Contacts of the helix formed by residues 350 - 360 (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 ASP 350 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE 3.1 6.6 - - - +
331A SER* 3.0 11.3 + - - -
332A GLY* 2.9 16.9 + - - +
346A ASN 3.4 17.7 - - - +
347A CYS* 4.6 1.2 - - - -
348A ASP 3.5 1.8 - - - +
349A VAL* 1.3 76.6 - - - +
351A VAL* 1.3 63.6 + - - +
352A SER* 3.4 4.9 + - - -
353A PHE* 3.1 32.5 + - + +
354A MET* 3.1 26.0 + - - +
373A TYR* 2.9 31.5 + - + -
380A THR* 5.6 1.2 - - - +
383A LEU* 3.2 14.6 - - - +
384A LYS* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PRO* 4.4 3.8 - - + +
295A ALA 3.8 9.2 - - - +
296A LEU* 3.1 35.4 - - + +
298A GLY* 4.7 2.9 - - - +
299A ALA 5.3 1.1 - - - +
329A ALA* 4.6 1.8 - - + -
330A PHE* 3.4 31.0 + - + +
350A ASP* 1.3 70.9 - - - +
352A SER* 1.3 65.9 + - - +
354A MET* 2.9 23.1 + - + +
355A TYR* 2.9 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 4.4 0.7 + - - +
329A ALA* 3.7 17.2 - - - +
330A PHE 4.1 2.7 + - - -
350A ASP* 3.4 10.9 + - - -
351A VAL* 1.3 78.2 - - - +
353A PHE* 1.3 62.1 + - - +
355A TYR* 3.5 5.0 + - - +
356A LEU* 3.3 24.0 + - - +
383A LEU* 3.9 18.4 - - - -
384A LYS* 3.7 26.8 - - - +
387A LEU* 3.6 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A CYS* 3.7 42.0 - - + -
350A ASP* 3.1 24.5 + - + +
352A SER* 1.3 73.6 - - - +
354A MET* 1.3 68.9 + - - +
356A LEU* 2.9 20.4 + - + +
357A THR* 3.0 26.9 + - - -
366A LEU* 3.4 40.4 - - + -
369A ILE* 4.2 17.5 - - + -
370A ARG* 3.6 40.8 - - + -
373A TYR* 5.2 0.9 - + + -
383A LEU* 4.1 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PRO* 3.3 34.8 - - + -
299A ALA* 5.1 10.3 - - + -
330A PHE* 5.9 0.2 - - + -
347A CYS 5.0 5.2 - - - +
348A ASP 3.5 19.7 - - - +
349A VAL* 3.5 11.2 - - + -
350A ASP 3.1 24.7 + - - +
351A VAL* 2.9 45.2 + - + +
353A PHE* 1.3 76.4 - - - +
355A TYR* 1.3 57.8 + - - +
357A THR* 2.9 31.9 + - - -
358A PHE* 3.1 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 4.6 4.4 - - + +
293A PHE* 3.4 37.3 - + + -
294A PRO* 3.3 33.1 + - + -
296A LEU* 3.3 36.4 + - + +
311A SER* 5.5 1.0 - - - -
312A ILE* 4.3 16.4 + - + +
351A VAL* 2.9 32.6 + - + -
352A SER 3.5 4.3 - - - +
353A PHE 3.1 0.2 - - - -
354A MET* 1.3 77.4 - - + +
356A LEU* 1.3 59.6 + - - +
357A THR 3.0 1.6 - - - -
358A PHE* 2.8 23.8 + - - +
359A PHE* 2.9 19.3 + + + +
387A LEU* 3.4 33.7 - - + -
391A LEU* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.5 6.1 + - - -
352A SER 3.3 11.4 + - - +
353A PHE* 2.9 12.1 + - + +
355A TYR* 1.3 77.3 - - - +
357A THR* 1.3 62.4 + - - +
359A PHE* 5.0 0.4 - - - +
360A LEU* 3.0 46.7 + - + +
366A LEU* 3.6 15.1 - - + +
369A ILE* 4.0 23.1 - - + -
383A LEU* 3.5 37.0 - - + +
386A ALA* 4.3 1.8 - - + +
387A LEU* 3.4 33.2 - - + +
390A VAL* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS* 4.3 1.2 - - - -
87A ARG* 3.0 57.2 + - + +
89A ILE* 3.8 17.3 - - + +
353A PHE* 3.0 29.7 + - - -
354A MET* 2.9 19.4 + - - -
355A TYR 3.0 0.2 - - - -
356A LEU* 1.3 77.7 - - - +
358A PHE* 1.3 60.2 + - + +
366A LEU* 4.3 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS* 2.9 28.6 + - - -
84A PHE* 3.4 13.5 - + - -
89A ILE* 3.7 34.3 - - + -
128A ILE* 3.4 35.2 - - + -
291A THR* 4.0 9.9 - - - -
292A PHE 3.4 24.9 - - - -
293A PHE* 3.5 31.4 - + - -
294A PRO* 3.6 16.6 - - + -
354A MET* 3.1 27.1 - - + -
355A TYR 2.8 6.8 + - - +
357A THR* 1.3 82.4 - - + +
359A PHE* 1.3 68.2 + - + +
360A LEU 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS* 4.9 0.4 - - - -
84A PHE* 5.5 0.2 - + - -
124A VAL* 3.3 39.9 - - + -
127A LEU* 4.6 1.6 - - + -
128A ILE* 3.6 16.8 - - + -
131A ILE* 3.6 29.6 - - + -
293A PHE* 3.5 28.9 - + - -
355A TYR* 2.9 25.2 + - + +
356A LEU* 5.3 0.2 - - - -
358A PHE* 1.3 76.9 - - + +
360A LEU* 1.3 59.9 + - - +
361A GLU* 3.4 12.2 + - - +
387A LEU* 5.7 1.3 - - + -
390A VAL* 3.4 24.9 - - + +
391A LEU* 4.0 15.3 - - + -
394A LEU* 3.7 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A HIS* 4.9 0.4 - - - -
87A ARG* 2.9 25.8 + - - -
356A LEU* 3.0 44.4 + - + +
358A PHE 5.1 0.9 - - - -
359A PHE* 1.3 75.2 - - - +
361A GLU* 1.3 61.9 + - - +
362A ASP* 3.3 15.3 + - + +
365A LYS* 4.4 24.9 - - + -
366A LEU* 4.4 10.1 - - + -
369A ILE* 3.7 25.8 - - + -
386A ALA 5.3 0.9 - - - +
390A VAL* 3.3 27.5 - - + +
----------------------------------------------------------
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