Contacts of the helix formed by residues 339 - 352 (chain E) in PDB entry 6CAJ
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 339 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E TYR 5.1 4.5 + - - -
337E GLY 4.2 0.8 + - - -
338E CYS* 1.3 80.6 - - - +
340E SER* 1.3 62.9 + - - +
341E LEU* 4.4 5.6 - - - -
342E VAL* 3.3 27.6 - - - +
343E SER* 3.1 25.4 + - - -
372E THR* 5.5 0.8 - - - -
404E GLY* 4.0 19.4 + - - -
406E HIS* 5.5 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E ASN* 3.5 26.9 + - - +
338E CYS* 5.5 0.8 - - - -
339E SER* 1.3 71.8 - - - +
341E LEU* 1.3 62.3 + - - +
343E SER* 4.0 5.4 - - - -
344E ARG* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E ASN* 4.6 13.8 - - - +
316E ALA* 3.8 39.9 - - + +
319E ILE* 4.0 28.9 - - + -
339E SER* 3.3 3.9 - - - +
340E SER* 1.3 79.6 + - - +
342E VAL* 1.3 62.2 + - + +
344E ARG* 3.3 7.6 + - + +
345E ILE* 2.9 36.2 + - + +
437E CYS* 3.4 38.4 - - + +
438E CYS* 4.0 1.6 - - - +
439E GLU* 4.0 14.8 - - + +
442E LYS* 6.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E VAL* 3.9 18.2 - - + -
339E SER* 3.3 22.2 + - - +
340E SER 3.5 0.2 - - - -
341E LEU* 1.3 76.4 - - + +
343E SER* 1.3 58.9 + - - +
345E ILE* 3.3 9.5 + - - +
346E LEU* 2.9 29.1 + - + +
402E LEU* 3.8 35.0 - - + -
403E LEU 3.4 28.9 - - - +
404E GLY* 4.0 3.1 - - - -
437E CYS* 4.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E CYS* 6.2 0.2 - - - -
339E SER 3.1 18.5 + - - -
340E SER* 4.0 5.8 - - - -
341E LEU 3.3 0.4 - - - -
342E VAL* 1.3 79.1 - - - +
344E ARG* 1.3 56.5 + - - +
346E LEU* 3.3 10.7 + - - +
347E GLN* 2.9 35.5 + - - +
372E THR* 2.9 30.8 + - - -
375E SER* 4.2 16.4 - - - -
376E LEU* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ILE* 5.5 2.4 - - - +
313E VAL* 4.3 18.8 + - - +
316E ALA* 3.5 34.9 - - - +
317E GLN* 3.5 34.9 - - - +
320E SER* 4.6 3.1 - - - +
340E SER 2.9 20.3 + - - +
341E LEU* 3.7 7.2 - - + +
343E SER* 1.3 73.1 - - - +
345E ILE* 1.3 60.4 + - - +
347E GLN* 3.9 10.7 - - - +
348E GLU* 2.9 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E ILE* 3.8 20.4 - - + -
320E SER* 3.7 32.2 + - - +
323E ALA* 3.7 24.7 - - + -
324E TYR 5.3 0.2 - - - +
327E ILE* 4.4 16.6 - - + -
341E LEU* 2.9 22.0 + - + +
342E VAL* 3.4 11.7 - - + +
344E ARG* 1.3 76.1 - - - +
346E LEU* 1.3 58.3 + - - +
348E GLU* 3.8 0.7 - - - +
349E ALA* 2.9 32.3 + - + +
402E LEU* 4.4 9.9 - - + -
437E CYS* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E ILE* 5.0 2.0 - - + -
333E ILE* 3.9 15.5 - - + -
335E VAL* 3.8 25.8 - - + -
342E VAL* 2.9 22.1 + - + +
343E SER* 3.7 6.1 - - - +
345E ILE* 1.3 75.5 - - - +
347E GLN* 1.3 57.5 - - - +
349E ALA* 3.4 0.6 + - - -
350E TRP* 2.9 29.3 + - - +
356E PHE* 3.5 31.7 - - + -
358E VAL* 4.1 4.3 - - + -
372E THR* 5.1 2.2 - - - +
376E LEU* 3.7 40.4 - - + -
381E VAL* 4.7 0.7 - - - +
402E LEU* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 347 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E SER 2.9 21.5 + - - +
344E ARG* 3.9 9.4 - - - +
346E LEU* 1.3 76.2 - - - +
348E GLU* 1.3 60.4 + - + +
350E TRP* 3.2 5.6 + - - +
351E THR* 2.9 37.6 + - + +
375E SER* 2.5 42.3 + - - +
376E LEU* 5.1 4.5 - - + -
379E ALA* 3.8 23.1 - - + +
381E VAL* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 348 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E GLN* 5.0 7.1 + - - +
320E SER* 2.6 36.6 + - - +
321E ARG* 6.1 0.3 - - - +
324E TYR* 4.1 5.0 - - - -
344E ARG* 2.9 52.7 + - + +
347E GLN* 1.3 77.0 - - + +
349E ALA* 1.3 58.0 + - - +
351E THR* 3.4 10.0 + - - +
352E GLU* 3.3 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E TYR* 3.7 22.6 - - + +
327E ILE* 4.7 15.0 - - + -
345E ILE* 2.9 20.3 + - + +
346E LEU* 3.8 4.3 - - - +
348E GLU* 1.3 78.7 - - - +
350E TRP* 1.3 63.4 + - - +
352E GLU 3.7 0.3 + - - -
353E GLY 3.7 3.6 + - - -
354E ARG* 3.1 29.9 + - + +
356E PHE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 350 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E LEU 2.9 17.9 + - - +
347E GLN* 3.2 5.1 + - - +
349E ALA* 1.3 78.7 - - - +
351E THR* 1.3 66.7 + - + +
352E GLU 3.5 0.2 + - - -
353E GLY 3.7 5.7 + - - -
354E ARG 3.2 21.3 - - - -
355E ARG* 3.7 35.3 + - - -
356E PHE* 3.3 44.1 - + + -
379E ALA* 3.2 24.1 + - + -
380E GLY* 3.2 25.5 + - - -
381E VAL* 3.6 19.7 - - + -
382E PRO* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 351 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E GLN* 2.9 23.8 + - + +
348E GLU* 3.4 14.4 + - - +
350E TRP* 1.3 84.7 - - + +
352E GLU* 1.3 68.5 + - - +
353E GLY* 3.6 0.7 + - - -
379E ALA* 5.5 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E TYR* 3.1 35.4 + - + +
348E GLU* 3.3 23.5 + - + +
349E ALA 3.7 0.4 + - - -
350E TRP 3.3 0.6 - - - -
351E THR* 1.3 85.0 + - - +
353E GLY* 1.3 55.6 + - - +
----------------------------------------------------------
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