Contacts of the helix formed by residues 331 - 342 (chain H) in PDB entry 4MNE
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 SER 331 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H GLU* 3.1 26.8 + - - -
330H PHE* 1.3 78.9 - - - +
332H LEU* 1.3 61.4 + - - +
333H GLU* 3.4 10.8 + - - +
334H PHE* 3.2 15.8 + - - +
335H GLN* 3.2 24.4 + - - +
363H ARG* 3.5 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H GLY* 5.7 4.3 - - - +
330H PHE 4.6 5.2 - - - +
331H SER* 1.3 76.8 - - - +
333H GLU* 1.3 64.4 + - + +
334H PHE 3.3 0.7 - - - -
335H GLN* 3.9 18.6 - - - +
336H ASP* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H SER* 3.3 11.2 - - - +
332H LEU* 1.3 83.1 - - + +
334H PHE* 1.3 51.8 + - - +
336H ASP* 3.4 2.0 + - - -
337H PHE* 2.8 30.0 + - - +
358H HIS* 3.1 14.7 - - - -
359H ALA* 3.2 35.6 - - + +
360H PHE* 3.9 19.3 - - + +
363H ARG* 4.2 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H GLU* 3.1 51.6 - - + +
166H LEU* 4.2 21.5 - - + -
253H LEU* 4.9 11.7 - - + -
257H ALA* 4.2 21.8 - - + -
325H LEU* 3.9 9.4 - - + -
330H PHE* 3.9 20.4 - + + -
331H SER* 3.2 12.2 + - - +
333H GLU* 1.3 74.0 - - - +
335H GLN* 1.3 64.8 + - - +
337H PHE* 3.0 6.1 + + - +
338H VAL* 3.0 42.4 + - + +
360H PHE* 3.4 38.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325H LEU* 3.6 27.0 + - + +
326H PRO 3.5 9.0 - - - +
327H SER* 3.2 39.9 - - - +
328H GLY 3.2 3.5 + - - -
330H PHE* 3.2 21.5 - - + +
331H SER 3.2 13.0 + - - +
332H LEU* 3.9 18.6 - - - +
334H PHE* 1.3 78.5 - - - +
336H ASP* 1.3 60.2 + - - +
338H VAL* 3.5 1.3 - - - +
339H ASN* 2.8 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 336 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H LEU 3.0 20.8 + - - +
333H GLU* 3.8 4.3 - - - +
335H GLN* 1.3 75.4 - - - +
337H PHE* 1.3 57.1 + - - +
339H ASN* 3.1 11.1 + - - +
340H LYS* 2.6 77.7 + - - +
358H HIS* 3.4 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 337 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H SER* 3.9 22.0 - - - -
174H ILE* 3.8 16.6 - - + -
249H MET* 4.7 2.0 - - + -
253H LEU* 3.9 19.5 - - + -
333H GLU 2.8 14.7 + - - +
334H PHE 3.2 9.2 - - - +
336H ASP* 1.3 76.2 - - - +
338H VAL* 1.3 62.6 + - + +
340H LYS* 3.0 7.3 + - - +
341H CYS* 2.9 36.6 + - - -
355H LEU* 3.2 36.1 - - + -
358H HIS* 3.5 27.0 + + + -
360H PHE* 3.4 23.1 - + + -
361H ILE* 3.3 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H GLY* 4.9 3.6 - - - +
253H LEU* 4.8 11.9 - - + -
254H VAL* 4.4 18.4 - - + -
324H LYS* 4.7 1.1 - - - -
325H LEU* 3.5 35.9 - - + +
334H PHE* 3.0 31.1 + - + +
335H GLN* 3.5 6.3 - - - +
337H PHE* 1.3 78.3 - - + +
339H ASN* 1.3 74.5 + - - +
341H CYS* 3.0 10.7 + - - +
342H LEU* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 339 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H PRO 4.8 1.6 - - - +
324H LYS* 3.7 26.0 - - - +
325H LEU 4.8 0.3 + - - -
335H GLN* 2.8 28.7 + - - +
336H ASP* 3.1 14.7 + - - +
338H VAL* 1.3 85.2 - - - +
340H LYS* 1.3 64.2 + - + +
342H LEU* 3.2 11.8 + - - +
343H ILE* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ASP* 2.6 57.6 + - - +
337H PHE* 3.3 7.6 - - - +
339H ASN* 1.3 79.0 - - + +
341H CYS* 1.3 58.6 + - - +
342H LEU 3.6 0.2 + - - -
343H ILE* 4.0 17.6 - - + +
349H ARG* 3.2 11.4 - - - +
350H ALA* 3.2 42.2 + - + -
355H LEU* 4.7 3.8 - - + -
358H HIS* 4.3 16.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 341 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H ILE* 3.8 24.2 - - - +
247H TRP* 3.4 15.2 + - - -
249H MET* 4.3 10.5 - - - -
250H GLY* 3.7 22.9 - - - -
337H PHE* 2.9 45.2 + - - -
338H VAL* 3.0 10.1 + - - +
340H LYS* 1.3 79.8 - - - +
342H LEU* 1.3 57.4 + - - +
343H ILE 3.5 0.2 - - - -
349H ARG* 2.9 20.1 - - - -
355H LEU* 4.2 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H TRP* 3.1 50.1 - - + +
250H GLY 4.2 2.0 - - - -
251H LEU* 3.4 31.6 - - + +
254H VAL* 3.8 26.9 - - + -
322H PRO* 3.1 23.8 - - + +
323H PRO* 3.4 28.5 - - + +
338H VAL* 2.9 21.7 + - + +
339H ASN* 3.2 6.2 + - - +
341H CYS* 1.3 78.6 - - - +
343H ILE* 1.3 63.9 + - - +
344H LYS 3.1 2.3 + - - -
----------------------------------------------------------
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