Contacts of the helix formed by residues 287 - 291 (chain B) in PDB entry 1YXU
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 HIS 287 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLU* 3.2 21.5 + - - +
265B HIS* 2.9 36.4 - + - -
266B LEU* 3.8 30.3 - - + +
269B TRP* 4.0 16.9 - + - -
283B GLU 3.3 6.8 + - - +
284B ILE 3.2 18.9 + - - +
285B GLN 3.3 0.4 - - - -
286B ASN* 1.3 81.6 - - - +
288B PRO* 1.3 82.9 - - + +
289B TRP* 3.2 34.5 - - + -
290B MET* 3.0 13.8 + - + +
291B GLN* 3.4 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 5.6 0.2 + - - -
262B GLU* 3.4 31.6 - - - +
286B ASN 3.7 4.5 - - - +
287B HIS* 1.3 101.0 - - + +
289B TRP* 1.3 60.7 + - - +
290B MET 3.3 0.7 + - - -
291B GLN* 3.4 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU* 2.7 52.2 + - + +
144B ALA* 3.8 3.1 - - + -
145B ARG* 2.7 81.7 + - + +
148B PHE* 4.3 1.8 - + - -
232B LEU* 3.7 36.3 - - + -
236B VAL* 4.9 0.2 - - + -
260B SER* 3.7 7.2 - - - -
262B GLU* 3.8 22.7 + - + +
263B CYS* 3.7 27.3 - - + +
266B LEU* 3.8 17.0 - - + -
287B HIS* 3.2 17.9 - - + -
288B PRO* 1.3 77.6 - - - +
290B MET* 1.3 72.4 + - + +
291B GLN 3.5 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 3.5 40.6 - - + +
148B PHE* 3.5 28.0 - - - -
149B TRP* 3.9 39.4 - - + +
152B LEU* 5.4 1.1 - - - -
266B LEU* 3.7 16.2 - - + -
284B ILE* 3.3 29.4 - - - +
285B GLN* 4.0 10.1 - - - +
287B HIS* 3.0 11.5 + - + +
289B TRP* 1.3 88.4 - - + +
291B GLN* 1.3 64.7 + - - +
292B ASP 4.0 0.3 + - - -
293B VAL* 4.3 5.4 + - - +
256C ARG 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 3.4 19.2 + - - -
149B TRP* 5.2 2.2 - - - -
285B GLN 3.4 18.7 + - - +
286B ASN* 4.1 8.0 - - - +
287B HIS 3.4 17.8 - - - +
288B PRO* 3.4 15.5 + - + +
289B TRP 3.3 2.9 - - - +
290B MET* 1.3 80.4 + - - +
292B ASP* 1.3 82.2 + - - +
256C ARG 4.9 3.2 + - - -
257C GLN* 3.2 34.5 + - - +
258C ARG* 5.2 2.0 - - - +
----------------------------------------------------------
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