Contacts of the helix formed by residues 310 - 316 (chain B) in PDB entry 1H3F
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 310 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ASP* 4.5 16.8 - - + +
272B LEU* 4.0 14.4 - - + +
276B GLU* 5.5 0.7 - - - +
295B LEU* 3.9 3.6 - - - +
308B ARG* 3.4 30.5 + - - +
309B ILE* 1.3 74.2 - - - +
311B ARG* 1.3 61.5 + - + +
312B ALA* 3.3 14.7 + - - +
313B PHE* 3.0 23.5 + - - +
314B TYR* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.7 10.3 - - + +
276B GLU* 3.8 28.6 + - - +
310B ASP* 1.3 79.2 - - + +
312B ALA* 1.3 56.4 + - - +
314B TYR* 2.9 9.1 + - - +
315B GLU* 2.8 58.6 + - + +
321B TRP* 3.3 49.2 - - + +
322B GLU* 3.9 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP* 3.3 15.9 + - - +
311B ARG* 1.3 80.7 - - - +
313B PHE* 1.3 56.1 - - - +
315B GLU* 3.4 8.4 + - - +
316B SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.7 39.0 - - + -
298B ALA* 4.3 0.9 - - + -
299B ALA* 4.0 26.0 - - + -
302B LEU* 4.4 12.3 - - + -
306B PRO* 3.8 28.5 - - + -
308B ARG 3.6 17.5 - - - +
309B ILE* 4.1 11.2 - - + -
310B ASP* 3.0 13.5 + - - +
312B ALA* 1.3 73.4 - - - +
314B TYR* 1.3 64.9 + - - +
316B SER* 2.8 26.9 + - - -
317B LEU* 3.2 44.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 6.0 0.2 - - + -
291B VAL* 4.0 27.2 - - + +
294B ARG* 2.9 43.9 + - + -
295B LEU* 3.9 26.0 - - + -
310B ASP 2.9 12.9 + - - +
311B ARG* 2.9 13.0 + - - +
313B PHE* 1.3 77.9 - - - +
315B GLU* 1.3 58.8 + - + +
317B LEU* 3.2 27.5 - - + +
319B TYR* 3.4 43.5 - + + +
320B ALA 4.1 15.5 - - - -
321B TRP* 4.0 31.0 - + + -
324B PHE* 6.3 0.2 - - - -
325B GLY 4.3 1.1 + - - -
327B ASP* 3.6 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 2.8 56.7 + - + +
312B ALA* 4.0 7.8 - - - +
314B TYR* 1.3 70.5 - - + +
316B SER* 1.3 55.6 + - - +
317B LEU 2.8 5.2 - - - -
318B GLY* 2.7 24.8 + - - -
319B TYR 3.6 18.6 + - - +
320B ALA* 4.9 0.7 - - - -
321B TRP* 3.6 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA 2.9 17.0 + - - -
313B PHE* 2.8 30.1 + - - -
315B GLU* 1.3 74.6 - - - +
317B LEU* 1.3 61.5 + - - +
318B GLY 3.2 0.8 + - - -
----------------------------------------------------------
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