Contacts of the helix formed by residues 301 - 312 (chain A) in PDB entry 1HMU
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 GLU 301 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 2.7 22.7 + - - +
272A TYR* 2.7 33.8 + - - -
273A LEU* 4.3 9.4 - - + -
276A ILE* 4.7 0.9 - - + -
298A LYS* 3.1 29.6 + - + +
299A LYS 3.3 0.8 - - - -
300A ALA* 1.3 78.4 - - - +
302A LYS* 1.3 62.7 + - - +
304A ARG* 2.8 39.9 + - - +
305A LEU* 3.0 28.4 + - + -
326A THR* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LYS 4.5 7.3 + - - +
300A ALA* 3.1 4.9 + - - +
301A GLU* 1.3 78.1 - - - +
303A LYS* 1.3 59.4 + - - +
304A ARG 3.1 0.2 - - - -
305A LEU* 3.6 13.7 - - + +
306A LEU* 2.8 49.0 + - + +
323A ILE* 4.2 25.4 - - + -
326A THR* 4.4 2.9 + - - +
327A ASP* 2.5 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 3.1 16.4 + - + +
301A GLU 3.0 0.6 + - - -
302A LYS* 1.3 82.5 - - + +
304A ARG* 1.3 64.1 + - + +
306A LEU* 4.1 7.0 - - - +
307A VAL* 3.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 2.9 24.8 + - - +
239A ILE* 3.9 12.6 - - - +
240A THR* 2.7 50.0 + - - +
243A LEU* 3.3 24.8 - - + +
268A TYR* 3.4 11.9 + - - +
272A TYR* 3.1 31.3 + - - -
300A ALA 5.8 0.4 - - - +
301A GLU* 2.8 31.7 + - - +
303A LYS* 1.3 80.8 - - + +
305A LEU* 1.3 66.0 + - - +
306A LEU 3.1 2.0 - - - -
307A VAL* 3.0 5.5 + - - -
308A ALA* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 3.5 22.4 + - + +
273A LEU* 3.9 26.5 - - + -
301A GLU* 3.0 26.8 + - + +
302A LYS* 3.8 4.3 - - - -
304A ARG* 1.3 75.7 - - - +
306A LEU* 1.3 57.5 + - - +
308A ALA* 3.2 6.3 + - - +
309A LYS* 2.9 31.4 + - - +
319A TRP* 3.9 16.9 - - + +
322A ALA* 3.7 9.2 - - + -
323A ILE* 3.5 49.6 - - + +
326A THR* 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LYS* 2.8 35.7 + - + +
303A LYS* 4.1 7.4 - - - +
305A LEU* 1.3 78.3 - - - +
307A VAL* 1.3 61.6 + - + +
309A LYS* 3.5 16.5 + - - +
310A MET* 3.2 26.8 + - - +
323A ILE* 3.3 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 5.4 7.2 - - - +
243A LEU* 4.0 15.5 - - + -
244A LYS* 5.6 1.1 - - - -
247A ASN* 3.7 43.1 - - + +
303A LYS 3.7 16.4 - - - +
304A ARG* 3.0 7.7 + - - +
306A LEU* 1.3 76.7 - - + +
308A ALA* 1.3 58.0 + - - +
310A MET* 2.7 34.6 + - + +
311A ILE* 2.9 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 4.0 14.3 - - + +
264A PHE* 5.2 2.0 - - + -
268A TYR* 4.1 11.9 - - + -
304A ARG 3.0 11.7 + - - +
305A LEU 3.5 8.3 - - - +
307A VAL* 1.3 77.8 - - - +
309A LYS* 1.3 54.3 + - - +
311A ILE* 4.5 2.2 - - - +
312A ASP* 2.7 39.5 + - + +
319A TRP* 3.6 35.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU 2.9 14.9 + - - +
306A LEU* 3.8 14.6 - - - +
308A ALA* 1.3 77.1 - - - +
310A MET* 1.3 60.6 + - + +
312A ASP 4.2 4.2 + - - +
313A LEU* 3.6 16.3 - - - +
316A THR* 4.0 26.4 + - + +
319A TRP* 3.7 23.0 - - + -
320A ALA* 4.4 20.2 - - - +
323A ILE* 3.7 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 5.2 10.3 - - - +
250A ARG* 5.4 15.2 - - - +
306A LEU* 3.2 17.3 - - - +
307A VAL* 2.7 19.2 + - + +
309A LYS* 1.3 79.8 - - + +
311A ILE* 1.3 61.1 + - + +
313A LEU* 2.9 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.7 17.7 - - + +
246A ALA* 3.8 11.0 - - + +
247A ASN* 3.2 54.1 - - + +
250A ARG* 4.5 14.8 - - + +
261A LEU* 3.7 30.9 - - + +
264A PHE* 6.4 0.9 - - + -
307A VAL* 2.9 21.0 + - + +
308A ALA* 4.1 3.8 - - - +
310A MET* 1.3 80.2 - - + +
312A ASP* 1.3 57.8 + - + +
313A LEU* 3.8 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.4 27.6 - - + +
264A PHE* 6.3 1.8 - - + -
265A SER* 2.6 27.4 + - - -
308A ALA* 2.7 19.7 + - - +
309A LYS 4.2 2.1 - - - +
310A MET 3.6 0.2 - - - -
311A ILE* 1.3 73.5 - - + +
313A LEU* 1.3 63.4 + - - +
314A LYS* 3.8 11.8 + - - +
315A HIS* 2.8 27.3 + - - -
316A THR 4.1 0.2 + - - -
319A TRP* 3.1 35.0 + - + +
----------------------------------------------------------
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