Contacts of the helix formed by residues 354 - 359 (chain B) in PDB entry 1HLG
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 354 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 6.1 2.2 - - - +
152B HIS* 4.1 19.7 - - + -
240B LEU* 3.5 43.7 - - + +
241B PHE* 3.8 27.6 - - + -
244B CYS* 3.9 25.3 + - + +
245B GLY 4.3 5.6 - - - +
251B PHE* 3.7 16.8 - - + -
352B ASN* 3.0 5.2 + - - +
353B HIS* 1.3 78.8 - - + +
355B ASP* 1.3 66.6 + - - +
356B PHE 3.1 2.5 - - - -
357B ILE* 3.2 7.1 + - + +
358B TRP* 3.1 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASP 4.9 0.2 - - - +
250B ASN* 2.9 38.1 + - - +
251B PHE* 3.3 20.3 - - - -
350B PHE 3.4 1.9 - - - +
351B TYR* 3.1 28.3 - - + -
352B ASN* 2.8 49.8 + - - +
354B LEU* 1.3 74.0 - - - +
356B PHE* 1.3 58.4 + - - +
357B ILE 2.8 3.8 + - - -
359B ALA* 2.8 34.7 + - + +
362B ALA* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B HIS* 4.2 8.3 - - + -
179B LEU* 3.8 33.3 - - + +
180B ALA* 4.0 13.7 - - + -
319B TRP* 3.4 30.1 - - + -
320B ASN 3.3 27.6 - - - -
321B GLY* 3.4 15.9 - - - -
324B ASP* 4.7 0.2 - - - -
348B ILE* 4.3 3.8 - - + -
351B TYR* 4.0 22.2 - + - -
352B ASN 3.4 21.3 - - - -
353B HIS 3.7 11.9 - - - +
354B LEU 3.1 0.8 - - - -
355B ASP* 1.3 76.0 - - - +
357B ILE* 1.3 60.6 + - - +
362B ALA* 4.4 1.7 - - - +
366B VAL* 4.0 17.7 - - + -
367B TYR* 2.8 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLY 5.4 0.2 - - - +
73B ASN* 3.2 57.4 - - + +
74B TRP* 4.2 20.4 - - + +
77B ASN* 3.9 6.8 + - - -
81B ASN 4.9 2.8 - - - +
82B SER* 5.8 1.2 - - - -
152B HIS* 2.8 50.5 - - + +
354B LEU* 3.2 7.4 + - + +
356B PHE* 1.3 86.0 - - + +
358B TRP* 1.3 73.6 + - + +
359B ALA 3.8 1.1 - - - +
362B ALA* 5.3 0.2 - - - -
367B TYR* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 3.6 25.2 + - - +
76B SER* 2.8 28.5 + - - -
77B ASN* 3.7 15.9 + - - +
240B LEU* 3.5 32.8 - - + -
241B PHE* 3.6 17.0 - + - -
251B PHE* 3.7 45.8 - + + -
252B ASN* 4.4 1.7 + - - +
259B TYR* 3.3 54.0 + + + +
263B ASN* 3.7 12.1 - - + -
354B LEU* 3.1 22.2 + - + +
357B ILE* 1.3 98.0 - - + +
359B ALA* 1.3 62.7 + - - +
360B MET* 3.6 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 5.8 0.5 + - - -
81B ASN* 5.3 4.0 - - - +
250B ASN* 3.3 12.6 - - + -
251B PHE* 4.4 0.2 - - - -
351B TYR* 3.3 29.8 - - + +
355B ASP* 2.8 41.0 + - + +
357B ILE 3.8 0.4 - - - -
358B TRP* 1.3 71.4 - - - +
360B MET* 1.3 66.4 + - - +
361B ASP* 3.7 4.9 - - - +
362B ALA* 3.0 18.6 + - - +
363B PRO* 4.3 1.2 - - - +
----------------------------------------------------------
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