Contacts of the helix formed by residues 339 - 349 (chain A) in PDB entry 6C90
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 339 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.5 39.5 - - + +
331A VAL* 2.9 17.1 + - - +
332A VAL 4.6 0.9 - - - +
333A ASP* 3.3 38.3 + - - +
334A GLU* 5.4 0.6 + - - -
337A ASP* 3.9 9.6 + - - +
338A PHE* 1.3 77.7 - - - +
340A GLU* 1.3 65.8 + - - +
341A ASP* 3.1 17.3 + - - +
342A ASN* 4.0 17.6 - - - +
343A PHE* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 3.4 30.7 + - + +
339A ARG* 1.3 73.3 - - - +
341A ASP* 1.3 62.5 + - - +
343A PHE* 3.8 1.4 - - + +
344A ASN* 2.9 44.0 + - - +
545A PRO* 3.9 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ARG* 3.5 23.7 + - - +
340A GLU* 1.3 72.5 + - - +
342A ASN* 1.3 87.6 + - - +
343A PHE 3.2 0.3 + - - -
344A ASN* 3.3 7.0 + - - +
345A THR* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A HIS* 3.9 9.7 - - + +
330A LEU* 2.9 44.5 + - - +
331A VAL* 4.3 1.8 - - - -
339A ARG* 3.4 27.0 + - - +
341A ASP* 1.3 97.0 + - - +
343A PHE* 1.3 56.5 + - - +
345A THR* 3.3 11.4 + - - +
346A ALA* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 3.6 30.3 - - + -
331A VAL* 3.8 11.8 - - + +
338A PHE* 3.6 25.4 - + + -
339A ARG 3.0 18.8 + - - +
340A GLU 3.8 4.0 - - - +
341A ASP 3.1 0.2 - - - -
342A ASN* 1.3 76.1 - - - +
344A ASN* 1.3 69.6 + - - +
346A ALA* 2.9 19.7 + - - +
347A MET* 2.9 26.3 + - + +
543A MET* 3.5 28.0 - - + -
544A SER 3.3 19.7 - - - -
545A PRO* 3.5 30.3 - - + -
548A GLY* 4.0 16.8 - - - -
552A LEU* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU* 2.9 32.4 + - - +
341A ASP* 3.9 4.3 - - - +
343A PHE* 1.3 80.0 - - - +
345A THR* 1.3 53.1 + - - +
347A MET* 3.1 9.4 + - - +
348A GLN* 2.7 34.9 + - - +
545A PRO* 3.5 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A HIS* 4.0 17.2 + - + +
341A ASP* 2.9 17.9 + - - +
342A ASN* 3.5 16.0 + - - +
343A PHE 3.2 0.2 - - - -
344A ASN* 1.3 76.2 - - - +
346A ALA* 1.3 60.7 + - - +
348A GLN* 3.3 32.2 + - - +
349A VAL* 3.6 11.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 4.1 26.5 - - + -
322A PRO* 3.4 23.6 - - + +
329A HIS* 3.8 29.1 - - + +
342A ASN 2.8 13.7 + - - +
343A PHE* 2.9 11.9 + - - +
345A THR* 1.3 74.4 - - - +
347A MET* 1.3 66.8 + - - +
349A VAL* 3.2 10.4 + - - +
350A LEU* 3.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 5.5 3.8 - - - -
322A PRO* 6.4 0.2 - - - -
343A PHE* 2.9 40.9 + - + +
344A ASN* 3.1 10.1 + - - +
346A ALA* 1.3 77.1 - - - +
348A GLN* 1.3 61.1 + - - +
350A LEU* 2.9 20.2 + - + +
351A ARG* 2.8 30.2 + - + +
539A VAL* 4.6 5.2 - - + -
541A GLU 3.6 17.3 - - - +
542A LYS* 3.7 5.6 - - + -
543A MET* 3.3 51.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASN 2.7 17.5 + - - +
345A THR* 3.3 29.3 - - - +
346A ALA 3.2 0.4 - - - -
347A MET* 1.3 72.2 - - - +
349A VAL* 1.3 64.9 + - + +
350A LEU 3.0 1.4 + - - -
351A ARG* 3.2 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 3.7 13.7 - - + -
323A ALA 4.0 9.2 - - - +
324A GLY 4.3 1.6 - - - -
325A GLY* 3.5 36.6 - - - +
329A HIS* 4.2 12.6 - - + +
345A THR* 3.6 15.0 - - + +
346A ALA 3.2 9.8 + - - +
347A MET 3.2 0.8 - - - -
348A GLN* 1.3 77.2 - - + +
350A LEU* 1.3 59.1 + - - +
351A ARG 4.7 0.7 - - - +
----------------------------------------------------------
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