Contacts of the helix formed by residues 383 - 404 (chain A) in PDB entry 1ULH
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 LEU 383 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 3.2 27.6 - - - +
352A SER* 3.9 12.3 - - - -
353A PHE* 4.1 10.3 - - + +
356A LEU* 3.5 22.9 - - + -
369A ILE* 3.4 30.3 - - + -
373A TYR* 3.5 32.5 - - + +
378A MET* 3.8 17.2 - - - +
379A LEU 3.4 8.9 + - - +
380A THR* 4.9 4.0 - - + +
382A GLU* 1.3 81.0 - - - +
384A LYS* 1.3 64.2 + - + +
386A ALA* 3.1 19.7 - - + +
387A LEU* 3.3 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 3.0 30.9 + - + +
326A ASN* 3.2 37.6 + - - +
327A LYS 5.4 0.2 - - - -
328A HIS 5.3 0.2 - - - +
329A ALA* 4.1 16.6 + - - +
330A PHE 5.0 7.0 + - - -
331A SER* 5.5 2.7 - - - -
335A ASP* 5.4 1.4 + - - -
350A ASP* 5.9 0.7 - - - -
352A SER* 3.7 24.0 - - - +
380A THR* 3.6 26.7 - - + +
381A GLY* 3.7 17.9 - - - +
382A GLU 3.3 0.2 - - - -
383A LEU* 1.3 74.4 - - + +
385A LYS* 1.3 57.5 + - - +
386A ALA 2.9 10.1 + - - -
387A LEU* 3.0 19.4 + - - +
388A ILE* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASN* 5.9 0.7 - - - +
381A GLY 3.2 15.6 + - - +
382A GLU* 3.7 26.0 - - - +
384A LYS* 1.3 77.6 - - - +
386A ALA* 1.3 56.0 + - - +
388A ILE* 3.7 20.1 - - + +
389A GLU* 2.6 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 4.3 4.8 - - + +
360A LEU* 5.2 1.3 - - + +
365A LYS* 5.4 9.9 + - - +
369A ILE* 4.7 20.0 - - + -
378A MET* 5.8 3.6 - - + -
382A GLU 3.5 12.3 + - - +
383A LEU* 3.1 17.7 + - - +
384A LYS 2.9 0.6 - - - -
385A LYS* 1.3 79.6 - - - +
387A LEU* 1.3 57.5 + - - +
389A GLU* 3.6 16.0 + - - +
390A VAL* 3.1 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 4.2 14.1 - - + -
351A VAL* 6.1 0.2 - - + -
352A SER* 3.6 33.9 - - - +
355A TYR* 3.4 40.2 - - + +
356A LEU* 3.4 30.0 - - + +
359A PHE* 5.7 0.7 - - + -
383A LEU 3.3 5.8 + - - +
384A LYS* 3.0 8.7 + - - +
386A ALA* 1.3 75.5 - - - +
388A ILE* 1.3 56.3 + - - +
389A GLU 3.1 1.8 - - - -
390A VAL* 2.7 28.4 + - + +
391A LEU* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 4.8 1.8 - - + -
322A LYS* 4.1 20.0 - - + +
325A VAL* 3.3 22.9 - - + -
326A ASN* 3.5 28.5 - - - +
384A LYS 3.0 12.8 + - - +
385A LYS* 3.7 24.2 - - + +
387A LEU* 1.3 76.8 - - - +
389A GLU* 1.3 58.3 + - + +
391A LEU* 4.5 7.9 - - - +
392A GLN* 3.1 69.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 5.6 4.0 + - - -
385A LYS* 2.6 47.9 + - - +
386A ALA* 3.6 13.3 + - - +
387A LEU 3.1 0.8 - - - -
388A ILE* 1.3 77.3 - - + +
390A VAL* 1.3 60.1 + - + +
392A GLN* 4.8 5.4 - - - +
393A PRO* 3.2 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 4.0 10.3 - - + -
359A PHE* 3.4 44.4 - - + +
360A LEU* 3.3 29.2 - - + +
365A LYS* 6.2 0.2 - - - -
386A ALA 3.1 20.2 - - - +
387A LEU* 2.7 10.3 + - + +
389A GLU* 1.3 82.8 - - + +
391A LEU* 1.3 63.3 + - + +
393A PRO* 3.4 4.7 - - - +
394A LEU* 3.2 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.3 11.2 - - + -
312A ILE* 4.0 17.0 - - + -
321A ILE* 4.0 15.5 - - + -
325A VAL* 3.9 27.8 - - + -
355A TYR* 4.4 7.4 - - + -
359A PHE* 4.0 20.0 - - + -
387A LEU* 2.9 36.1 + - + +
388A ILE* 4.2 2.0 - - - +
390A VAL* 1.3 73.1 - - - +
392A GLN* 1.3 55.5 + - - +
393A PRO 3.1 1.8 - - - -
394A LEU* 2.6 46.2 + - + -
395A ILE* 2.7 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 2.9 43.2 + - + +
319A LYS* 5.1 3.2 - - - +
321A ILE* 4.0 20.1 - - + +
322A LYS* 4.0 6.3 - - - +
388A ILE* 3.1 42.7 + - + +
389A GLU* 4.8 4.3 + - - +
391A LEU* 1.3 77.1 - - - +
393A PRO* 1.4 61.4 - - + +
396A ALA* 3.1 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLU* 3.2 30.1 - - - +
390A VAL* 3.4 7.0 - - - +
391A LEU 3.4 4.0 - - - -
392A GLN* 1.4 93.1 - - + +
394A LEU* 1.3 58.1 + - - +
396A ALA* 5.0 2.0 - - + -
397A GLU* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.5 32.3 - - + -
127A LEU* 4.5 12.1 - - + -
131A ILE* 5.1 6.1 - - + -
359A PHE* 3.7 35.9 - - + +
390A VAL* 3.2 15.0 + - + +
391A LEU* 2.6 23.5 + - + +
393A PRO* 1.3 71.9 - - - +
395A ILE* 1.3 67.3 + - + +
397A GLU* 3.7 4.6 - - - +
398A HIS* 3.1 20.8 + - - +
401A ARG* 5.2 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.7 6.5 - - + -
312A ILE* 3.6 27.6 - - + +
313A PHE 3.9 7.2 - - - +
314A LEU* 3.6 31.2 - - + +
316A ASP 3.8 9.9 - - - +
317A THR 4.7 0.4 - - - +
321A ILE* 3.5 26.2 - - + -
391A LEU* 2.7 25.7 + - + +
394A LEU* 1.3 78.7 - - + +
396A ALA* 1.3 58.9 + - - +
398A HIS* 2.6 36.9 + - - +
399A GLN* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR 6.1 1.3 - - - +
318A ALA* 6.2 4.0 - - + -
321A ILE* 5.3 0.8 - - + +
392A GLN 3.1 20.9 + - - +
393A PRO* 5.0 1.1 - - + -
395A ILE* 1.3 78.6 - - - +
397A GLU* 1.3 60.6 + - - +
399A GLN* 3.3 19.6 + - - +
400A ALA* 3.1 21.7 + - - +
403A LYS* 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PRO 3.1 22.4 + - - +
394A LEU* 3.4 4.2 + - - +
395A ILE 3.0 1.0 + - - -
396A ALA* 1.3 74.8 - - - +
398A HIS* 1.3 66.3 + - - +
400A ALA* 3.5 10.3 + - - +
401A ARG* 3.0 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 4.5 8.6 - - + +
174A ASP* 3.0 52.3 + - + -
177A ALA* 3.6 16.9 + - + +
178A CYS* 4.5 9.8 - - - -
314A LEU* 3.2 45.9 - - + +
394A LEU* 3.1 12.0 + - + +
395A ILE* 2.6 21.7 + - - +
397A GLU* 1.3 71.8 - - - +
399A GLN* 1.3 59.9 + - - -
401A ARG* 3.0 19.3 + - - +
402A ARG* 2.9 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU 2.8 28.7 + - - +
315A THR* 3.7 7.0 + - - +
316A ASP 2.9 27.4 + - - +
317A THR* 4.9 4.1 - - - +
395A ILE* 3.2 17.8 - - - +
396A ALA* 3.5 18.1 - - - +
398A HIS* 1.3 78.4 - - + +
400A ALA* 1.3 59.1 + - - +
402A ARG* 3.5 10.0 + - - +
403A LYS* 3.1 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA 3.1 15.3 + - - +
397A GLU* 3.8 13.0 - - - +
398A HIS 3.1 0.2 - - - -
399A GLN* 1.3 74.2 - - - +
401A ARG* 1.3 66.3 + - - +
403A LYS* 3.0 30.3 + - + +
404A GLU* 3.4 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 5.9 2.2 - - - +
177A ALA* 3.4 33.0 + - + +
178A CYS* 4.6 14.3 + - - +
179A GLY* 5.7 2.2 - - - -
394A LEU* 5.2 5.3 + - - +
397A GLU* 3.0 51.5 + - - +
398A HIS* 3.0 17.2 + - - +
400A ALA* 1.3 77.2 - - - +
402A ARG* 1.3 60.4 + - - +
404A GLU* 3.4 21.0 + - - +
405A VAL* 3.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 4.5 10.5 + - - -
170A GLU* 3.0 34.8 + - - +
173A LYS* 3.3 52.3 - - + +
174A ASP* 3.6 29.0 + - - +
177A ALA* 3.7 12.1 - - + +
398A HIS* 2.9 18.0 + - - +
399A GLN* 3.7 9.6 - - - +
400A ALA 3.1 0.2 - - - -
401A ARG* 1.3 74.0 - - - +
403A LYS* 1.3 64.2 + - - +
404A GLU 3.2 0.7 - - - -
405A VAL* 3.4 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA 5.4 0.6 + - - -
399A GLN* 3.1 47.2 + - - +
400A ALA* 3.0 16.8 + - - +
402A ARG* 1.3 79.3 - - - +
404A GLU* 1.3 59.8 + - + +
405A VAL 3.1 8.2 + - - +
406A THR* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ALA* 3.4 20.3 + - - +
401A ARG* 3.8 12.2 - - - +
402A ARG 3.2 0.8 - - - -
403A LYS* 1.3 78.3 - - + +
405A VAL* 1.3 58.3 + - - +
406A THR* 3.4 15.6 + - - +
409A ILE* 5.2 4.0 - - - +
----------------------------------------------------------
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