Contacts of the helix formed by residues 315 - 330 (chain J) in PDB entry 5G04
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 LYS 315 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309J TYR* 3.6 45.2 - - + +
312J VAL* 4.1 17.3 - - + -
313J GLY 2.9 5.4 + - - +
314J HIS* 1.3 82.1 + - + +
316J ASN* 1.3 57.6 + - - +
317J GLU* 3.3 8.9 + - - +
318J HIS* 2.9 43.4 + - + +
319J ALA* 2.9 13.2 + - - +
26M TYR 6.0 0.4 - - - +
28M ASP* 3.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 316 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309J TYR 3.9 2.6 + - - -
310J LEU* 3.2 44.2 + - - +
313J GLY* 4.9 1.6 - - - -
314J HIS* 3.2 17.9 + - - +
315J LYS* 1.3 74.8 - - - +
317J GLU* 1.3 65.0 + - - +
319J ALA* 3.8 2.6 - - - +
320J ARG* 2.9 52.4 + - - +
343J SER* 4.4 6.1 - - - +
346J VAL* 3.9 22.4 - - - +
347J GLU* 5.1 4.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314J HIS 4.9 5.5 + - - +
315J LYS* 5.1 7.3 + - - +
316J ASN* 1.3 76.7 - - - +
318J HIS* 1.3 91.5 + - - +
320J ARG* 4.1 20.1 - - - +
321J ARG* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 318 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309J TYR* 4.2 19.1 - + + -
315J LYS* 2.9 36.9 + - + +
317J GLU* 1.3 101.6 + - - +
319J ALA* 1.3 64.1 + - - +
321J ARG* 3.0 30.5 + - - +
322J TYR* 3.0 45.3 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306J GLY* 3.3 29.0 - - - +
309J TYR* 3.8 14.3 - - + +
310J LEU* 3.6 26.7 - - + +
315J LYS 2.9 8.7 + - - +
316J ASN* 3.8 7.2 - - - +
318J HIS* 1.3 74.7 - - - +
320J ARG* 1.3 64.2 + - - +
322J TYR* 3.3 2.1 + - - -
323J LEU* 2.9 31.0 + - + +
343J SER* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316J ASN* 2.9 41.0 + - - +
317J GLU* 4.1 16.8 - - - +
319J ALA* 1.3 77.1 - - - +
321J ARG* 1.3 53.5 + - - +
323J LEU* 3.8 3.9 - - - +
324J SER* 2.7 38.6 + - - -
340J TYR* 3.2 35.4 - - + +
343J SER* 3.7 20.1 + - - +
344J PHE* 3.3 36.9 - - + -
347J GLU* 3.9 23.8 - - - +
349J GLU* 4.3 8.7 + - - -
352J GLN* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317J GLU* 3.3 16.2 + - - +
318J HIS* 3.0 32.5 + - - +
320J ARG* 1.3 79.5 - - - +
322J TYR* 1.3 65.9 + - + +
324J SER* 3.4 8.8 - - - -
325J LYS* 3.2 22.2 + - - +
33M LEU* 4.8 13.5 - - - +
36M LEU* 3.9 37.2 - - + +
37M PRO* 3.9 20.8 + - + +
39M PRO* 4.5 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 322 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J TRP* 3.4 43.5 - + + +
305J VAL* 3.6 14.4 - - + -
306J GLY* 3.9 9.9 - - - +
309J TYR* 3.6 30.7 + + - -
318J HIS* 3.0 47.1 + + - -
319J ALA 4.7 0.2 - - - -
321J ARG* 1.3 77.5 + - + +
323J LEU* 1.3 61.5 + - - +
324J SER 3.2 1.1 - - - -
325J LYS* 3.3 5.5 + - - +
326J ALA* 3.0 26.9 + - - +
29M VAL 5.1 0.7 + - - -
31M ILE* 3.7 27.0 - - + +
33M LEU* 5.1 2.9 - - - +
36M LEU* 3.5 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J PHE* 3.8 36.8 - - + +
306J GLY* 3.7 28.0 - - - +
307J CYS* 4.3 0.7 - - - +
310J LEU* 4.5 8.1 - - + -
319J ALA* 2.9 36.8 + - + +
320J ARG* 3.8 7.9 - - - +
322J TYR* 1.3 72.0 - - - +
324J SER* 1.3 56.0 + - - +
326J ALA* 3.1 3.3 + - - +
327J THR* 2.8 39.6 + - - +
336J ALA* 4.1 21.9 - - + +
339J ALA* 4.2 16.2 - - + -
340J TYR* 4.4 14.8 - - + +
343J SER* 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 324 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320J ARG 2.7 25.0 + - - -
321J ARG* 3.4 8.8 - - - -
323J LEU* 1.3 77.9 - - - +
325J LYS* 1.3 56.7 + - - +
327J THR* 3.3 9.3 - - - +
328J THR* 2.9 43.2 + - - +
340J TYR* 3.9 21.3 + - - -
37M PRO* 6.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J TRP* 3.4 30.1 - - + +
321J ARG 3.2 4.1 + - - +
322J TYR* 3.5 10.1 - - - +
323J LEU 3.3 0.2 - - - -
324J SER* 1.3 80.8 - - - +
326J ALA* 1.3 56.3 + - - +
328J THR* 3.5 9.4 + - - +
329J LEU* 3.1 55.2 + - - +
35M GLU* 3.0 51.9 + - - +
36M LEU* 3.7 27.1 - - + -
37M PRO* 4.3 10.2 - - + +
49M SER* 5.0 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J PRO* 3.5 32.6 - - + +
302J TRP* 3.6 11.7 - - + -
303J PHE* 3.7 9.2 - - - +
322J TYR 3.0 13.7 + - - +
323J LEU* 3.1 7.6 + - - +
325J LYS* 1.3 72.8 - - - +
327J THR* 1.3 65.9 + - - +
329J LEU* 3.5 5.2 + - - +
330J GLU 3.1 19.4 + - - +
333J TYR* 4.8 1.1 - - + +
336J ALA* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 327 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323J LEU 2.8 21.6 + - - +
324J SER* 3.3 16.4 - - - +
326J ALA* 1.3 75.2 - - - +
328J THR* 1.3 62.9 + - + +
330J GLU 3.0 4.7 - - - -
331J LYS* 2.8 39.8 + - - +
333J TYR* 4.6 2.1 + - - -
336J ALA* 4.4 12.8 - - - +
337J TRP* 2.8 61.5 + - + -
340J TYR* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324J SER* 2.9 32.0 + - - +
325J LYS* 3.5 15.2 + - - +
327J THR* 1.3 80.1 - - + +
329J LEU* 1.3 67.9 + - - +
331J LYS* 4.3 27.4 + - - +
37M PRO* 5.2 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J PRO 4.8 0.4 - - - +
297J SER* 3.0 33.7 - - - +
298J ASN 4.7 0.4 - - - +
299J PRO* 4.1 20.9 - - + -
302J TRP* 5.0 2.0 - - + -
325J LYS* 3.1 48.0 + - - +
326J ALA* 3.7 7.0 - - - +
327J THR 3.3 0.2 - - - -
328J THR* 1.3 79.8 + - - +
330J GLU* 1.3 60.3 + - + +
331J LYS 4.2 0.5 + - - -
35M GLU* 4.1 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J HIS* 4.9 11.8 - - + -
299J PRO* 3.7 32.0 - - + +
326J ALA 3.1 4.9 + - - +
327J THR* 3.0 6.9 - - - +
329J LEU* 1.3 81.8 - - + +
331J LYS* 1.4 83.5 + - - +
332J THR* 3.9 7.4 + - - +
333J TYR* 3.1 32.7 + - + +
----------------------------------------------------------
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