Contacts of the helix formed by residues 299 - 311 (chain A) in PDB entry 5DX1
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 299 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PHE* 3.8 11.5 - - + -
298A THR* 1.3 75.3 + - - +
300A GLU* 1.3 62.5 + - - +
301A GLN* 3.5 12.0 + - - +
302A LEU* 3.1 23.2 + - + +
303A TYR* 3.1 20.3 + - - +
343A PHE* 5.2 1.4 - - - +
347A ILE* 4.4 9.2 - - + +
385A HIS* 3.0 14.5 + - - +
419A ARG* 2.7 35.4 + - - +
421A LEU* 5.3 0.2 - - - +
475A ARG* 4.6 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 4.9 0.4 + - - -
299A ASP* 1.3 74.7 + - - +
301A GLN* 1.3 63.8 + - - +
303A TYR* 3.4 2.0 + - + +
304A MET* 3.0 47.5 + - + +
383A LEU* 5.7 6.4 - - - +
385A HIS* 3.6 23.5 - - + +
308C THR* 5.3 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP* 3.3 8.8 + - - +
300A GLU* 1.3 77.1 - - - +
302A LEU* 1.3 64.7 + - - +
304A MET* 3.6 4.4 + - - +
305A GLU* 3.1 27.0 + - - +
475A ARG* 4.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PHE* 4.3 5.6 - - + -
299A ASP* 3.1 22.7 + - - +
301A GLN* 1.3 73.9 - - - +
303A TYR* 1.3 67.4 + - - +
305A GLU* 3.2 6.6 + - - +
306A GLN* 3.1 27.4 + - + +
339A VAL* 3.9 24.0 - - + -
419A ARG* 3.5 37.2 - - + +
421A LEU* 4.0 26.0 - - + -
475A ARG* 3.6 41.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP 3.1 5.2 + - - +
300A GLU* 3.6 7.2 - - + +
301A GLN 3.4 0.2 - - - -
302A LEU* 1.3 80.9 - - - +
304A MET* 1.3 81.3 + - + +
306A GLN* 3.4 2.6 + - - +
307A PHE* 2.9 59.5 + + - +
335A PHE* 3.6 22.0 - + - -
385A HIS* 3.6 33.9 - + + +
421A LEU* 4.3 13.6 - - + +
422A PHE 3.3 26.0 - - - -
423A GLN 2.5 23.0 + - - -
425A PRO* 3.7 16.5 - - + +
314C TYR* 4.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.0 41.0 + - + +
301A GLN* 4.2 3.8 - - - +
303A TYR* 1.3 95.0 - - + +
305A GLU* 1.3 55.8 + - - +
307A PHE* 3.7 14.7 - - + +
308A THR* 2.6 45.0 + - - +
304C MET* 3.9 23.6 - - + -
308C THR* 3.9 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 3.1 20.1 + - + +
302A LEU* 3.4 6.1 - - - +
304A MET* 1.3 78.3 - - - +
306A GLN* 1.3 67.9 + - - +
308A THR* 3.7 5.3 - - - -
309A LYS* 3.4 32.7 + - - +
473A PHE* 3.6 16.8 - - - -
475A ARG* 2.8 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.1 12.2 + - + +
303A TYR 3.9 5.4 - - - +
305A GLU* 1.3 78.7 - - - +
307A PHE* 1.3 63.4 + - - +
309A LYS* 2.9 36.9 + - - +
310A ALA* 3.2 20.3 + - - +
334A TYR* 3.9 30.7 + - + +
335A PHE* 4.1 20.4 - - + -
337A GLN* 4.4 10.1 + - - +
339A VAL* 4.8 4.4 - - + +
421A LEU* 3.6 24.0 - - + -
473A PHE* 3.3 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 2.9 45.8 + + + +
304A MET* 3.7 23.6 - - + +
306A GLN* 1.3 76.8 - - - +
308A THR* 1.3 64.1 + - - +
310A ALA* 3.2 6.6 + - - +
311A ASN* 3.1 51.6 + - - -
331A VAL* 4.2 21.5 - - + -
335A PHE* 4.1 17.2 - + + -
423A GLN 5.4 0.2 - - - -
304C MET* 5.4 2.5 - - + -
307C PHE* 4.1 15.5 - + - -
311C ASN* 4.1 10.8 - - + -
314C TYR* 4.7 18.6 - + - -
327C ARG* 4.5 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 2.6 31.7 + - - +
305A GLU* 3.7 6.4 - - - -
307A PHE* 1.3 75.0 - - - +
309A LYS* 1.3 63.4 + - + +
311A ASN* 3.2 17.8 + - - +
312A PHE* 3.7 6.6 + - - +
300C GLU* 5.3 9.9 + - - +
304C MET* 5.1 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLU* 3.4 20.9 + - - +
306A GLN* 2.9 36.4 + - - +
308A THR* 1.3 77.3 - - + +
310A ALA* 1.3 63.8 + - - +
311A ASN 3.3 0.3 + - - -
312A PHE* 3.4 6.4 + - - +
334A TYR* 3.6 30.9 - - + +
473A PHE* 3.2 30.9 - - - -
160B GLN* 3.1 29.6 + - - +
12G NMM 4.8 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLN 3.2 8.0 + - - +
307A PHE* 3.2 12.2 + - + +
309A LYS* 1.3 79.2 - - - +
311A ASN* 1.3 59.3 + - - +
312A PHE 3.1 0.7 - - - -
313A TRP* 3.0 29.1 + - - +
327A ARG* 4.9 2.6 - - - +
330A ALA* 3.7 3.8 - - - +
331A VAL* 3.7 36.1 - - + +
334A TYR* 3.5 26.2 - - + -
335A PHE* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.1 43.9 + - - +
308A THR* 3.2 10.1 + - - +
309A LYS 3.2 1.2 - - - -
310A ALA* 1.3 75.6 - - - +
312A PHE* 1.3 65.6 + - - +
313A TRP 3.0 1.3 - - - -
314A TYR* 3.1 35.5 + - + +
315A GLN* 4.0 5.4 + - - +
327A ARG* 4.6 10.2 - - - +
331A VAL* 4.7 4.0 - - - +
304C MET* 6.2 0.4 - - - +
307C PHE* 3.4 33.7 - - + -
327C ARG* 5.5 1.7 + - - -
----------------------------------------------------------
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