Contacts of the strand formed by residues 241 - 247 (chain B) in PDB entry 2AFW
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 MET 241 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 4.4 3.6 - - - +
134B HIS* 3.8 6.7 - - + -
136B VAL* 4.1 23.8 - - + -
194B GLN* 5.2 0.4 - - - +
196B ILE* 4.7 5.4 - - + -
223B MET* 3.8 17.7 - - + -
237B GLN 3.8 9.0 - - - +
238B LEU* 3.1 18.1 + - - +
239B HIS 4.3 4.1 - - - +
240B GLY* 1.3 74.6 - - - +
242B ASP* 1.3 65.8 + - - +
243B LEU 3.3 2.1 + - - +
244B LEU* 3.9 26.5 - - + -
310B PHE* 3.6 41.1 - - + -
315B VAL* 3.9 25.2 - - + +
316B PRO* 3.9 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.7 27.8 - - - +
133B ARG* 2.7 56.7 + - - +
134B HIS 3.0 17.8 + - - +
135B LEU* 4.5 0.7 - - - -
191B LEU* 4.0 8.0 - - - +
239B HIS 5.6 0.6 - - - +
240B GLY 3.2 5.0 + - - +
241B MET* 1.3 73.4 - - - +
243B LEU* 1.3 62.2 + - + +
316B PRO* 3.4 21.0 - - - +
358B TYR* 2.6 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.8 14.3 - - + +
136B VAL* 3.0 29.1 + - - +
241B MET 3.3 3.0 - - - -
242B ASP* 1.3 82.5 - - + +
244B LEU* 1.3 60.2 + - - +
245B VAL* 4.0 18.4 - - + -
264B SER* 4.2 10.5 - - - -
267B TRP* 4.0 24.0 - - + +
315B VAL* 4.9 2.0 - - - -
316B PRO* 3.4 31.9 - - + +
317B VAL 4.0 2.0 - - - -
318B LEU* 3.9 18.8 - - + +
354B PHE* 4.0 26.9 - - + -
358B TYR* 4.2 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.6 28.7 - - + +
138B ALA* 4.0 20.0 - - + -
196B ILE* 5.0 2.9 - - + -
198B PHE* 5.2 4.9 - - + -
241B MET* 3.9 9.0 - - + -
243B LEU* 1.3 70.9 - - - +
245B VAL* 1.3 57.3 + - - +
246B LEU* 4.6 9.2 - - + +
306B ASP 4.8 0.9 - - - +
307B HIS* 3.8 33.9 - - + -
310B PHE* 3.9 27.6 - - + -
315B VAL* 4.1 11.0 - - + +
316B PRO 2.8 14.6 + - - +
317B VAL* 3.3 8.5 - - + +
318B LEU 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.0 7.9 - - + -
136B VAL 2.8 17.5 + - - +
137B LEU* 3.4 20.7 - - + -
138B ALA 3.0 24.8 + - - +
243B LEU* 4.0 25.4 - - + -
244B LEU* 1.3 73.2 - - - +
246B LEU* 1.3 60.4 + - - +
247B LEU* 3.7 9.7 - - + +
318B LEU* 3.3 20.2 - - + +
320B LEU* 3.7 30.1 - - + -
351B LEU* 4.6 6.7 - - + -
354B PHE* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ALA* 3.5 29.2 - - + +
139B CYS* 3.9 11.2 - - - +
140B HIS 5.2 0.2 - - - +
198B PHE* 4.5 1.8 - - + -
244B LEU* 3.6 9.5 + - + +
245B VAL* 1.3 73.3 - - - +
247B LEU* 1.3 61.9 + - - +
248B ASP* 4.8 1.3 - - + -
305B ASP* 3.6 28.9 - - - +
306B ASP* 3.9 15.3 - - + +
307B HIS* 3.4 37.5 - - + +
317B VAL* 5.0 0.2 - - + -
318B LEU 3.0 7.8 + - - +
319B HIS* 3.7 19.8 - - + +
320B LEU* 2.7 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 4.9 6.1 - - + -
138B ALA 2.9 18.2 + - - +
139B CYS* 3.3 24.0 - - + +
140B HIS 4.8 0.5 + - - -
160B SER* 4.5 0.3 + - - -
163B PRO* 3.8 32.7 - - + +
166B MET* 4.1 21.1 - - + -
167B MET* 4.3 7.2 - - + -
245B VAL* 3.7 28.7 - - + +
246B LEU* 1.3 73.3 - - - +
248B ASP* 1.3 63.2 + - - +
250B ILE* 3.9 10.8 - - + -
320B LEU* 3.6 13.5 - - + -
351B LEU* 4.0 29.2 - - + -
----------------------------------------------------------
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