Contacts of the helix formed by residues 329 - 348 (chain A) in PDB entry 6B0Z
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 PRO 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.7 24.5 - - + -
327A THR 3.3 10.8 - - - +
328A ASN* 1.3 91.6 - - - +
330A ILE* 1.3 57.4 + - - +
331A ALA 3.4 2.5 - - - -
332A SER* 3.3 7.6 + - - +
333A ILE* 2.8 35.6 + - + +
373A THR* 4.2 1.1 - - + -
394A THR* 5.4 1.8 - - + +
397A PHE* 3.6 35.0 - - + -
398A MET* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.6 25.6 - - + -
290A MET* 3.7 25.1 - - + -
328A ASN* 3.1 19.4 + - - +
329A PRO* 1.3 77.2 - - - +
331A ALA* 1.3 52.6 + - - +
333A ILE* 2.9 7.2 + - + +
334A PHE* 2.7 53.3 + - + -
363A SER* 3.7 26.0 - - - +
364A ILE* 6.3 0.2 - - + -
367A ILE* 4.0 11.7 - - + -
397A PHE* 3.7 26.5 - - + -
401A LEU* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 4.5 9.0 - - - -
289A GLY 3.0 26.2 + - - +
291A MET 3.3 28.9 - - - +
292A THR* 3.9 5.9 + - - -
307A ALA* 3.7 17.1 - - + +
309A HIS* 3.8 8.7 - - + +
329A PRO 3.4 0.4 - - - -
330A ILE* 1.3 74.5 - - - +
332A SER* 1.3 62.1 + - - +
334A PHE* 3.4 3.8 + - - +
335A ALA* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 4.5 9.1 + - - +
22A ILE* 4.3 12.6 - - - +
23A TRP* 4.2 13.7 - - - -
26A ILE* 3.6 17.5 - - - -
307A ALA* 3.9 7.5 - - - +
309A HIS* 3.9 20.3 + - - -
328A ASN 5.0 0.3 + - - -
329A PRO* 3.3 12.3 + - - +
330A ILE 3.2 0.4 - - - -
331A ALA* 1.3 77.0 - - - +
333A ILE* 1.3 63.2 + - - +
335A ALA* 3.2 19.5 + - - +
336A TRP* 3.5 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.6 24.0 - - + -
30A LEU* 3.7 15.7 - - + -
329A PRO* 2.8 30.3 + - + +
330A ILE* 3.3 12.8 - - + +
332A SER* 1.3 75.7 - - - +
334A PHE* 1.3 60.5 + - + +
336A TRP* 2.9 23.7 + - + +
337A THR* 3.1 13.2 + - + +
359A LEU* 3.9 31.6 - - + -
363A SER* 4.0 13.2 - - - +
398A MET* 4.5 2.0 - - - -
401A LEU* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.7 39.7 - - + -
292A THR* 3.9 15.7 + - - +
330A ILE* 2.7 42.5 + - + +
331A ALA 3.9 2.0 - - - +
332A SER 3.3 0.2 - - - -
333A ILE* 1.3 75.0 - - + +
335A ALA* 1.3 60.7 + - - +
337A THR* 3.0 8.3 + - - -
338A ARG* 3.0 51.4 + - - +
360A GLU* 3.3 55.0 - - + -
363A SER* 3.8 19.3 - - - -
364A ILE* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 4.5 13.2 - - + -
71A VAL* 3.4 7.6 - - - +
292A THR* 4.0 3.3 + - - -
305A ALA* 3.3 19.9 - - - +
306A GLU* 3.6 35.7 - - - +
307A ALA 4.1 1.1 - - - +
331A ALA 3.1 8.6 + - - +
332A SER* 3.3 13.2 - - - +
333A ILE 3.1 0.6 - - - -
334A PHE* 1.3 77.9 - - - +
336A TRP* 1.3 60.5 + - - +
339A GLY 3.2 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.7 4.3 - - + -
12A GLU* 3.9 15.7 - - + -
23A TRP* 3.3 46.6 - + - -
26A ILE* 3.7 22.6 - - + +
27A LYS* 3.6 37.4 - - + +
31A ILE* 4.1 34.1 - - + -
32A PHE* 5.5 1.8 - + - -
37A LEU* 4.0 22.9 - - + -
39A LEU* 4.7 5.2 - - + -
71A VAL* 4.0 18.8 - - + +
332A SER 3.5 16.6 - - - -
333A ILE 2.9 9.1 + - - +
335A ALA* 1.3 76.7 - - - +
337A THR* 1.3 60.9 + - + +
339A GLY* 3.3 0.9 + - - -
340A LEU* 2.8 48.2 + - + +
359A LEU* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 3.1 15.4 + - + +
334A PHE* 3.0 16.6 + - + -
336A TRP* 1.3 75.7 - - - +
338A ARG* 1.3 54.3 + - - +
340A LEU* 4.6 2.0 - - + -
341A ALA* 2.7 38.6 + - - +
356A ALA* 3.5 28.9 - - - +
359A LEU* 3.7 31.0 - - + -
360A GLU* 2.7 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 3.2 26.6 + - - -
112A ILE* 6.0 1.0 - - - +
203A LYS* 3.7 25.4 - - - +
292A THR* 3.5 25.1 - - + +
294A VAL* 5.6 12.4 - - + +
303A VAL* 5.2 2.6 - - + +
305A ALA* 4.3 11.9 - - + -
334A PHE* 3.0 39.2 + - - +
335A ALA 4.3 1.6 - - - +
337A THR* 1.3 83.2 + - - +
339A GLY* 1.3 62.6 + - - +
341A ALA* 3.8 5.0 - - - +
342A HIS* 3.0 24.3 + - - +
360A GLU* 2.7 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.4 23.0 - - - +
70A GLY 5.0 0.7 - - - -
71A VAL* 3.9 14.8 - - - -
303A VAL* 5.2 3.4 - - - -
305A ALA* 4.1 6.6 - - - +
335A ALA 3.2 17.1 + - - -
336A TRP 3.7 2.0 - - - -
338A ARG* 1.3 77.4 - - - +
340A LEU* 1.3 57.2 + - - +
342A HIS* 3.2 4.6 + - - +
343A ARG 2.8 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.0 26.2 - - + -
31A ILE* 4.4 18.6 - - + -
35A VAL* 5.0 1.8 - - + -
37A LEU* 4.1 20.6 - - + -
71A VAL* 6.0 0.9 - - + -
336A TRP* 2.8 38.0 + - + +
337A THR* 4.0 4.3 - - + +
339A GLY* 1.3 71.9 - - - -
341A ALA* 1.3 58.0 + - - +
343A ARG* 3.2 5.1 + - - +
344A ALA* 2.8 29.8 + - - +
352A LEU* 3.5 29.9 - - + +
355A PHE* 4.2 25.4 - - + -
356A ALA* 4.3 6.7 - - + -
359A LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A THR 2.7 24.0 + - - +
338A ARG* 3.8 6.1 - - - +
340A LEU* 1.3 72.3 - - - +
342A HIS* 1.3 57.1 - - - +
344A ALA* 3.3 7.6 + - - +
345A LYS* 3.0 26.9 + - - +
353A ALA* 5.1 5.3 - - + +
356A ALA* 3.9 15.4 - - + +
357A ASN 5.8 0.2 - - - +
360A GLU* 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN 3.7 16.6 - - - -
69A VAL* 3.8 5.6 - - + -
300A GLY 4.0 16.2 - - - -
301A LYS 2.7 27.5 + - - -
303A VAL* 3.7 35.7 - - + +
338A ARG 3.0 17.6 + - - +
339A GLY* 3.6 4.5 - - - +
341A ALA* 1.3 74.2 - - - +
343A ARG* 1.3 65.8 + - - +
345A LYS* 3.2 25.5 + - - +
346A LEU* 3.1 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 3.2 27.6 - - - +
9A SER* 2.8 43.2 + - - +
10A VAL* 4.2 4.9 - - + -
67A HIS 2.9 24.9 + - - -
68A ASN* 5.0 3.2 + - - -
69A VAL* 3.5 25.4 - - + +
339A GLY 2.8 16.9 + - - +
340A LEU* 3.4 11.4 - - - +
342A HIS* 1.3 73.7 - - - +
344A ALA* 1.3 61.6 - - - +
346A LEU* 3.4 19.6 + - - +
347A ASP* 2.8 59.6 + - + +
352A LEU* 3.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU 2.8 19.2 + - - +
341A ALA 3.6 5.4 - - - +
343A ARG* 1.3 74.4 - - - +
345A LYS* 1.3 57.0 + - - +
347A ASP 3.2 0.2 + - - -
348A ASN* 2.8 28.6 + - - -
349A ASN* 3.0 38.4 + - - +
352A LEU* 3.9 6.3 - - + -
353A ALA* 3.4 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.2 38.0 + - - +
300A GLY 5.6 3.7 + - - -
341A ALA 3.0 13.8 + - - +
342A HIS* 3.2 32.1 + - - +
344A ALA* 1.3 78.0 - - - +
346A LEU* 1.3 65.6 + - + +
347A ASP 3.4 0.3 + - - -
348A ASN* 3.6 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 3.7 21.1 - - + +
69A VAL* 4.2 4.5 - - + -
300A GLY 4.9 2.5 - - - +
301A LYS* 3.7 25.8 - - + +
342A HIS* 3.1 51.8 + - + +
343A ARG* 3.8 17.9 - - - +
344A ALA 3.3 0.2 - - - -
345A LYS* 1.3 81.4 - - - +
347A ASP* 1.3 67.2 + - - +
348A ASN* 3.6 4.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
7A GLY 4.4 4.5 - - - +
8A GLY* 4.8 5.2 - - - -
9A SER 5.2 0.2 + - - -
343A ARG* 2.8 58.7 + - - +
344A ALA 3.2 2.0 + - - +
346A LEU* 1.3 81.1 - - - +
348A ASN* 1.3 73.2 + - - +
349A ASN* 4.3 14.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA 2.8 12.3 + - - -
345A LYS* 3.6 12.7 + - - +
346A LEU 3.6 4.0 + - - +
347A ASP* 1.3 77.8 + - - +
349A ASN* 1.3 57.7 + - - +
350A LYS* 3.4 13.7 + - + +
----------------------------------------------------------
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