Contacts of the strand formed by residues 304 - 310 (chain A) in PDB entry 4DGX
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 TYR 304 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 4.2 4.3 - - + -
268A GLY* 3.4 29.7 - - - -
273A ASN* 3.4 46.0 - - + +
276A LYS* 3.8 26.9 - - + +
277A ASN* 2.5 28.8 + - - -
284A PRO* 3.1 36.1 - - + +
289A ARG* 3.9 18.4 - - - +
292A LEU* 4.3 6.2 - - - +
302A SER* 3.4 9.3 + - - +
303A ASP* 1.3 85.6 - - - +
305A ILE* 1.3 65.9 + - - +
306A ASN* 3.8 13.6 + - - -
340A ASP* 4.1 15.9 - - - +
343A ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 5.8 1.6 - - - -
284A PRO* 4.2 2.3 - - - +
289A ARG* 5.3 1.2 + - - +
290A VAL* 3.8 26.2 + - + +
292A LEU* 4.2 15.5 - - + -
303A ASP 4.0 0.8 + - - -
304A TYR* 1.3 91.1 - - - +
306A ASN* 1.3 67.7 + - - +
307A ALA* 2.8 27.1 + - + +
330A THR* 4.5 4.0 - - - +
331A GLN* 6.0 2.7 - - + +
337A THR* 5.2 5.6 - - - +
340A ASP* 3.8 12.6 - - + +
341A PHE* 3.7 37.2 - - + +
344A MET* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS 4.2 3.4 + - - +
277A ASN* 2.9 31.8 + - - +
278A ARG 4.7 0.2 - - - +
282A ILE* 3.0 24.4 + - - +
283A LEU 4.4 0.2 - - - -
284A PRO* 3.6 17.1 - - - +
304A TYR* 3.8 6.6 + - - -
305A ILE* 1.3 73.2 - - - +
307A ALA* 1.3 51.4 + - - +
330A THR* 2.6 26.6 + - - -
331A GLN* 3.7 37.4 + - - +
461A ALA 5.9 0.2 - - - -
501A ARG* 2.4 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO* 3.8 3.9 - - - +
289A ARG* 3.4 5.4 - - - -
290A VAL* 2.8 32.3 + - + -
305A ILE* 2.8 16.5 + - + +
306A ASN* 1.3 73.2 - - - +
308A ASN* 1.3 59.8 + - - +
328A ILE* 4.0 2.9 - - + -
329A ALA 3.3 7.9 - - - -
330A THR* 3.4 17.7 - - - +
344A MET* 3.6 28.7 - - - -
501A ARG* 3.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO* 3.1 20.9 - - - +
285A PHE 3.3 18.7 + - - +
288A THR* 2.8 33.9 + - - +
289A ARG* 3.4 4.8 - - - +
290A VAL* 4.1 4.9 - - - -
307A ALA* 1.3 72.1 - - - +
309A ILE* 1.3 64.4 + - - +
310A ILE* 3.9 2.3 - - + +
328A ILE* 3.4 2.8 - - - -
329A ALA 2.9 33.1 + - - +
500A GLN 3.3 19.2 + - - +
501A ARG* 2.8 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 2.9 25.6 + - + +
289A ARG 4.8 3.8 - - - +
290A VAL* 3.6 22.6 - - + +
308A ASN* 1.3 76.5 - - - +
310A ILE* 1.3 76.4 + - - +
311A MET* 4.2 20.6 - - + +
326A SER* 4.9 4.5 - - - +
327A TYR 3.4 6.1 - - - +
328A ILE* 3.6 19.3 - - + -
348A GLU* 4.8 10.5 - - - +
454A PRO* 4.8 8.1 - - + -
500A GLN* 3.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ASN* 3.9 3.4 - - + +
309A ILE* 1.3 84.4 - - - +
311A MET* 1.3 65.3 + - - +
312A PRO 4.2 0.2 - - - -
326A SER* 3.4 5.0 - - - -
327A TYR* 2.6 53.1 + - + +
329A ALA* 3.6 35.0 - - + +
470A ILE* 4.2 14.6 - - + -
474A ILE* 5.0 2.2 - - + -
497A VAL* 4.1 26.7 - - + +
500A GLN* 3.6 22.4 - - + +
501A ARG* 4.1 13.0 - - + -
504A MET* 4.1 13.2 - - + -
----------------------------------------------------------
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