Contacts of the strand formed by residues 307 - 313 (chain A) in PDB entry 2EWY
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 ARG 307 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 4.0 0.7 - - - +
302A ASP* 3.1 25.4 + - + -
304A ASN* 2.6 39.7 + - - +
305A SER 3.2 6.1 - - - +
306A SER* 1.3 82.1 + - - +
308A SER* 1.3 59.0 + - - +
385A PRO* 3.6 36.6 - - + +
386A PHE 3.3 8.3 - - - +
387A SER* 5.5 0.7 - - - -
388A THR* 2.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.0 13.5 - - - -
299A TYR* 3.9 12.7 - - - -
300A LEU 3.3 17.5 - - - -
302A ASP* 3.6 6.1 - - - +
307A ARG* 1.3 76.6 - - - +
309A PHE* 1.3 62.7 + - - +
385A PRO* 3.1 7.0 - - - +
386A PHE* 2.6 45.7 + - - +
387A SER 4.8 1.7 + - - -
388A THR* 3.5 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TRP* 3.6 58.3 - + + -
203A TYR 3.4 28.7 - - - -
204A THR* 4.1 11.7 - - - -
299A TYR* 3.6 4.1 - - - -
300A LEU* 3.0 66.4 + - + +
301A ARG 4.2 1.6 - - - -
302A ASP* 4.2 6.5 - - - -
308A SER* 1.3 73.7 - - - +
310A ARG* 1.3 71.4 + - - +
311A ILE* 4.1 14.4 - - + -
366A PHE* 4.2 8.7 - + - -
382A ILE* 4.3 6.7 - - + -
383A SER 3.5 13.0 - - - +
384A GLY* 4.3 0.4 - - - -
386A PHE* 4.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 3.0 13.9 + - - -
297A SER* 4.2 13.2 - - - -
298A ILE 3.4 11.4 - - - +
299A TYR* 2.9 50.2 + - + -
309A PHE* 1.3 78.2 - - - +
311A ILE* 1.3 63.0 + - - +
312A THR* 4.0 12.4 + - - +
381A GLU* 4.0 4.7 + - - +
382A ILE* 3.3 5.0 - - - +
383A SER* 2.9 44.1 + - - +
386A PHE* 3.9 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A SER* 3.4 0.3 - - - -
298A ILE* 3.0 56.4 + - + +
300A LEU* 4.4 11.2 - - + -
309A PHE* 4.1 11.2 - - + -
310A ARG* 1.3 72.8 - - - +
312A THR* 1.3 66.8 + - - +
345A ILE* 5.1 4.3 - - + -
349A VAL* 4.3 20.0 - - + -
353A PHE* 3.5 23.1 - - + -
366A PHE* 4.1 35.4 - - + -
381A GLU 3.5 4.3 - - - -
382A ILE* 4.1 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LYS* 4.0 23.1 - - + -
296A ILE 3.3 10.3 - - - +
297A SER* 2.6 28.6 + - - +
310A ARG* 4.0 13.9 + - - +
311A ILE* 1.3 76.1 + - - +
313A ILE* 1.3 74.9 + - - +
314A LEU* 4.7 2.9 - - + -
353A PHE* 3.4 3.0 - - - -
380A SER* 3.1 9.0 - - - -
381A GLU* 2.7 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.8 4.7 - - + -
295A LYS* 3.9 1.6 - - - -
296A ILE* 3.1 44.5 + - + +
312A THR* 1.3 80.7 - - - +
314A LEU* 1.3 66.1 + - - +
317A LEU* 3.5 26.0 - - + -
318A TYR* 4.0 29.7 - - + -
348A THR* 4.2 7.0 - - - +
349A VAL* 4.1 34.3 - - + +
353A PHE* 4.1 16.8 - - + -
379A VAL 3.8 3.1 - - - -
----------------------------------------------------------
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