Contacts of the strand formed by residues 307 - 313 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 4.8 11.2 + - - -
81A PHE* 5.9 3.2 - - + +
301C ARG* 4.0 1.2 - - - +
302C ASP* 3.1 25.2 + - + -
304C ASN* 2.6 40.0 + - + +
305C SER 3.2 5.4 - - - +
306C SER* 1.3 81.9 + - - +
308C SER* 1.3 59.4 + - - +
385C PRO* 3.6 37.0 - - + +
386C PHE 3.3 8.7 - - - +
387C SER* 5.5 0.9 - - - -
388C THR* 2.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 4.0 13.9 - - - -
299C TYR* 3.9 13.1 - - - -
300C LEU 3.3 17.3 - - - -
302C ASP* 3.6 6.7 - - - +
307C ARG* 1.3 77.0 - - - +
309C PHE* 1.3 63.7 + - - +
385C PRO* 3.1 7.0 - - - +
386C PHE* 2.6 46.0 + - - +
387C SER 4.8 1.6 + - - -
388C THR* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TRP* 3.6 56.3 - + + -
203C TYR 3.4 29.6 - - - -
204C THR* 4.1 11.9 - - - -
299C TYR* 3.6 3.4 - - - -
300C LEU* 3.0 64.4 + - + +
301C ARG 4.2 1.6 - - - -
302C ASP* 4.2 7.4 - - - -
308C SER* 1.3 75.5 - - - +
310C ARG* 1.3 72.7 + - - +
311C ILE* 4.1 15.0 - - + -
366C PHE* 4.2 9.0 - + - -
382C ILE* 4.3 6.1 - - + -
383C SER 3.5 12.6 - - - +
384C GLY* 4.3 0.4 - - - -
386C PHE* 4.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 4.2 8.7 + - - -
93A THR* 3.0 34.4 + - - +
119A PHE* 5.5 0.8 - - - -
120A GLU* 3.5 19.1 + - - +
220C GLU* 3.0 15.0 + - - -
297C SER* 4.2 12.6 - - - -
298C ILE 3.4 11.2 - - - +
299C TYR* 2.9 48.2 + - + -
309C PHE* 1.3 80.7 - - - +
311C ILE* 1.3 63.1 + - - +
312C THR* 4.0 12.7 + - - +
381C GLU* 4.0 2.2 + - - +
382C ILE* 3.3 5.7 - - - +
383C SER* 2.9 41.4 + - - +
386C PHE* 3.8 16.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE 4.1 0.2 - - - +
297C SER* 3.4 0.7 - - - -
298C ILE* 3.0 56.4 + - + +
300C LEU* 4.4 11.4 - - + -
309C PHE* 4.1 11.9 - - + -
310C ARG* 1.3 73.7 - - - +
312C THR* 1.3 66.9 + - - +
345C ILE* 5.1 3.6 - - + -
349C VAL* 4.3 20.6 - - + -
353C PHE* 3.5 22.9 - - + -
366C PHE* 4.1 34.8 - - + -
381C GLU 3.5 4.3 - - - -
382C ILE* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LYS* 4.0 24.9 - - + -
296C ILE 3.3 10.5 - - - +
297C SER* 2.6 27.4 + - - +
310C ARG* 4.0 14.0 + - - +
311C ILE* 1.3 76.1 + - - +
313C ILE* 1.3 74.9 + - - +
314C LEU* 4.7 2.9 - - + -
353C PHE* 3.4 2.8 - - - -
380C SER* 3.1 9.0 - - - -
381C GLU* 2.7 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LEU* 4.8 4.7 - - + -
295C LYS* 3.9 1.0 - - - -
296C ILE* 3.1 45.9 + - + +
312C THR* 1.3 81.4 - - - +
314C LEU* 1.3 66.7 + - - +
317C LEU* 3.5 27.1 - - + -
318C TYR* 4.0 29.2 - - + -
348C THR* 4.2 6.5 - - - +
349C VAL* 4.1 35.2 - - + +
353C PHE* 4.1 15.7 - - + -
379C VAL 3.8 3.8 - - - -
----------------------------------------------------------
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