Contacts of the helix formed by residues 278 - 289 (chain B) in PDB entry 4A04
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 278 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.3 30.7 + - - +
129B GLU* 3.3 17.9 + - - +
172B TYR* 3.5 30.8 + - + +
177B SER* 5.5 2.2 + - - -
179B TRP* 5.6 1.4 - - - +
276B TYR* 4.4 2.1 - - - +
277B GLN* 1.3 76.3 - - - +
279B HIS* 1.3 69.9 + - - +
280B ARG* 3.1 28.4 + - - +
281B ILE* 3.1 25.9 + - + +
282B THR* 3.5 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR* 5.1 0.2 + - - -
174B PHE* 6.4 2.5 - + - -
277B GLN 3.5 5.8 + - - +
278B ASN* 1.3 74.1 + - - +
280B ARG* 1.4 89.2 + - + +
282B THR* 3.4 12.6 + - - -
283B GLN* 3.1 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.8 37.0 - - + +
278B ASN* 3.1 14.3 + - - +
279B HIS* 1.4 99.3 + - + +
281B ILE* 1.4 61.8 + - - +
283B GLN* 3.5 17.6 - - - +
284B LEU* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.9 22.8 - - + +
126B LEU* 3.7 22.2 - - + -
127B GLY 3.4 29.8 - - - +
128B THR* 3.9 3.8 - - - -
129B GLU* 3.7 21.1 - - + +
276B TYR* 3.8 31.0 - - + -
278B ASN* 3.1 22.5 + - + +
280B ARG* 1.4 73.8 - - - +
282B THR* 1.4 58.8 + - - +
284B LEU* 3.1 5.5 + - - +
285B LYS* 2.9 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TYR* 3.2 34.7 - - + +
278B ASN 3.5 6.5 + - - -
279B HIS* 3.4 13.0 + - - -
281B ILE* 1.4 75.2 - - - +
283B GLN* 1.4 53.7 + - - +
285B LYS* 3.3 4.9 + - - +
286B ILE* 2.9 44.7 + - + +
17D G 3.5 31.0 - - - +
18D T 3.6 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B HIS* 3.1 46.7 + - - +
280B ARG* 3.5 20.7 - - - +
281B ILE 3.3 0.2 - - - -
282B THR* 1.4 74.2 - - - +
284B LEU* 1.3 57.1 + - - +
286B ILE* 3.6 7.9 + - - +
287B ALA* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 4.8 2.7 - - + -
122B GLU* 3.3 46.4 - - + +
123B PHE* 3.9 39.9 - - + +
126B LEU* 3.9 16.2 - - + -
280B ARG 3.2 9.2 + - - +
281B ILE 3.1 9.6 + - - +
283B GLN* 1.3 76.8 - - - +
285B LYS* 1.4 55.2 + - - +
287B ALA* 3.4 8.0 + - + +
288B SER* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.8 25.5 - - + -
128B THR* 5.2 0.2 - - - +
129B GLU 3.1 27.2 + - - -
130B MET* 3.7 10.3 - - - +
131B ILE 5.1 0.4 - - - +
140B PHE* 2.6 44.2 + - + +
276B TYR* 3.2 34.7 + - + +
281B ILE* 2.9 22.6 + - - +
282B THR* 3.5 8.3 - - - +
284B LEU* 1.4 75.1 - - - +
286B ILE* 1.4 56.7 + - - +
288B SER* 4.3 1.1 - - - -
289B ASN* 2.9 36.9 + - + +
292B ALA* 4.6 2.2 - - - -
17D G 3.5 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 2.9 29.8 + - + +
283B GLN* 3.9 6.7 - - - +
285B LYS* 1.4 76.8 - - - +
287B ALA* 1.3 51.4 + - + +
289B ASN 3.6 3.8 - - - +
292B ALA* 3.7 20.6 - - + +
295B PHE* 3.8 31.4 - - + +
296B ARG* 2.7 51.2 + - + -
17D G 3.6 38.6 - - - +
18D T 4.0 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLN 3.1 19.6 + - - +
284B LEU* 3.9 10.5 - - + +
286B ILE* 1.3 77.1 - - - +
288B SER* 1.4 56.7 + - - +
296B ARG* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.9 29.9 - - - +
123B PHE* 4.1 1.0 - - - -
140B PHE* 3.2 27.4 - - - -
284B LEU* 2.7 25.3 + - - -
287B ALA* 1.4 77.6 - - - +
289B ASN* 1.4 59.0 + - - +
290B PRO* 3.5 9.4 - - - +
296B ARG* 3.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE* 3.6 36.8 - - + +
285B LYS* 2.9 23.4 + - + +
286B ILE 3.6 4.5 - - - +
288B SER* 1.4 72.2 + - - +
290B PRO* 1.4 74.3 - - - +
291B PHE* 3.2 18.5 + - - -
292B ALA* 3.1 15.1 + - + +
296B ARG* 3.0 12.2 + - - -
16D T 3.1 46.6 + - - -
17D G 4.9 2.8 + - - -
----------------------------------------------------------
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