Contacts of the helix formed by residues 339 - 351 (chain A) in PDB entry 1JD7
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 TRP 339 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 3.7 32.8 - - + -
281A GLY* 3.9 22.0 - - - -
284A TYR* 3.8 17.7 - + + -
285A ASP* 3.3 23.6 - - - +
329A PHE* 3.8 18.4 - + - +
334A LYS* 3.2 31.6 + - - -
335A CYS 3.3 13.9 - - - -
336A GLU* 3.0 28.2 + - + +
338A ARG* 1.3 75.6 - - - +
340A SER* 1.3 66.8 - - - +
341A TYR 3.3 0.7 - - - -
342A ILE* 2.9 21.7 + - + -
343A ALA 2.8 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG 3.1 6.8 + - - -
339A TRP* 1.3 68.6 - - - +
341A TYR* 1.3 74.9 + - - -
343A ALA* 3.8 3.5 - - - +
344A GLY* 2.7 34.1 + - - -
404A VAL 4.5 1.2 - - - +
405A LEU 3.8 13.5 + - - +
406A LYS* 5.3 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 3.7 30.0 + - - -
285A ASP* 3.6 37.4 + - + +
286A LEU* 5.2 1.8 - - + -
289A VAL* 4.1 20.3 - - + +
292A LEU* 4.9 0.2 - - - +
339A TRP* 3.3 1.4 - - - +
340A SER* 1.3 92.8 + - - +
342A ILE* 1.3 56.6 + - - +
344A GLY* 3.8 0.9 - - - -
345A GLY* 2.9 24.4 + - - -
405A LEU* 3.5 43.5 - - + +
406A LYS* 3.2 23.3 - - + -
437A ASP* 2.7 32.0 + - - -
438A ALA* 4.4 10.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
29A TYR* 4.3 3.8 - - - +
284A TYR* 3.7 20.9 - - + -
285A ASP* 4.2 7.9 - - - +
288A ASN* 3.6 43.1 - - + +
292A LEU* 3.2 15.0 - - + +
301A VAL* 3.8 31.4 - - + -
336A GLU* 3.3 33.2 - - + +
339A TRP* 2.9 22.3 + - + +
341A TYR* 1.3 69.2 - - - +
343A ALA* 1.3 64.8 + - - +
345A GLY 3.0 10.0 + - - -
346A VAL* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.0 30.5 - - + +
27A LYS* 5.2 10.9 - - + +
29A TYR* 4.2 8.3 - - + +
337A HIS 3.6 13.1 + - - +
338A ARG 4.5 1.8 - - - +
339A TRP 2.8 16.3 + - - +
340A SER* 4.1 3.8 - - - +
342A ILE* 1.3 72.6 - - - +
344A GLY* 1.3 63.5 + - - +
346A VAL* 3.2 6.7 + - - +
347A ASP* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER 2.7 19.4 + - - -
341A TYR 3.8 1.3 - - - -
343A ALA* 1.3 74.5 - - - +
345A GLY* 1.3 61.1 + - - +
347A ASP* 3.1 9.9 + - - +
348A PHE* 3.0 21.7 + - - +
404A VAL* 3.3 29.8 - - - +
405A LEU* 3.9 7.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
289A VAL* 5.3 4.7 - - - -
292A LEU* 3.6 30.9 - - - +
293A ALA 5.7 0.2 - - - -
341A TYR 2.9 14.5 + - - -
342A ILE 3.0 4.9 + - - -
344A GLY* 1.3 77.2 - - - +
346A VAL* 1.3 59.2 - - - +
348A PHE* 3.2 9.2 + - - +
349A ARG 3.0 18.2 + - - -
405A LEU* 3.9 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 4.1 25.4 - - + +
27A LYS* 4.3 11.2 - - + +
28A GLY 4.6 4.3 - - - +
29A TYR* 3.7 39.3 - - + +
292A LEU* 3.6 10.5 - - + +
301A VAL* 4.4 2.2 - - + -
342A ILE 3.1 13.3 + - - +
343A ALA* 3.4 8.1 - - - +
345A GLY* 1.3 74.1 - - - +
347A ASP* 1.3 66.1 + - - +
349A ARG* 3.2 6.0 + - - +
350A ASN* 2.9 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS 5.1 6.6 + - - +
343A ALA 3.1 12.3 + - - +
344A GLY* 3.1 12.3 + - - +
346A VAL* 1.3 76.3 - - - +
348A PHE* 1.3 63.6 + - - +
350A ASN* 3.3 7.6 + - - +
351A ASN* 2.9 42.1 + - - +
404A VAL* 3.7 14.1 - - + +
408A GLU* 6.1 1.4 - - - +
442A HIS* 2.8 25.2 + - - -
445A ALA* 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU 4.3 0.4 - - - -
293A ALA* 3.6 47.6 - - + -
344A GLY 3.0 11.7 + - - +
345A GLY* 3.2 11.7 - - - +
347A ASP* 1.3 74.0 + - - +
349A ARG* 1.3 60.4 + - - +
351A ASN* 3.1 9.4 + - - +
352A THR* 2.8 43.0 + - + +
371A PHE* 5.6 0.7 - + - -
372A GLY 5.6 0.2 - - - -
373A ARG* 3.8 25.1 - - + -
377A GLY 4.2 0.2 - - - -
378A HIS* 3.6 24.7 - - - -
379A MET* 4.5 4.3 - - + -
404A VAL* 4.5 5.6 - - + -
440A ALA* 4.0 18.8 - - + -
441A ILE 3.2 31.4 - - - -
442A HIS* 3.9 10.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.3 29.5 + - + +
4A THR* 3.5 14.8 - - - +
291A MET 3.0 9.0 + - - -
292A LEU* 2.7 40.1 + - - +
293A ALA 4.2 0.8 + - - -
294A TYR 2.6 30.9 + - - -
296A TYR 3.3 15.8 + - - +
297A GLY 3.0 24.4 + - - -
299A PRO* 3.3 22.6 - - - +
345A GLY 3.0 10.3 + - - +
346A VAL* 3.8 6.3 - - - +
348A PHE* 1.3 75.9 - - - +
350A ASN* 1.3 63.3 + - - +
352A THR* 3.2 19.9 + - - +
353A ALA* 3.2 9.2 + - - +
356A TRP* 3.7 27.7 - - + -
373A ARG* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR* 3.1 52.7 + - - +
3A THR* 2.7 36.3 + - - +
4A THR 4.4 0.4 - - - +
27A LYS 3.9 2.9 - - - +
28A GLY* 3.4 27.7 + - - +
346A VAL* 2.9 37.4 + - - +
347A ASP* 3.4 9.1 - - - +
349A ARG* 1.3 77.2 - - - +
351A ASN* 1.3 63.4 + - - +
352A THR 3.7 0.2 + - - -
353A ALA* 4.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR 5.8 1.6 - - - +
347A ASP* 2.9 32.9 + - - +
348A PHE 3.1 3.2 + - - +
350A ASN* 1.3 81.8 + - - +
352A THR* 1.3 64.9 + - - +
353A ALA 3.6 1.6 - - - -
354A ASP* 4.3 1.2 - - - +
376A SER* 3.9 13.0 - - - +
442A HIS* 3.4 32.2 - - + +
443A LYS* 4.0 14.0 - - - +
444A ASN* 2.6 36.4 + - - +
----------------------------------------------------------
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