Contacts of the helix formed by residues 327 - 344 (chain A) in PDB entry 5X61
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 327 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLY 4.3 1.0 + - - -
316A PHE* 3.9 19.3 + - - +
326A GLY* 1.3 73.8 - - - +
328A ALA* 1.3 64.7 + - - +
329A GLY 3.2 2.7 - - - -
330A LEU* 2.9 38.7 + - + +
331A PHE* 3.0 27.6 + - + -
452A VAL 4.6 0.3 - - - +
453A PRO* 3.5 3.7 - - - +
454A VAL* 2.7 52.4 + - - +
456A ASP* 3.8 15.4 + - - +
459A PHE* 4.1 8.1 - - - +
460A LEU* 4.6 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE 3.6 24.9 - - - +
207A ARG 3.9 3.6 - - - +
208A HIS* 4.4 10.5 - - + +
310A ARG* 3.8 24.6 + - - +
314A LEU 4.6 0.2 - - - +
315A GLY* 3.1 16.5 + - - +
316A PHE* 5.4 0.2 - - - -
326A GLY 3.2 5.1 - - - -
327A ASN* 1.3 74.9 - - - +
329A GLY* 1.3 58.6 + - - +
331A PHE* 3.1 5.3 + - - +
332A ASP* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 3.4 4.5 - - - +
310A ARG 3.4 25.4 - - - -
315A GLY* 2.7 17.3 + - - -
316A PHE* 3.9 6.9 - - - -
327A ASN 3.2 0.2 - - - -
328A ALA* 1.3 72.8 - - - +
330A LEU* 1.3 60.3 + - - +
332A ASP* 3.3 12.5 - - - +
333A GLN* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.3 0.7 - - + -
316A PHE* 3.6 19.9 - - + -
327A ASN* 2.9 38.5 + - + +
329A GLY* 1.3 72.7 - - - +
331A PHE* 1.3 61.6 + - - +
332A ASP 3.2 0.2 - - - -
333A GLN* 3.2 27.1 + - - +
334A ASN* 2.8 27.3 + - - +
365A SER* 4.1 10.5 - - - +
368A LEU* 3.8 21.5 - - + -
369A HIS* 4.1 0.9 - - + -
453A PRO* 3.8 16.2 - - + -
459A PHE* 3.7 38.0 - - + -
460A LEU* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A HIS* 3.1 42.8 - + + +
209A PRO* 3.4 22.0 - - + +
327A ASN* 3.0 28.0 + - + -
328A ALA 3.6 3.8 - - - +
330A LEU* 1.3 73.7 - - - +
332A ASP* 1.3 60.1 + - - +
334A ASN* 3.7 12.1 + - - +
335A LEU* 2.9 30.5 + - - +
338A ARG* 5.1 0.7 + - - -
374A LEU* 3.5 22.9 - - + -
456A ASP* 3.6 13.9 - - - -
458A ALA* 3.7 22.0 - - + -
459A PHE* 3.6 24.5 - + + -
374B LEU* 4.1 20.2 - - + -
458B ALA* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 3.2 27.5 + - - +
209A PRO* 3.2 15.8 - - - +
256A LEU* 3.6 11.5 - - - +
309A TYR* 3.9 7.2 - - + -
310A ARG* 2.8 65.3 + - - +
328A ALA 2.8 14.3 + - - +
329A GLY 3.3 9.6 - - - +
331A PHE* 1.3 77.3 - - - +
333A GLN* 1.3 62.6 + - - +
335A LEU* 3.8 0.2 - - - +
336A ALA* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 3.7 11.0 - - + +
307A LEU* 3.9 20.5 - - + +
309A TYR* 3.5 42.7 - - + -
329A GLY 3.1 12.0 + - - +
330A LEU* 3.4 18.2 - - - +
332A ASP* 1.3 77.7 - - - +
334A ASN* 1.3 58.1 + - - +
336A ALA* 3.2 4.7 + - - +
337A LEU* 2.9 33.7 + - - +
365A SER* 3.0 35.3 + - - -
369A HIS* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 2.8 16.2 + - - +
331A PHE* 3.7 20.6 + - + +
332A ASP 3.3 0.2 - - - -
333A GLN* 1.3 76.0 - - - +
335A LEU* 1.3 61.5 + - - +
337A LEU* 3.1 8.8 + - - +
338A ARG* 3.0 54.7 + - - +
369A HIS* 4.1 6.5 - - - -
374A LEU* 3.9 13.9 - - - +
375A SER* 3.3 26.7 + - - -
378A LEU* 3.4 14.1 - - - +
459A PHE* 4.3 12.3 - - + -
374B LEU* 4.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 3.6 26.0 - - + +
197A ALA* 3.7 19.7 - - + -
209A PRO* 3.7 20.4 - - + +
210A ARG 3.8 12.3 - - - +
211A PRO* 4.5 12.8 - - + -
331A PHE 2.9 17.4 + - - +
332A ASP 3.8 4.0 - - - +
334A ASN* 1.3 75.1 - - - +
336A ALA* 1.3 57.3 + - - +
338A ARG* 3.2 34.5 + - + +
339A TRP* 3.0 26.1 + - + +
373B ALA 5.9 0.2 - - - +
377B ASP* 4.4 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TYR* 3.7 22.6 - - + -
258A ILE* 3.8 17.4 - - + +
274A LEU* 5.6 0.2 - - - -
307A LEU* 3.8 22.9 - - + -
332A ASP 3.1 14.6 + - - +
333A GLN 3.2 9.4 + - - +
335A LEU* 1.3 77.7 - - - +
337A LEU* 1.3 59.5 + - - +
339A TRP* 3.4 4.5 + - - +
340A VAL* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.5 34.3 - - + -
276A ILE* 5.2 2.7 - - + -
307A LEU* 4.8 3.1 - - + -
333A GLN 2.9 17.4 + - - +
334A ASN* 3.1 7.2 + - - +
336A ALA* 1.3 75.6 - - - +
338A ARG* 1.3 58.4 + - - +
340A VAL* 3.2 7.8 + - - +
341A ARG* 3.0 27.2 + - - +
354A VAL* 5.4 1.8 - - + -
356A LEU* 3.6 31.4 - - + -
369A HIS* 4.0 27.1 - - + +
375A SER* 4.1 13.9 - - - -
378A LEU* 3.8 26.5 - - + +
379A PHE* 4.5 4.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
209A PRO* 6.1 0.2 - - - +
331A PHE* 5.1 1.2 + - - -
334A ASN* 3.0 36.2 + - - +
335A LEU* 3.2 38.7 + - + +
337A LEU* 1.3 72.9 - - - +
339A TRP* 1.3 64.8 + - - +
341A ARG* 3.4 6.6 - - + +
342A ASP* 3.1 34.3 + - - +
378A LEU* 3.7 27.1 - - + -
338B ARG* 4.0 34.1 - - - +
373B ALA 5.3 1.4 + - - -
374B LEU* 3.5 47.8 + - - +
377B ASP* 5.1 11.9 + - - +
378B LEU* 5.6 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 4.0 15.6 + - + -
171A ASP* 4.2 7.2 + - - -
172A LYS* 6.1 4.1 - - + +
194A ILE* 3.7 40.6 - - + +
195A PRO 4.8 4.6 + - - -
196A TYR* 4.2 19.7 - - + +
215A TRP* 6.0 1.6 - - - -
258A ILE* 3.7 29.8 - - + -
260A VAL* 4.1 15.5 - - + -
335A LEU* 3.0 12.7 + - + +
336A ALA* 3.4 9.4 - - - +
337A LEU 3.2 0.2 - - - -
338A ARG* 1.3 77.1 - - - +
340A VAL* 1.3 70.3 + - + +
342A ASP* 3.1 2.7 + - - -
343A ASN* 2.9 68.2 + - + +
344A ILE* 4.8 4.5 - - + -
347A PHE* 3.5 24.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 4.7 2.5 - - + -
272A VAL* 4.4 4.3 - - + -
274A LEU* 3.7 27.6 - - + -
305A VAL* 4.0 16.4 - - + -
336A ALA* 3.1 14.7 + - + +
337A LEU 3.2 7.4 + - - +
339A TRP* 1.3 92.6 - - + +
341A ARG* 1.3 62.1 + - - +
344A ILE* 2.9 54.5 + - + +
354A VAL* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU 3.0 12.5 + - - +
338A ARG* 3.4 15.0 - - + +
340A VAL* 1.3 79.4 - - - +
342A ASP* 1.3 67.5 + - - +
343A ASN 3.6 0.2 + - - -
351A PRO* 3.5 56.4 + - - +
352A SER* 5.0 5.3 - - - +
377A ASP* 3.1 31.5 + - - +
378A LEU* 4.1 24.9 + - + +
171B ASP* 3.7 18.6 + - - +
342B ASP* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP* 4.7 7.6 - - + +
338A ARG* 3.1 19.4 + - - +
339A TRP* 3.1 2.5 + - - -
341A ARG* 1.3 86.3 - - - +
343A ASN* 1.3 69.8 + - - +
345A HIS* 6.5 0.2 - - - -
346A ARG* 3.2 21.8 + - - -
341B ARG* 3.1 41.4 + - - +
342B ASP* 5.0 4.9 - - - +
377B ASP* 4.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A THR* 3.4 5.9 - - + -
171A ASP* 2.7 44.7 + - - +
339A TRP* 2.9 60.9 + - + +
340A VAL 3.4 0.2 + - - -
342A ASP* 1.3 85.7 - - - +
344A ILE* 1.3 65.9 + - - +
345A HIS* 3.1 5.1 + - - -
346A ARG* 3.1 36.3 + - - +
347A PHE* 3.3 14.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 4.2 14.4 - - + -
272A VAL* 3.7 24.9 - - + -
303A ILE* 4.0 10.3 - - + -
305A VAL* 3.6 29.2 - - + -
339A TRP* 4.8 5.4 - - + -
340A VAL* 2.9 39.3 + - + +
341A ARG 4.7 0.4 + - - -
343A ASN* 1.3 77.6 - - - +
345A HIS* 1.3 61.6 + - - +
346A ARG 3.3 0.2 - - - -
347A PHE* 3.3 16.0 + - + +
348A GLY 3.3 0.3 + - - -
349A GLY* 2.8 28.5 + - - -
351A PRO* 3.8 29.2 - - + -
354A VAL* 4.9 0.2 - - + -
----------------------------------------------------------
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