Contacts of the helix formed by residues 338 - 351 (chain A) in PDB entry 2MBG
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 ASN 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 5.1 1.4 - - - +
332A GLU* 2.8 18.8 + - - +
333A LEU* 5.4 6.9 - - - +
337A MET* 1.3 79.4 - - - +
339A ILE* 1.3 83.7 + - - +
340A GLN* 3.9 17.6 - - + +
341A ASN* 2.7 38.0 + - - +
342A ILE 3.5 0.2 + - - -
358A TYR* 6.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ILE* 3.2 26.1 - - + +
332A GLU* 3.4 7.7 + - - -
338A ASN* 1.3 83.2 + - - +
340A GLN* 1.3 53.4 + - - +
341A ASN 3.3 0.2 + - - -
342A ILE* 3.4 2.9 + - - +
343A SER* 2.7 39.1 + - - +
358A TYR* 3.5 45.5 - - + +
361A PHE* 3.8 29.6 - - + -
362A THR* 5.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASN* 3.0 16.6 - - - +
339A ILE* 1.3 80.0 - - - +
341A ASN* 1.3 83.9 + - - +
343A SER* 3.2 8.3 + - - -
344A ILE* 3.0 58.7 + - + +
354A ASN* 5.1 7.2 - - - +
358A TYR* 5.0 5.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.9 26.6 + - - +
332A GLU* 3.5 8.5 - - - +
337A MET* 4.1 19.7 - - + +
338A ASN* 2.7 42.0 + - - +
340A GLN* 1.3 88.9 + - - +
342A ILE* 1.3 62.3 + - - +
344A ILE* 3.1 18.1 + - - +
345A VAL* 3.3 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE 3.5 25.1 - - - +
231A TYR* 3.7 16.8 - - + -
325A MET* 3.6 17.9 - - + -
328A VAL* 4.2 12.3 - - + -
329A ILE* 3.7 10.8 - - + -
332A GLU* 3.3 29.6 - - + +
337A MET* 4.3 2.5 - - + -
338A ASN 3.5 0.6 + - - -
339A ILE 3.4 7.1 + - - +
341A ASN* 1.3 79.2 - - - +
343A SER* 1.3 52.2 + - - +
345A VAL* 3.1 7.8 - - + +
346A LEU* 2.7 44.9 + - + +
361A PHE* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 2.7 25.5 + - - +
340A GLN* 3.4 8.9 - - - -
341A ASN 3.2 0.2 - - - -
342A ILE* 1.3 77.6 - - - +
344A ILE* 1.3 61.3 + - - +
347A SER* 3.1 24.8 + - - -
354A ASN* 3.3 33.4 + - - -
357A LEU* 3.7 13.4 - - - +
358A TYR* 3.1 28.0 + - - +
361A PHE* 4.2 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 4.0 24.9 - - - +
340A GLN* 3.0 50.6 + - + +
341A ASN* 3.1 8.9 + - - +
343A SER* 1.3 77.0 - - - +
345A VAL* 1.3 59.7 + - + +
347A SER* 3.8 3.1 - - - -
348A PRO* 3.0 23.2 - - - +
354A ASN* 3.3 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 3.0 34.5 - - + +
232A ARG* 3.6 40.6 - - - +
268A LYS* 3.0 21.1 + - - +
341A ASN 3.4 11.0 - - - +
342A ILE* 3.1 23.6 - - + +
344A ILE* 1.3 77.7 - - + +
346A LEU* 1.3 62.5 + - + +
347A SER 3.4 0.2 - - - -
348A PRO* 3.5 11.5 - - - +
349A THR* 2.9 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 5.3 8.7 - - + -
268A LYS* 6.0 0.9 - - + -
321A LEU* 4.7 19.7 - - + -
322A ILE* 4.5 9.2 - - + -
325A MET* 4.2 15.9 - - + -
342A ILE* 2.7 23.4 + - + +
345A VAL* 1.3 78.4 - - + +
347A SER* 1.3 67.1 + - - +
348A PRO 3.5 0.4 - - - -
349A THR* 3.0 41.1 + - + +
350A VAL* 3.4 10.4 + - + +
357A LEU* 3.5 29.3 - - + +
361A PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER 3.1 18.2 + - - -
344A ILE* 3.8 4.3 - - - -
346A LEU* 1.3 77.1 - - - +
348A PRO* 1.4 63.7 - - - +
349A THR 3.0 0.5 + - - -
351A GLN* 3.0 27.2 + - - -
352A ILE 2.6 34.9 + - - -
353A SER* 3.8 1.6 - - - -
354A ASN* 3.6 15.3 + - - +
357A LEU* 3.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LYS* 6.1 2.2 - - + +
272A ARG* 3.4 26.1 + - - +
344A ILE 3.0 21.3 - - - +
345A VAL* 3.5 12.8 - - - +
347A SER* 1.4 92.9 - - - +
349A THR* 1.3 52.5 + - - +
351A GLN* 2.7 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LYS* 3.6 36.4 - - + +
271A LEU* 3.8 25.8 - - + +
272A ARG* 3.6 19.3 + - - +
321A LEU* 4.8 1.3 - - + -
345A VAL 2.9 22.5 + - - -
346A LEU* 3.0 34.6 - - + +
347A SER 3.0 0.4 - - - -
348A PRO* 1.3 74.9 - - - +
350A VAL* 1.3 63.0 + - + +
351A GLN* 2.8 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 5.3 2.7 - - + -
277A ASN* 3.6 5.5 + - - +
278A LEU* 3.6 31.9 - - + +
279A LEU* 4.6 7.7 - - + +
284A MET* 3.3 17.3 - - - +
318A ILE* 5.7 2.0 - - + -
321A LEU* 3.7 19.5 - - + -
322A ILE* 5.9 2.0 - - + -
346A LEU* 3.4 12.0 + - + +
349A THR* 1.3 82.2 - - + +
351A GLN* 1.3 74.3 + - - +
352A ILE* 3.8 26.7 - - + +
357A LEU* 4.5 14.1 - - + -
360A PHE* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 3.9 21.8 + - - +
277A ASN* 3.9 13.5 - - - +
284A MET* 3.5 20.1 - - + +
347A SER 3.0 7.9 + - - -
348A PRO* 2.7 31.3 + - - +
349A THR 2.8 20.2 + - - -
350A VAL* 1.3 81.4 - - - +
352A ILE* 1.3 63.4 + - - +
----------------------------------------------------------
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