16.7 + - + +
293D ASP* 1.3 75.6 - - + +
295D LEU* 1.3 56.1 - - - +
297D ASP* 3.0 25.5 + - - +
298D LEU* 2.8 29.5 + - - +
304D LYS* 5.6 3.2 - - - +
305D PHE* 4.6 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D MET* 4.0 20.2 - - + +
146D ASN* 5.7 0.4 - - - -
147D VAL* 4.3 8.5 - - + +
148D ALA* 3.2 14.2 - - + +
289D PHE* 3.4 33.9 - - + +
291D GLN 3.6 1.1 + - - +
292D ILE 2.9 12.9 + - - +
293D ASP 2.8 3.2 + - - -
294D ARG* 1.3 75.9 - - - +
296D GLU* 1.3 48.7 + - - +
298D LEU* 2.9 10.8 + - + +
299D SER* 2.7 33.4 + - - -
405D LEU* 3.6 29.2 - - + -
415D ILE* 4.0 12.6 - - + -
454D ILE* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ALA* 3.8 5.6 - - + -
149D VAL* 4.0 25.3 + - + +
292D ILE* 3.3 43.4 - - + +
293D ASP* 2.5 20.1 + - - +
295D LEU* 1.3 70.8 - - - +
297D ASP* 1.3 58.9 + - - +
299D SER* 3.2 23.2 - - - -
300D LYS* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ASP* 2.8 15.5 + - - +
294D ARG* 3.0 47.7 + - - +
296D GLU* 1.3 76.6 - - - +
298D LEU* 1.3 60.4 + - - +
299D SER 3.0 5.1 + - - -
300D LYS* 3.5 26.0 + - - +
301D ASP* 4.0 5.2 + - - +
304D LYS* 5.0 8.7 - - + +
305D PHE* 5.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.5 40.8 - - + +
145D MET* 4.7 2.9 - - + -
146D ASN* 3.2 16.4 - - - +
289D PHE* 3.4 27.8 - - + -
294D ARG 2.8 15.4 + - - +
295D LEU* 3.3 7.4 - - + +
297D ASP* 1.3 73.8 - - - +
299D SER* 1.3 63.5 + - - +
301D ASP 3.6 20.2 - - - +
302D PRO* 3.1 34.1 - - + +
304D LYS* 5.8 0.2 - - - -
305D PHE* 3.3 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ASN* 4.1 8.0 - - - +
148D ALA* 2.9 45.6 + - - +
149D VAL* 4.1 12.6 - - - -
295D LEU 2.7 4.3 + - - -
296D GLU* 3.2 13.9 - - - -
297D ASP 3.0 0.4 - - - -
298D LEU* 1.3 77.7 - - - +
300D LYS* 1.3 63.2 + - - +
301D ASP 3.2 4.9 + - - -
302D PRO* 3.3 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D VAL* 5.8 3.1 - - + -
296D GLU* 3.2 28.4 + - - +
297D ASP* 3.5 15.8 + - - +
299D SER* 1.3 77.9 - - - +
301D ASP* 1.3 69.9 + - - +
302D PRO* 4.0 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