Contacts of the strand formed by residues 249 - 255 (chain D) in PDB entry 5B2G
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 GLN 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ALA* 4.3 17.6 - - + +
247D THR 3.6 16.2 + - - +
248D GLY* 1.3 86.0 + - - +
250D LYS* 1.3 60.6 + - - +
251D TYR* 3.5 32.7 - - + +
290D SER* 5.4 0.9 - - - -
291D LEU 2.7 28.5 + - - +
318D LYS* 3.4 31.4 - - - +
319D PHE 4.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D GLN* 1.3 73.8 + - - +
251D TYR* 1.3 70.2 + - - +
288D ASP* 4.7 9.0 + - + +
289D ILE* 3.5 24.7 - - - +
290D SER* 3.9 28.7 - - - +
318D LYS* 3.9 1.7 - - - +
319D PHE* 3.1 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 4.6 13.2 - - + -
212D THR* 4.4 5.1 + - - -
215D LEU* 3.7 28.0 - - + -
244D ILE* 3.7 41.2 - - + +
246D ALA* 3.8 13.6 + - - +
249D GLN* 3.5 33.8 - - + +
250D LYS* 1.3 83.2 - - - +
252D ARG* 1.3 64.4 + - - +
253D ILE* 5.3 8.6 - - + +
287D VAL 4.0 0.3 - - - +
288D ASP* 3.9 12.3 - - - -
289D ILE 3.9 8.1 + - - +
291D LEU* 4.1 24.2 - - + -
316D PHE* 5.8 4.5 - - + -
317D GLN 3.2 16.4 - - - +
318D LYS* 4.2 13.6 - - + -
319D PHE* 3.7 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 3.1 31.1 + - - +
41C VAL* 3.6 20.6 - - + +
251D TYR* 1.3 74.9 - - - +
253D ILE* 1.3 66.3 + - - +
254D LEU* 5.1 0.7 - - + -
286D TYR* 3.5 36.9 + - + -
287D VAL 3.5 3.6 - - - -
288D ASP* 3.1 33.1 + - - +
315D LEU 3.1 7.3 - - - +
316D PHE* 3.5 2.9 - - - +
317D GLN* 2.8 61.7 + - + +
319D PHE* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LEU* 5.3 4.3 - - + -
251D TYR* 5.3 6.7 - - + -
252D ARG* 1.3 75.5 - - - +
254D LEU* 1.3 61.0 + - - +
261D PHE* 3.8 25.7 - - + -
263D ILE* 3.7 31.0 - - + -
286D TYR* 3.1 4.9 - - - -
287D VAL* 2.9 36.2 + - + +
289D ILE* 5.6 3.8 - - + -
291D LEU* 5.6 9.0 - - + -
298D LEU* 4.1 17.3 - - + -
314D ILE* 3.6 25.1 - - + -
315D LEU 3.7 3.1 - - - -
316D PHE* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER 4.8 4.7 - - - +
39C ASN* 3.9 31.0 - - + +
40C ILE* 5.1 2.7 - - + -
153C ALA* 5.1 5.6 - - + -
156C GLN* 4.0 10.3 - - + +
252D ARG* 3.9 1.3 + - + -
253D ILE* 1.3 72.2 - - - +
255D ALA* 1.3 63.5 + - - +
284D ASP* 3.9 20.9 - - + +
285D HIS 3.6 19.7 - - - +
286D TYR* 3.7 16.4 - - + -
313D SER 4.6 0.3 - - - +
314D ILE* 3.8 6.5 - - - -
315D LEU* 3.0 63.6 + - + +
317D GLN* 4.7 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ALA* 4.3 4.6 - - - +
253D ILE 4.0 1.6 + - - -
254D LEU* 1.3 83.5 - - - +
256D SER* 1.3 67.4 + - - +
259D VAL* 4.3 7.4 - - + -
261D PHE* 3.2 37.5 - - + -
284D ASP* 4.2 3.8 - - - +
285D HIS* 3.1 25.4 + - + +
313D SER 4.7 1.8 - - - -
314D ILE* 4.1 19.5 - - + -
----------------------------------------------------------
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