Contacts of the helix formed by residues 321 - 340 (chain S) in PDB entry 5L4K
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 ALA 321 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99S ARG* 5.4 4.4 - - - +
316S ALA* 4.1 9.4 - - + -
317S PRO* 3.6 12.8 - - + +
320S THR* 1.3 80.4 - - - +
322S VAL* 1.3 72.0 + - - +
323S GLY 3.0 3.3 + - - -
324S PHE* 3.1 13.9 + - - +
325S LYS* 3.3 34.4 + - + +
19Y PHE* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320S THR* 4.8 12.1 - - + -
321S ALA* 1.3 81.0 - - - +
323S GLY* 1.3 60.4 + - - +
325S LYS* 3.6 4.1 + - - +
326S GLN* 2.9 34.4 + - + +
352S SER* 5.5 4.9 - - - -
353S LEU* 5.5 4.7 - - + +
24Y ALA* 3.7 21.8 - - + -
25Y GLU 3.9 9.6 - - - +
26Y ASP* 3.9 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 323 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321S ALA 3.4 0.8 - - - -
322S VAL* 1.3 76.3 - - - +
324S PHE* 1.3 66.5 + - - +
326S GLN* 2.8 16.8 + - - +
327S THR* 2.9 14.7 + - - +
22Y PHE* 4.1 8.7 - - - -
23Y PRO 3.3 27.2 - - - +
24Y ALA* 3.8 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286S ALA* 3.5 37.0 - - + -
287S ARG* 4.1 15.0 - - + -
290S TYR* 3.9 13.7 - + + -
291S TYR* 6.0 0.4 - + - -
312S ALA* 4.9 7.9 - - + -
313S LEU* 6.1 0.2 - - - -
316S ALA* 4.2 15.3 - - + -
321S ALA* 3.1 9.0 + - + +
323S GLY* 1.3 72.3 - - - +
325S LYS* 1.3 65.3 + - + +
327S THR* 2.9 24.8 - - - +
328S VAL* 3.0 31.0 + - + +
19Y PHE* 3.6 48.2 - + + +
21Y GLU* 4.7 0.2 - - - -
22Y PHE* 3.6 36.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313S LEU* 3.7 34.1 - - + +
316S ALA* 3.0 28.8 + - + +
317S PRO 2.4 32.7 + - - -
318S GLN* 4.0 14.1 + - - +
320S THR 6.0 0.2 - - - -
321S ALA* 3.3 14.5 + - + +
322S VAL* 3.9 7.0 - - - +
324S PHE* 1.3 79.0 - - + +
326S GLN* 1.3 63.6 + - - +
327S THR 3.0 1.6 + - - -
328S VAL* 3.2 11.8 - - + +
329S HIS* 3.0 31.2 + - + +
353S LEU* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322S VAL* 2.9 20.6 + - + +
323S GLY* 2.8 13.5 + - - +
325S LYS* 1.3 72.2 - - - +
327S THR* 1.3 56.0 + - - -
329S HIS* 4.0 4.9 - - - +
330S LYS* 3.0 35.1 + - - +
353S LEU* 4.2 28.8 - - + +
356S SER* 3.0 34.3 + - - -
357S LEU* 4.3 3.1 - - + +
23Y PRO 4.7 3.4 + - - -
24Y ALA* 3.9 8.7 - - - +
25Y GLU* 3.1 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 327 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S TYR* 3.7 16.8 + - + +
323S GLY 2.9 12.4 + - - +
324S PHE* 2.9 27.6 - - - +
326S GLN* 1.3 75.9 - - - +
328S VAL* 1.3 75.6 + - + +
329S HIS 2.9 1.6 - - - -
330S LYS* 2.8 36.8 + - - +
331S LEU* 3.1 10.2 + - - +
389S ASP* 5.5 1.0 + - - -
22Y PHE* 4.2 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S TYR* 3.8 32.3 - - + -
309S MET* 4.2 9.1 - - - +
312S ALA* 5.1 3.8 - - + -
313S LEU* 3.4 38.6 - - + +
324S PHE* 3.0 39.8 + - + +
325S LYS* 3.2 14.4 - - - +
327S THR* 1.3 79.4 - - + +
329S HIS* 1.3 59.8 + - - +
331S LEU* 3.3 1.8 + - - +
332S LEU* 2.8 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 329 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313S LEU* 3.3 41.5 - - + +
325S LYS* 3.0 25.7 + - + +
326S GLN 4.0 6.1 - - - +
327S THR 2.9 1.0 + - - -
328S VAL* 1.3 74.3 - - - +
330S LYS* 1.3 64.2 + - - +
331S LEU 2.8 5.0 + - - -
332S LEU* 3.0 10.5 + - + +
333S ILE* 2.9 34.6 + - + +
347S GLN* 4.6 17.5 - - + +
350S GLN* 3.1 33.7 + - - -
353S LEU* 3.8 16.8 - - + -
357S LEU* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326S GLN* 3.0 46.3 + - - +
327S THR* 2.8 31.1 + - - +
329S HIS* 1.3 72.4 - - - +
331S LEU* 1.3 59.4 + - - +
333S ILE* 4.5 2.9 - - - +
334S VAL* 3.9 9.7 + - - +
356S SER* 4.4 12.5 + - - +
357S LEU* 3.9 13.0 - - + +
360S TYR* 3.4 57.1 + - + +
389S ASP* 4.0 18.8 - - - +
391S THR* 4.5 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S TYR* 3.8 16.2 - - + +
294S ARG* 3.4 39.5 - - - +
297S ALA* 5.0 2.0 - - + -
309S MET* 3.3 32.5 - - + -
327S THR 3.1 8.8 + - - +
328S VAL 3.8 5.8 - - - +
329S HIS 2.8 1.8 + - - -
330S LYS* 1.3 75.7 - - - +
332S LEU* 1.3 65.5 + - - +
333S ILE 3.2 1.6 - - - -
334S VAL* 2.9 6.7 + - + -
335S VAL* 2.9 34.6 + - + +
391S THR* 4.8 8.5 - - + -
394S LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306S ARG* 4.6 3.4 - - + +
309S MET* 3.7 21.6 - - + +
310S THR* 3.7 28.9 - - + +
313S LEU* 4.2 26.0 - - + -
328S VAL* 2.8 21.7 + - + +
329S HIS* 3.8 10.1 - - - +
331S LEU* 1.3 71.5 - - - +
333S ILE* 1.3 63.5 + - + +
335S VAL* 3.1 15.7 - - + +
336S GLU* 3.0 43.2 + - + +
347S GLN* 3.7 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329S HIS* 2.9 30.3 + - + +
330S LYS* 4.6 5.6 - - - +
332S LEU* 1.3 75.9 - - - +
334S VAL* 1.3 59.6 + - + +
336S GLU* 4.0 2.3 + - - +
337S LEU* 3.2 27.2 + - + +
343S PRO* 4.3 14.7 - - + +
347S GLN* 3.3 26.0 - - + +
348S PHE* 3.5 39.5 - - + -
357S LEU* 4.1 23.8 - - + -
360S TYR* 4.3 20.2 - - + -
364S THR* 4.4 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330S LYS 3.9 5.6 + - - +
331S LEU* 2.9 11.0 + - + +
333S ILE* 1.3 79.2 - - - +
335S VAL* 1.3 61.8 + - + +
336S GLU 3.3 0.4 - - - -
337S LEU* 3.7 10.0 - - + +
338S LEU* 2.9 33.8 + - + +
360S TYR* 3.9 33.0 - - + -
363S LEU* 4.8 6.3 - - + -
391S THR* 4.7 4.3 - - + -
394S LEU* 4.2 35.0 - - + +
395S ILE* 4.6 14.4 - - + -
398S LEU* 5.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297S ALA* 4.5 14.6 - - + -
302S TYR* 4.2 9.0 - - + +
305S ALA* 4.8 8.7 - - + -
306S ARG* 4.2 20.2 - - + +
309S MET* 4.1 12.1 - - + -
331S LEU* 2.9 38.7 + - + +
332S LEU* 3.1 34.5 - - + +
334S VAL* 1.3 74.8 - - + +
336S GLU* 1.3 61.5 + - - +
338S LEU* 3.9 8.1 - - + +
339S LEU* 2.9 30.3 + - - +
394S LEU* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306S ARG* 3.4 41.8 + - + +
310S THR* 5.5 0.3 + - - -
332S LEU* 3.0 29.4 + - + +
333S ILE 4.3 3.6 - - - +
335S VAL* 1.3 75.2 - - - +
337S LEU* 1.3 66.1 + - - +
339S LEU* 3.1 7.9 + - - +
340S GLY 3.0 6.2 + - - -
341S GLU* 2.9 32.5 + - + +
342S ILE 3.2 8.3 - - - +
343S PRO* 3.1 32.2 - - + +
344S ASP* 4.4 5.5 + - - +
347S GLN* 3.9 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333S ILE* 3.2 22.1 + - + +
334S VAL* 3.4 12.5 + - + +
335S VAL 3.4 0.4 - - - -
336S GLU* 1.3 77.0 - - - +
338S LEU* 1.3 64.1 + - - +
340S GLY* 2.9 13.9 + - - -
341S GLU 3.4 7.3 + - - +
342S ILE* 4.6 5.4 - - + -
343S PRO* 3.8 23.8 - - + -
360S TYR* 6.4 0.2 - - + -
363S LEU* 4.7 6.7 - - + -
364S THR* 4.1 26.0 - - + +
367S VAL* 3.7 35.2 - - + +
398S LEU* 3.9 28.6 - - + +
401S ASN* 3.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297S ALA* 5.2 1.1 - - + +
302S TYR* 3.1 53.5 - - + +
334S VAL* 2.9 24.2 + - + +
335S VAL* 3.9 7.9 - - + +
337S LEU* 1.3 72.1 - - - +
339S LEU* 1.3 62.6 + - - +
394S LEU* 4.5 24.2 - - + +
397S ARG* 3.9 36.1 - - + +
398S LEU* 3.5 19.1 - - + +
401S ASN* 2.4 29.0 + - - +
404S LYS* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302S TYR* 3.6 43.3 - - + +
303S SER* 4.3 8.1 - - - +
306S ARG* 3.7 30.5 - - + +
335S VAL 2.9 17.7 + - - +
336S GLU* 3.1 5.8 + - - +
338S LEU* 1.3 76.1 - - - +
340S GLY* 1.3 57.2 + - - +
341S GLU* 3.5 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337S LEU 2.9 13.5 + - - -
338S LEU 3.1 1.5 + - - -
339S LEU* 1.3 77.4 - - - +
341S GLU* 1.3 68.4 + - - +
342S ILE* 6.2 0.2 - - - -
401S ASN* 4.7 5.8 - - - -
408S ARG* 4.1 19.0 + - - -
----------------------------------------------------------
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