Contacts of the helix formed by residues 300 - 308 (chain A) in PDB entry 1MRA
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 GLN 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.6 0.4 - - - +
298A LEU 3.3 3.5 - - - -
299A PHE* 1.3 74.6 - - - +
301A GLU* 1.3 77.0 + - - +
303A SER* 4.2 3.6 - - - -
304A ALA* 3.0 26.0 + - - +
316A LEU* 3.7 27.3 - - + +
317A GLU 3.8 3.8 - - - +
318A ARG* 3.3 8.7 - - - +
319A LEU 2.7 37.2 + - - +
320A ASP* 3.3 36.2 + - - +
330A LEU* 3.7 17.8 - - + +
332A PHE* 4.1 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 2.8 33.9 + - - -
299A PHE* 2.9 5.4 + - - +
300A GLN* 1.3 91.9 + - + +
302A ILE* 1.3 59.7 + - - +
304A ALA* 3.8 5.5 + - - +
305A HIS* 3.2 20.6 + - - -
320A ASP* 4.5 8.1 - - - +
321A LEU 5.6 0.5 + - - -
322A ALA* 4.2 6.2 + - - +
326A ILE* 3.4 31.6 - - + +
329A THR* 5.7 3.1 - - - +
330A LEU* 4.3 24.7 - - + +
340A PRO* 5.9 0.2 - - - +
345A VAL* 4.2 17.5 - - + +
346A GLY 6.2 0.9 - - - -
347A ILE* 4.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A MET* 4.1 31.0 - - + +
123A LEU* 4.1 8.7 - - + -
271A ALA* 4.0 16.4 - - + -
277A VAL* 3.9 23.1 - - + -
299A PHE* 3.1 25.5 + - + +
301A GLU* 1.3 77.8 + - - +
303A SER* 1.3 70.3 + - - +
304A ALA 3.1 0.7 - - - -
305A HIS* 3.0 5.7 + - - +
306A LEU* 2.8 35.3 + - + +
345A VAL* 3.6 34.3 - - + -
347A ILE* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ALA* 4.6 5.9 - - - +
280A TRP* 5.1 4.0 - - - -
296A SER* 3.4 33.0 + - - -
297A HIS 4.9 0.2 + - - -
298A LEU 3.0 15.1 + - - -
299A PHE* 2.5 31.3 + - - +
300A GLN* 4.2 3.6 - - - -
302A ILE* 1.3 76.2 - - - +
304A ALA* 1.3 55.3 + - - +
306A LEU* 4.2 7.9 - - - -
307A LEU* 2.8 36.8 + - - +
316A LEU* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.1 11.5 - - + +
300A GLN 3.0 18.0 + - - +
301A GLU 3.9 3.1 - - - +
302A ILE 3.1 0.2 - - - -
303A SER* 1.3 77.9 - - - +
305A HIS* 1.3 61.4 + - + +
308A ALA* 3.5 13.7 + - - +
316A LEU* 3.6 17.6 - - + +
330A LEU* 3.7 23.8 - - + -
337A ALA* 4.6 6.7 - - + -
339A ILE* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 4.5 4.9 - - + -
123A LEU* 3.8 17.4 - - + +
124A VAL* 3.2 50.3 + - + +
127A LEU* 5.0 1.2 - - - +
301A GLU 3.2 25.5 + - - -
302A ILE* 3.0 8.8 + - - +
304A ALA* 1.3 74.3 - - + +
306A LEU* 1.3 69.6 + - + +
308A ALA* 3.2 9.7 + - - -
309A ALA* 3.6 8.1 + - - +
339A ILE* 3.1 33.3 - - + +
340A PRO* 4.4 5.3 - - + +
342A LEU 5.1 0.7 - - - -
344A GLY 3.5 19.7 - - - -
345A VAL* 2.8 29.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.8 3.1 - - + -
127A LEU* 3.9 23.6 - - + -
271A ALA* 4.5 7.6 - - + -
276A GLY 4.7 4.9 - - - +
277A VAL* 4.2 20.9 - - + +
280A TRP* 3.7 57.8 + - + -
281A ILE* 5.5 0.9 - - + -
302A ILE* 2.8 41.9 + - + +
303A SER* 3.7 4.7 - - - +
305A HIS* 1.3 79.7 - - + +
307A LEU* 1.3 57.5 + - - +
309A ALA* 3.0 23.8 + - - +
310A THR* 3.0 14.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
132A ARG* 2.9 18.3 + - - -
134A VAL* 4.3 15.5 - - + -
280A TRP* 3.8 22.4 - - + -
294A MET 3.5 25.1 - - - +
295A SER* 4.2 7.9 - - - -
296A SER* 3.9 11.0 - - - +
303A SER 2.8 23.3 + - - +
304A ALA 4.2 3.1 - - - +
306A LEU* 1.3 72.4 - - - +
308A ALA* 1.3 59.3 + - - +
310A THR* 3.0 11.0 + - + +
313A ALA* 3.0 22.7 - - + +
314A HIS 4.6 0.9 - - - +
315A TRP 3.8 14.4 - - - +
316A LEU* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.2 8.3 - - + -
129A ALA* 3.9 11.8 - - - +
130A ASN 4.0 18.6 - - - +
132A ARG* 3.4 45.8 + - + +
134A VAL* 4.9 2.2 - - + +
304A ALA 3.5 11.3 + - - +
305A HIS 3.2 9.8 + - - +
306A LEU 3.2 1.4 - - - -
307A LEU* 1.3 77.7 - - - +
309A ALA* 1.3 55.4 + - - +
310A THR 3.3 1.1 - - - -
339A ILE* 4.4 4.9 - - + -
----------------------------------------------------------
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