Contacts of the helix formed by residues 300 - 307 (chain A) in PDB entry 2HD1
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 ASN 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A IBM 6.3 2.9 - - + -
296A HIS* 4.8 3.0 - - + +
299A TYR* 1.3 76.0 - - - +
301A ASN* 1.3 62.7 + - - +
302A THR* 3.0 13.7 + - - +
303A TYR 2.8 23.5 + - - +
304A GLN* 3.0 18.5 + - - +
321A LEU* 3.7 13.0 - - + -
424A TYR* 5.7 3.6 - - + -
427A GLN* 3.0 28.1 + - - +
441A PHE* 4.9 3.1 - - - -
442A MET* 3.1 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASN* 1.3 73.8 - - - +
302A THR* 1.3 61.6 + - - +
304A GLN* 3.1 5.5 + - - +
305A ILE* 2.8 43.4 + - + +
319A SER* 4.2 0.8 - - - +
320A PRO* 3.3 18.8 - - + +
321A LEU* 2.9 37.7 + - - +
322A GLU* 2.9 29.4 + - - -
364A ASP* 3.6 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASN* 3.0 16.0 + - - +
301A ASN* 1.3 77.4 - - - +
303A TYR* 1.3 58.1 + - - +
305A ILE* 3.4 7.0 + - - +
306A ASN* 2.9 50.4 + - - +
427A GLN* 4.8 1.1 - - - +
431A GLU* 4.8 7.4 - - - +
437A PRO 5.8 0.4 - - - +
439A ALA* 6.1 5.4 - - + -
442A MET* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR* 3.5 22.9 - + + -
300A ASN* 2.8 21.3 - - - +
302A THR* 1.3 77.2 - - - +
304A GLN* 1.3 70.2 + - - +
306A ASN* 4.9 2.2 - - + -
307A ALA* 2.9 46.8 + - + +
309A THR* 4.0 11.4 - - + +
427A GLN* 3.7 16.8 - - + +
430A ARG* 2.9 48.0 + - + -
431A GLU* 3.8 28.5 - - + -
434A GLU* 2.8 28.4 + - - -
436A LEU* 3.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO* 3.5 14.9 - - - +
299A TYR* 3.1 26.1 - - - +
300A ASN 3.0 18.4 + - - +
301A ASN* 3.5 10.8 - - - +
303A TYR* 1.3 77.6 - - - +
305A ILE* 1.3 57.4 + - - +
308A ARG 3.1 6.8 + - - -
309A THR* 2.6 69.5 + - - +
311A LEU* 3.8 17.5 - - + +
312A ALA* 3.1 14.0 - - + +
320A PRO* 4.3 9.4 - - + -
321A LEU* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN* 2.8 33.3 + - + +
302A THR* 3.8 5.4 - - - +
304A GLN* 1.3 71.1 - - - +
306A ASN* 1.3 74.9 + - - +
308A ARG* 3.0 19.9 + - - +
312A ALA* 3.9 8.5 - - + -
317A ASP* 3.6 56.5 - - + +
320A PRO* 4.6 5.6 - - + -
350B LYS* 5.4 8.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 2.9 44.5 + - - +
303A TYR* 4.3 2.7 - - + +
305A ILE* 1.3 77.7 - - - +
307A ALA* 1.3 59.3 + - - +
308A ARG* 3.5 11.4 + - - +
431A GLU* 5.0 2.4 + - - +
436A LEU* 3.6 22.1 - - + +
437A PRO* 3.3 42.0 + - + +
350B LYS* 3.6 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TYR* 2.9 42.0 + - + +
306A ASN* 1.3 75.1 - - - +
308A ARG* 1.3 73.2 + - - +
309A THR* 3.1 7.7 + - + +
434A GLU* 4.4 1.3 - - - +
436A LEU* 3.5 23.8 - - + -
----------------------------------------------------------
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