Contacts of the helix formed by residues 389 - 401 (chain A) in PDB entry 1HNY
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 ARG 389 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ARG 3.3 3.8 + - - -
388A TRP* 1.3 70.2 - - - +
390A GLN* 1.3 79.5 + - - +
392A ARG* 4.1 19.9 - - - +
393A ASN* 2.9 52.3 + - - +
452A VAL 4.3 0.7 - - - +
453A ILE 2.9 27.9 + - - -
454A SER* 3.4 20.9 + - - +
455A GLY* 3.7 15.5 - - - -
456A ASP* 3.5 22.2 - - - +
485A ASP* 4.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LYS* 3.5 42.5 - - + +
326A GLY* 5.6 0.3 - - - -
388A TRP* 3.9 10.4 - - - +
389A ARG* 1.3 103.2 + - - +
391A ILE* 1.3 59.7 + - - +
393A ASN* 4.5 0.4 - - - -
394A MET* 3.2 30.8 + - - +
452A VAL 4.8 0.2 - - - -
453A ILE* 3.5 39.1 - - + +
485A ASP* 2.8 27.5 + - - +
487A PHE* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TYR* 4.0 25.4 - - + -
322A LYS* 4.6 11.9 - - + +
325A VAL* 3.9 30.3 - - + -
329A LEU* 4.3 0.2 - - - +
338A VAL* 4.0 26.9 - - + -
385A GLU* 3.4 29.6 - - + +
386A HIS* 4.6 2.9 - - - -
388A TRP* 2.9 29.5 + - + +
390A GLN* 1.3 79.2 - - - +
392A ARG* 1.3 67.3 + - - +
394A MET* 3.1 6.3 + - - +
395A VAL* 3.0 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 3.1 32.3 + - + +
35A LYS* 3.8 39.6 - - + +
37A PHE* 4.3 7.0 - - + -
376A THR* 5.0 8.7 + - - +
386A HIS 3.4 13.6 + - - +
387A ARG 4.4 6.9 + - - -
388A TRP 2.9 14.3 + - - +
389A ARG* 4.1 22.7 - - - +
391A ILE* 1.3 72.2 - - - +
393A ASN* 1.3 97.9 + - - +
395A VAL* 3.1 18.4 + - - +
396A ILE* 3.2 19.0 + - + +
456A ASP* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 2.9 22.8 + - - +
390A GLN 4.7 1.6 - - - +
392A ARG* 1.3 99.8 + - - +
394A MET* 1.3 60.0 - - - +
396A ILE* 3.4 15.1 + - - +
397A PHE* 3.0 23.6 + - - +
452A VAL* 2.9 49.6 + - + +
453A ILE* 5.4 0.4 - - + -
455A GLY 3.1 8.9 + - - -
456A ASP* 2.8 24.2 + - - +
491A HIS* 4.6 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLY* 3.3 36.1 - - - +
329A LEU* 3.7 30.0 - - + +
330A ALA* 3.8 8.1 - - + +
390A GLN 3.2 20.3 + - - +
391A ILE* 3.1 3.2 + - - +
393A ASN* 1.3 75.7 - - - +
395A VAL* 1.3 66.3 + - - +
396A ILE 3.1 0.7 - - - -
397A PHE* 3.4 33.5 - - + +
398A ARG* 3.1 18.2 + - - +
427A ILE* 3.6 15.7 - - + -
452A VAL* 4.8 1.3 - - - -
453A ILE* 3.6 13.2 - - + -
487A PHE* 4.6 0.2 - - + -
489A ALA* 3.8 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 4.4 0.7 + - - -
12A SER* 4.5 15.6 + - - +
35A LYS 4.4 4.0 - - - +
36A GLY 4.3 12.6 - - - +
37A PHE* 3.9 48.2 - - + -
329A LEU* 4.2 10.5 - - + -
338A VAL* 4.1 23.3 - - + -
391A ILE* 3.0 17.7 + - + +
392A ARG 3.1 9.4 + - - +
394A MET* 1.3 79.5 - - - +
396A ILE* 1.3 61.3 + - - +
398A ARG* 3.4 5.2 + - - +
399A ASN* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.2 38.4 - - + +
36A GLY* 5.2 0.4 - - - -
392A ARG* 3.2 33.2 + - - +
393A ASN* 3.6 14.8 - - - +
394A MET 3.1 0.2 - - - -
395A VAL* 1.3 74.1 - - - +
397A PHE* 1.3 64.8 + - - +
399A ASN* 3.0 14.9 + - + +
400A VAL* 3.0 30.6 + - + +
491A HIS* 4.4 16.8 - - + +
493A GLU* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA* 3.6 34.5 - - + -
393A ASN 3.0 14.9 + - - +
394A MET* 3.3 37.0 + - + +
396A ILE* 1.3 75.4 - - - +
398A ARG* 1.3 63.4 + - - +
400A VAL* 3.1 2.6 + - - +
401A VAL* 3.0 46.0 + - + +
421A ARG* 4.3 5.2 - - + -
425A GLY* 4.0 9.6 - - - -
426A PHE* 3.7 29.2 - - - -
427A ILE* 4.5 2.9 - - + -
452A VAL* 4.9 0.2 - - + -
489A ALA* 4.1 11.2 - - + -
490A ILE 3.5 20.6 - - - -
491A HIS* 3.8 30.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.1 27.1 + - + +
12A SER* 4.0 4.7 - - - -
328A MET 3.3 7.3 + - - -
329A LEU* 2.8 43.0 + - + +
330A ALA 4.3 0.2 - - - -
331A HIS 2.7 30.9 + - - -
332A PRO* 3.8 7.6 + - - +
333A TYR 3.5 7.5 + - - -
334A GLY 2.9 28.3 + - - -
335A PHE* 5.5 0.2 - - - +
336A THR* 3.2 34.2 + - - +
394A MET 3.1 7.9 + - - +
395A VAL* 3.5 9.6 - - - +
396A ILE 3.2 0.2 - - - -
397A PHE* 1.3 80.4 - - - +
399A ASN* 1.3 61.7 + - - +
401A VAL* 3.9 6.8 - - - +
402A ASP* 3.2 24.1 + - - +
421A ARG* 4.5 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY* 3.1 26.8 + - - +
11A THR* 2.7 44.8 + - - -
12A SER 4.6 0.5 + - - -
35A LYS 4.8 0.2 + - - -
36A GLY* 2.9 35.2 + - - +
395A VAL* 3.3 13.3 + - - +
396A ILE* 3.0 16.0 + - + +
398A ARG* 1.3 80.9 - - - +
400A VAL* 1.3 63.1 + - + +
401A VAL 3.4 0.2 + - - -
402A ASP* 3.5 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 3.0 23.3 + - + +
397A PHE 3.1 6.7 + - - +
399A ASN* 1.3 78.4 - - + +
401A VAL* 1.3 59.5 + - - +
402A ASP 3.8 1.7 + - - +
404A GLN* 5.1 0.2 - - - +
424A ARG* 2.8 61.6 + - - +
491A HIS* 3.8 30.7 - - + +
492A ALA* 4.0 11.0 - - + -
493A GLU* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PHE* 3.0 34.6 + - + +
398A ARG* 3.9 6.1 - - - +
400A VAL* 1.3 79.8 - - + +
402A ASP* 1.3 67.8 + - - +
403A GLY 3.2 0.2 + - - -
404A GLN* 2.8 27.5 + - - +
421A ARG* 3.5 48.4 + - + +
424A ARG* 3.6 34.5 - - + +
425A GLY* 3.8 9.4 - - - +
491A HIS* 4.7 1.1 - - + -
----------------------------------------------------------
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