Contacts of the helix formed by residues 315 - 330 (chain A) in PDB entry 1JIQ
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 ASN 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 4.3 2.8 + - - -
306A HIS* 3.7 2.1 - - - +
307A PHE* 2.9 30.9 - - - +
310A THR* 2.9 27.3 - - - +
311A PRO 3.4 12.6 - - - +
312A LEU* 3.1 12.1 + - - +
313A GLU 3.7 0.4 - - - -
314A LYS* 1.3 73.9 - - - +
316A ALA* 1.3 59.0 + - - +
317A PRO* 3.1 24.7 - - - +
318A VAL* 3.1 24.7 + - + +
319A LEU* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.5 22.2 - - + -
44A LEU* 4.2 10.8 - - + -
53A VAL* 4.3 7.8 - - + +
303A MET* 5.1 0.4 - - - -
306A HIS* 3.0 21.5 - - + -
314A LYS 3.6 3.2 + - - -
315A ASN* 1.3 69.8 - - - +
317A PRO* 1.3 71.1 - - + +
319A LEU* 3.2 3.0 + - - +
320A LEU* 2.9 28.9 + - - +
493A MET* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 4.5 6.3 - - - -
306A HIS* 3.9 8.1 - - - +
307A PHE* 3.9 19.3 - - + -
315A ASN* 3.1 17.9 - - - +
316A ALA* 1.3 95.9 - - + +
318A VAL* 1.3 55.1 + - - +
320A LEU* 3.4 1.7 + - + -
321A ALA* 2.9 29.5 + - - +
493A MET* 3.5 35.0 - - + +
496A HIS* 3.6 21.3 - - + -
497A LYS* 3.5 12.4 - - + +
500A VAL* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 4.6 6.7 - - + -
77A VAL* 4.8 1.3 - - + -
307A PHE* 3.9 20.0 - - + -
312A LEU* 3.9 37.0 - - + +
315A ASN* 3.1 34.9 + - + +
317A PRO* 1.3 77.8 - - - +
319A LEU* 1.3 57.2 + - - +
321A ALA* 3.2 2.9 + - - +
322A LEU* 2.9 49.3 + - + +
500A VAL* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.2 17.0 - - + -
53A VAL* 6.4 1.3 - - + -
55A TYR* 3.4 42.4 - - + +
65A MET* 4.0 20.4 - - + -
69A VAL* 4.6 8.7 - - + -
312A LEU 3.7 17.3 - - - +
313A GLU* 3.5 23.1 - - - +
314A LYS* 4.4 0.2 - - - -
315A ASN 2.8 21.5 + - - +
316A ALA* 3.8 4.3 - - - +
318A VAL* 1.3 70.2 - - - +
320A LEU* 1.3 68.1 + - + +
322A LEU* 3.7 8.3 - - + +
323A LEU* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.1 22.7 - - + -
55A TYR* 5.7 0.2 - - + -
316A ALA 2.9 20.0 + - - +
317A PRO* 3.8 4.7 - - + +
319A LEU* 1.3 79.0 - - + +
321A ALA* 1.3 60.8 + - - +
323A LEU* 3.5 8.4 + - + +
324A GLY 3.2 15.9 + - - -
405A ASP* 5.0 3.4 - - - +
475A ASN* 3.7 28.2 - - - +
477A ILE* 4.4 11.7 - - + -
493A MET* 3.9 41.1 - - + -
494A TYR* 4.7 12.3 - - + -
497A LYS* 3.9 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO 2.9 13.0 + - - +
318A VAL 3.4 8.1 - - - +
320A LEU* 1.3 75.5 - - - +
322A LEU* 1.3 57.3 + - - +
324A GLY 3.0 2.8 + - - -
325A ILE* 2.9 28.4 + - - +
497A LYS* 3.4 28.4 - - - +
500A VAL* 3.6 19.1 - - + -
501A GLN* 3.1 24.8 + - + +
504A ILE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 5.5 1.8 - - + -
68A LEU* 3.4 60.7 - - + +
69A VAL* 3.8 17.0 - - + +
71A LEU* 4.6 5.4 - - + -
72A ALA* 4.2 6.1 - - + +
318A VAL* 2.9 42.8 + - + +
319A LEU* 3.2 11.2 + - + +
321A ALA* 1.3 72.7 - - + +
323A LEU* 1.3 63.3 + - + +
325A ILE* 3.2 7.1 + - + +
326A TRP* 3.1 22.3 + - - +
504A ILE* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.7 35.0 - - + -
58A ASN* 4.0 17.7 - - + +
60A VAL* 3.8 30.1 - - + -
65A MET* 4.2 16.2 - - + -
68A LEU* 4.8 1.6 - - + -
319A LEU* 2.9 27.7 + - + +
320A LEU* 3.8 9.4 - - + +
322A LEU* 1.3 75.8 - - - +
324A GLY* 1.3 62.5 + - - +
326A TRP* 3.3 7.5 - - + +
327A TYR* 3.1 39.5 + - + -
475A ASN* 3.9 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU 3.2 8.1 + - - -
321A ALA 3.0 8.4 + - - -
323A LEU* 1.3 74.9 - - - +
325A ILE* 1.3 59.1 + - - +
327A TYR* 3.3 6.6 + - - +
328A ILE* 2.8 39.8 + - - +
336A HIS* 5.9 5.4 - - - -
497A LYS* 5.4 2.7 - - - -
501A GLN* 3.5 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.4 0.7 - - + -
10A PHE* 4.9 6.3 - - + -
13A LEU* 4.9 2.2 - - + -
68A LEU* 4.9 4.7 - - + -
71A LEU* 4.0 23.8 - - + -
321A ALA 2.9 18.7 + - - +
322A LEU* 3.5 9.6 - - + +
324A GLY* 1.3 74.5 - - - +
326A TRP* 1.3 59.4 + - - +
328A ILE* 4.5 1.3 - - - +
329A ASN* 2.7 45.5 + - + +
330A CYS* 3.7 0.4 + - - -
501A GLN* 3.9 10.3 - - + +
504A ILE* 4.0 32.3 - - + -
505A TRP* 3.3 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.7 34.5 - - + -
16A TRP* 3.9 15.3 - + - -
17A TYR* 4.4 23.3 - + + -
24A LEU* 3.8 15.5 - - + -
59A LEU* 2.7 30.9 + - - +
60A VAL* 3.4 16.1 - - + +
64A VAL* 3.6 33.9 - - + -
68A LEU* 4.2 10.3 - - + -
322A LEU 3.1 13.1 + - - +
323A LEU* 3.3 10.8 - - + +
325A ILE* 1.3 77.2 - - - +
327A TYR* 1.3 81.4 + + - +
330A CYS* 3.0 41.3 + - + +
331A PHE* 3.1 22.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 2.7 36.0 + - + +
59A LEU* 3.0 30.1 + - + -
323A LEU* 3.1 30.8 + - + +
324A GLY* 3.9 6.7 - - - +
326A TRP* 1.3 92.8 - + - +
328A ILE* 1.3 59.6 + - + +
331A PHE* 3.4 25.8 + + + +
332A GLY 2.9 10.6 + - - -
333A CYS* 2.9 26.8 + - + -
401A MET* 4.5 5.4 - - - -
403A PRO* 3.6 39.9 - - + -
473A PRO* 3.1 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLY* 2.8 30.2 + - - +
325A ILE 4.1 1.1 - - - +
327A TYR* 1.3 75.3 - - + +
329A ASN* 1.3 67.6 + - - +
332A GLY* 3.2 22.5 - - - -
333A CYS* 3.9 18.3 - - + +
335A THR 5.9 0.9 - - - +
336A HIS* 6.3 0.2 - - + -
374A GLN* 3.6 26.8 - - + +
375A THR 3.5 17.7 - - - +
377A PRO* 3.8 38.4 - - + -
501A GLN* 4.6 4.9 - - - +
505A TRP* 3.8 20.0 - - + -
400B LYS* 4.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.0 7.4 - - - +
10A PHE* 3.8 28.7 - - + -
14A GLN* 5.0 4.2 - - - +
325A ILE* 2.7 34.3 + - - +
328A ILE* 1.3 74.1 - - - +
330A CYS* 1.3 62.4 + - - +
332A GLY* 5.4 0.4 - - - -
373A HIS* 3.9 11.1 + - - +
374A GLN* 3.1 40.8 + - - +
505A TRP* 2.8 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.6 10.1 - - - -
13A LEU* 4.5 17.5 - - - -
14A GLN* 4.6 15.3 - - - -
17A TYR* 3.3 49.5 + - + -
326A TRP* 3.0 39.0 + - + +
329A ASN* 1.3 84.4 - - - +
331A PHE* 1.3 61.6 + - + +
332A GLY 3.3 1.5 + - - -
----------------------------------------------------------
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