Contacts of the strand formed by residues 234 - 242 (chain B) in PDB entry 1ATT
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 234 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B SER* 3.0 27.9 + - - +
233B GLU* 1.4 76.7 - - + +
235B THR* 1.3 58.6 + - - +
236B ARG* 4.1 6.5 + - - +
254B TYR* 3.2 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 5.6 0.7 - - - +
231B SER 3.8 3.8 + - - -
232B PRO* 2.9 24.5 + - - +
233B GLU 4.0 6.6 - - - +
234B ASN* 1.3 78.1 - - - +
236B ARG* 1.3 59.1 + - - +
251B LEU* 4.0 24.0 - - + +
252B MET 3.2 35.0 - - - +
253B MET* 4.1 7.8 - - + +
254B TYR 5.1 0.2 + - - -
323B ARG* 4.8 3.4 - - - +
378B GLU* 3.7 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ASN 4.5 5.6 - - - +
235B THR* 1.3 75.6 - - - +
237B LYS* 1.3 67.1 + - - +
238B GLU* 2.7 30.4 + - - -
251B LEU* 4.6 2.9 - - - -
252B MET* 3.0 60.9 + - - +
253B MET 3.8 0.6 + - - -
254B TYR* 2.9 47.8 - - - +
320B HIS* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ARG* 1.3 77.6 - - - +
238B GLU* 1.3 67.5 + - - +
249B SER* 5.1 12.3 + - - -
250B VAL 4.0 13.5 - - - +
251B LEU* 3.8 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ARG* 2.7 38.7 + - - +
237B LYS* 1.3 82.2 - - - +
239B LEU* 1.3 74.8 + - - +
240B PHE 3.5 0.3 + - - -
248B CYS 3.5 0.7 - - - +
249B SER* 3.6 1.6 - - - -
250B VAL* 2.8 38.3 + - - +
252B MET* 3.8 24.0 - - + +
320B HIS* 3.0 14.9 + - - -
404B LYS* 2.8 25.0 + - - -
406B ASN* 4.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 1.3 80.4 + - - +
240B PHE* 1.3 64.3 + - - +
241B TYR* 3.5 36.9 - - + +
247B SER* 4.2 19.7 - - - +
248B CYS 3.0 14.6 - - - +
249B SER* 3.9 19.3 - - - +
250B VAL* 4.6 0.4 - - - -
252B MET* 5.9 0.2 - - - -
406B ASN* 3.5 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU 3.5 2.4 + - - -
239B LEU* 1.3 71.4 - - - +
241B TYR* 1.4 67.1 + - - +
242B LYS* 4.0 4.7 - - + -
248B CYS* 2.7 26.9 + - + -
250B VAL* 3.7 15.4 - - + +
252B MET* 5.1 0.4 - - + -
322B PRO* 3.8 12.1 - - + -
405B ALA 3.7 10.3 - - - -
406B ASN* 2.8 48.3 - - + +
407B ARG* 3.2 32.3 - - - -
408B PRO* 3.3 22.0 - - + -
409B PHE* 4.2 4.7 - + - -
427B VAL 4.4 4.0 - - - -
428B ALA 3.5 20.0 - - - -
430B PRO* 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 3.5 39.6 - - + +
240B PHE* 1.4 88.4 - - - +
242B LYS* 1.3 70.8 + - - +
245B GLY 4.3 10.1 - - - +
246B GLU 4.1 0.7 - - - -
247B SER* 4.0 20.4 - - - +
248B CYS 3.8 7.5 - - - +
406B ASN* 3.7 22.0 - - - +
407B ARG* 3.3 26.4 - - + +
408B PRO* 3.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASN* 3.7 12.3 + - - +
240B PHE* 4.2 7.9 - - + -
241B TYR* 1.3 80.4 - - - +
243B ALA* 1.3 67.2 + - - +
244B ASP* 2.9 36.5 + - - +
245B GLY* 2.9 15.6 + - - -
246B GLU* 2.9 36.8 + - - +
247B SER 4.0 6.1 - - - -
248B CYS* 3.6 34.3 - - + -
408B PRO* 4.5 0.2 - - - -
428B ALA 4.1 13.2 - - - +
429B ASN* 3.8 25.1 + - - +
----------------------------------------------------------
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