Contacts of the strand formed by residues 301 - 307 (chain A) in PDB entry 2Q8F
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 ILE 301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 5.4 1.1 - - + -
248A PRO* 3.9 15.7 - - + +
249A GLU 2.8 11.5 + - - +
250A LEU* 3.5 6.6 - - + +
251A GLU 2.9 25.3 + - - +
281A PHE* 3.8 19.5 - - + +
284A ALA* 3.6 22.0 - - + -
285A MET* 3.3 44.4 - - + +
288A THR* 4.4 8.7 - - - +
300A PRO* 1.3 74.3 - - - +
302A GLN* 1.3 60.9 + - - +
303A VAL* 4.4 2.0 - - + -
316A MET* 3.5 31.6 - - + -
317A SER 3.6 7.0 - - - +
318A ASP* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 3.3 33.4 + - + +
300A PRO* 4.4 11.4 - - + +
301A ILE* 1.3 74.8 - - - +
303A VAL* 1.3 61.5 + - - +
304A HIS 4.2 0.4 + - - -
315A LYS 3.6 1.6 - - - +
316A MET* 3.5 1.6 - - - -
317A SER* 2.7 54.9 + - - +
319A ARG* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 4.3 6.3 - - + -
250A LEU* 3.7 9.9 - - + -
251A GLU 2.8 11.0 + - - +
252A LEU* 3.5 24.4 - - + -
253A GLU* 2.8 28.8 + - - +
281A PHE* 3.7 33.4 - - + -
301A ILE* 4.4 0.9 - - + -
302A GLN* 1.3 77.4 - - - +
304A HIS* 1.3 62.1 + - - +
305A VAL* 4.1 5.8 - - + -
314A VAL* 3.8 23.1 - - + -
315A LYS 3.2 8.5 - - - +
316A MET* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 3.4 37.6 + - + +
254A GLU 4.4 1.8 - - - -
255A LEU* 4.1 19.0 + - + +
302A GLN 4.2 0.8 - - - -
303A VAL* 1.3 75.6 - - - +
305A VAL* 1.3 82.4 + - - +
306A THR* 3.7 16.2 + - - -
313A THR* 3.7 2.1 + - - +
314A VAL* 3.6 1.6 - - - -
315A LYS* 2.9 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 4.1 7.6 - - + -
226A LEU* 3.9 20.6 - - + -
229A ILE* 3.4 31.0 - - + -
252A LEU* 4.1 6.3 - - + -
253A GLU 2.8 12.5 + - - +
254A GLU* 3.2 2.8 - - + -
255A LEU 2.7 32.7 + - - +
264A ILE* 3.9 18.3 - - + +
303A VAL* 4.1 11.4 - - + -
304A HIS* 1.3 75.7 - - - +
306A THR* 1.3 58.7 + - - +
312A LEU* 3.9 21.3 - - + -
313A THR 3.4 5.6 - - - +
314A VAL* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 3.3 25.7 - - + +
257A ALA* 4.8 5.6 - - + -
304A HIS* 3.7 20.6 + - - -
305A VAL* 1.3 76.4 + - - +
307A LEU* 1.3 70.0 + - - +
308A GLY* 4.0 3.4 - - - +
311A ASP 3.8 1.6 - - - +
312A LEU* 3.4 7.9 - - - +
313A THR* 2.8 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU 2.9 9.4 + - - +
256A ASN* 3.9 27.4 - - - +
257A ALA* 3.0 24.6 + - - +
258A LYS* 3.3 23.1 + - + +
263A PRO 5.4 0.2 - - - +
264A ILE* 4.2 24.1 - - + +
265A GLN 4.3 15.3 - - - +
266A VAL* 4.2 10.1 - - + -
306A THR* 1.3 74.5 - - - +
308A GLY* 1.3 62.5 + - - +
312A LEU* 4.0 20.4 - - + -
391A ALA* 3.8 28.5 - - + -
----------------------------------------------------------
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