Contacts of the strand formed by residues 239 - 244 (chain B) in PDB entry 1NYE
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 LYS 239 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS* 5.5 0.7 - - - -
231B TRP* 3.6 6.1 - - - -
232B GLU* 3.0 41.5 + - + +
237B ARG 4.6 9.6 - - - +
238B GLY* 1.3 77.1 - - - +
240B GLY* 1.3 57.9 + - - +
241B THR* 6.5 0.2 - - + -
254B TYR 4.5 1.1 - - - -
255B GLY* 5.5 0.2 - - - -
257B ASN* 5.7 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS* 3.1 13.7 - - - -
231B TRP* 3.7 6.0 - - - -
239B LYS* 1.3 77.4 - - - +
241B THR* 1.3 62.4 + - - +
253B PRO* 3.3 6.1 - - - +
254B TYR* 2.7 53.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA* 3.0 5.9 - - - +
230B HIS* 2.7 51.3 + - + +
239B LYS* 5.9 0.4 - - + -
240B GLY* 1.3 80.4 - - - +
242B VAL* 1.3 60.3 + - - +
243B SER* 5.0 1.0 + - - -
251B GLN* 3.1 52.2 + - + +
252B GLN 3.0 8.5 - - - +
253B PRO* 4.3 6.1 - - + -
254B TYR* 3.4 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 4.0 9.2 - - + +
78A ALA* 3.1 35.4 - - + -
228B GLN 3.4 3.6 - - - +
229B ALA* 4.0 4.9 - - + -
241B THR* 1.3 76.2 - - - +
243B SER* 1.3 65.2 + - - +
249B LEU* 3.8 23.7 - - + +
250B ASN 3.7 0.3 - - - +
251B GLN* 3.7 1.0 - - - -
252B GLN* 2.9 36.3 + - + +
254B TYR* 3.9 10.1 - - + -
266B THR* 4.1 18.6 - - - +
271B LEU* 4.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.8 8.2 - - - +
227B GLY* 3.5 3.3 - - - -
228B GLN* 2.7 51.4 + - - +
229B ALA* 5.6 0.3 - - - -
241B THR* 5.0 0.9 + - - -
242B VAL* 1.3 74.5 - - - +
244B THR* 1.3 64.5 + - - +
249B LEU* 3.0 7.6 - - - -
250B ASN 2.3 25.7 + - - -
251B GLN* 3.5 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 2.8 36.1 + - - +
71A LEU* 4.1 8.1 - - - +
74A ALA* 4.3 4.0 - - - +
226B LYS 4.0 3.4 - - - -
227B GLY* 5.1 0.4 - - - -
228B GLN* 6.1 0.7 - - - -
243B SER* 1.3 78.5 + - - +
245B GLU* 1.3 62.1 + - - +
246B SER* 3.0 28.7 - - - +
247B GLY* 3.2 16.6 + - - +
248B VAL* 3.5 12.6 - - + +
249B LEU* 2.9 22.5 + - - +
----------------------------------------------------------
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