Contacts of the helix formed by residues 339 - 355 (chain A) in PDB entry 3M6L
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 ALA 339 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 1.3 76.4 - - - +
340A THR* 1.3 59.6 + - - +
341A ARG* 4.0 4.9 - - + -
342A ASP* 2.9 37.4 + - - +
343A SER 3.2 8.8 + - - -
498A SER* 3.6 7.4 - - - +
499A ARG 3.4 19.7 - - - +
500A GLN 3.3 26.5 - - - +
501A LYS* 3.7 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 3.7 2.6 + - + -
339A ALA* 1.3 69.9 - - - +
341A ARG* 1.3 59.8 + - - +
343A SER* 3.2 13.8 + - - +
344A ASN* 2.9 31.0 + - - +
473A PRO* 3.6 27.9 + - + +
475A ASP* 3.9 27.6 - - - +
479A ASN* 3.4 0.7 + - - -
496A VAL 4.7 0.2 + - - -
497A LEU* 3.3 20.8 - - - +
498A SER* 2.8 33.7 + - - -
502A LEU* 3.9 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA* 4.0 7.0 - - + +
340A THR* 1.3 80.1 + - - +
342A ASP* 1.3 66.8 + - - +
344A ASN* 3.8 3.8 - - - +
345A GLY 3.2 18.9 + - - -
368A SER* 2.9 36.5 + - - +
369A ASN 4.0 5.4 - - - +
370A LYS* 3.5 33.4 - - + +
440A THR* 3.9 21.3 - - + -
441A HIS* 3.6 15.8 + - - -
497A LEU* 3.9 8.9 - - - +
498A SER 3.1 23.2 + - - +
499A ARG* 3.3 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.8 6.4 - - + +
339A ALA* 2.9 26.6 + - - +
341A ARG* 1.3 82.8 + - - +
343A SER* 1.3 66.1 + - - +
344A ASN 3.1 1.1 - - - -
345A GLY* 3.2 1.4 + - - +
346A GLU* 3.1 28.6 + - + +
370A LYS* 2.8 42.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
333A PHE* 3.7 17.3 - - - -
338A LEU* 3.3 36.2 - - - +
339A ALA 3.2 3.2 + - - -
340A THR* 3.2 8.5 + - - -
342A ASP* 1.3 76.6 - - - +
344A ASN* 1.3 61.6 + - - +
346A GLU* 3.3 4.3 + - - +
347A ILE* 3.0 24.8 + - - +
476A GLY* 3.7 16.0 - - - -
479A ASN* 2.7 26.4 + - - -
----------------------------------------------------------
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 THR 2.9 20.8 + - - +
341A ARG 3.8 3.1 - - - +
343A SER* 1.3 78.4 - - - +
345A GLY* 1.3 57.6 + - - +
347A ILE* 3.0 4.6 + - - +
348A LEU* 2.9 39.9 + - - +
369A ASN 5.6 1.2 - - - +
371A THR* 5.4 0.3 - - - +
438A ILE* 3.7 17.4 - - - +
479A ASN* 3.1 20.7 + - - +
483A TRP* 2.9 32.9 - - - +
495A PHE* 4.4 6.5 - - - -
497A LEU* 3.4 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG 3.2 12.9 + - - -
342A ASP 3.2 3.2 + - - -
344A ASN* 1.3 76.1 + - - +
346A GLU* 1.3 62.2 + - - +
348A LEU* 3.3 8.9 + - - +
349A ASN* 2.9 34.0 + - - -
369A ASN 5.5 0.4 + - - -
370A LYS* 3.1 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PRO* 4.4 8.1 - - + +
333A PHE* 3.9 24.4 - - + -
342A ASP* 3.1 16.1 + - + +
343A SER 3.5 7.6 - - - +
345A GLY* 1.3 77.2 - - - +
347A ILE* 1.4 60.7 + - - +
349A ASN* 3.3 8.5 + - - +
350A VAL* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TYR* 3.9 19.1 - - + -
331A PRO* 4.2 6.3 - - + -
333A PHE* 4.0 8.1 - - + -
343A SER 3.0 14.4 + - - +
344A ASN* 3.4 6.1 - - - +
346A GLU* 1.4 72.5 - - - +
348A LEU* 1.3 59.0 + - - +
350A VAL* 3.1 7.8 + - - +
351A LEU* 2.8 32.1 + - + +
479A ASN* 3.5 38.1 - - + +
480A VAL* 3.5 36.8 - - + +
483A TRP* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASN* 2.9 35.6 + - - +
345A GLY* 3.6 10.5 - - - +
347A ILE* 1.3 72.9 - - - +
349A ASN* 1.3 57.6 + - - +
351A LEU* 3.4 3.3 + - - +
352A ALA* 3.0 29.5 + - - +
358A PHE* 3.7 23.6 - - + -
371A THR* 3.8 34.3 - - + +
373A LEU* 3.6 15.4 - - + +
410A PHE* 4.1 23.3 - - + -
438A ILE* 4.6 3.6 - - + -
483A TRP* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLY* 2.9 29.1 + - - -
346A GLU* 3.6 11.2 - - - +
347A ILE 3.2 0.2 - - - -
348A LEU* 1.3 76.2 - - - +
350A VAL* 1.3 64.8 + - + +
352A ALA* 3.3 4.8 + - - +
353A LYS* 3.1 32.9 + - + +
370A LYS 5.3 0.2 + - - -
371A THR 5.4 0.2 - - - -
372A GLU 3.0 22.1 + - - -
373A LEU* 3.4 8.8 - - - +
374A HIS* 2.7 47.9 + - - +
376A MSE 4.9 3.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
328A ILE* 3.9 12.1 - - + -
329A ALA 3.5 24.2 - - - +
330A TYR* 4.4 7.2 - - + -
331A PRO* 3.9 20.9 - - + -
346A GLU 3.1 14.9 + - - +
347A ILE* 3.5 9.2 - - - +
349A ASN* 1.3 72.1 - - + +
351A LEU* 1.4 66.2 + - - +
353A LYS* 3.2 14.4 + - - +
354A ASN* 2.9 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.8 24.2 - - + -
330A TYR* 3.7 28.9 - - + +
347A ILE* 2.8 29.6 + - + +
348A LEU 3.8 0.2 - - - +
349A ASN 3.3 0.2 - - - -
350A VAL* 1.4 74.8 - - - +
352A ALA* 1.3 56.4 + - - +
354A ASN* 3.2 2.0 + - - -
355A LEU* 2.9 38.7 + - + +
358A PHE* 3.7 37.2 - - + -
483A TRP* 3.6 38.8 - - + -
487A LEU* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU 3.0 17.6 + - - +
349A ASN 3.3 3.3 + - - +
351A LEU* 1.3 75.3 - - - +
353A LYS* 1.3 61.7 + - - +
355A LEU 3.5 5.4 + - - +
356A GLU* 5.0 0.5 - - - -
358A PHE* 3.8 11.4 - - + -
373A LEU* 4.0 17.5 - - + -
376A MSE 3.7 22.6 - - - +
383A LYS* 3.1 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASN* 3.1 21.2 + - + +
350A VAL* 3.7 15.0 - - - +
351A LEU 3.1 1.0 - - - -
352A ALA* 1.3 80.1 - - - +
354A ASN* 1.4 67.5 - - - +
355A LEU 5.4 0.2 - - - -
356A GLU* 6.0 1.4 - - - +
376A MSE 4.3 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS* 5.1 3.3 - - - +
328A ILE* 3.9 40.4 - - + +
329A ALA 4.9 3.2 + - - +
350A VAL* 2.9 42.8 + - - +
351A LEU 4.0 2.2 - - - +
353A LYS* 1.4 88.2 - - - +
355A LEU* 1.3 66.3 + - + +
356A GLU* 4.1 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 3.9 28.5 - - + -
324A ASP 4.7 7.2 - - - +
325A PHE* 3.9 25.8 - - + -
328A ILE* 4.1 21.3 - - + -
351A LEU* 2.9 24.1 + - + +
352A ALA 3.5 2.9 - - - +
353A LYS 3.6 1.0 - - - -
354A ASN* 1.3 85.7 - - + +
356A GLU* 1.3 62.2 + - - +
357A GLY 3.0 3.0 + - - +
358A PHE* 3.0 26.2 + - + +
383A LYS* 2.8 21.6 + - - -
408A LEU* 4.0 13.7 - - + -
487A LEU* 4.7 3.1 - - + -
----------------------------------------------------------
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