Contacts of the strand formed by residues 268 - 273 (chain B) in PDB entry 3IFS
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 ILE 268 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A THR* 5.5 0.9 - - - +
268A ILE* 3.9 31.2 - - + -
301A PHE* 3.9 30.3 - - + -
266B LYS 3.5 0.2 - - - -
267B THR* 1.3 88.1 - - - +
269B GLU* 1.3 64.5 + - - +
270B MSE 4.2 2.5 - - + -
300B ILE* 4.1 1.3 - - - -
301B PHE* 3.5 13.0 - - + +
303B SER* 4.0 20.9 - - - -
324B ASP* 3.0 16.6 + - + +
325B LEU* 3.3 31.2 - - + -
326B PHE* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 2.5 24.3 + - - -
258B ARG* 2.8 33.7 + - - -
268B ILE* 1.3 74.0 - - - +
270B MSE 1.3 62.4 + - - +
285B TRP* 3.5 18.1 - - + -
300B ILE* 3.5 10.6 - - + +
301B PHE 2.9 7.5 + - - +
302B PRO* 3.7 1.0 - - - +
303B SER 2.8 33.8 + - - +
326B PHE* 3.3 36.4 - - + +
328B THR* 2.5 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 4.0 20.0 - - + -
268B ILE* 4.2 8.7 - - + -
269B GLU* 1.3 75.7 - - - +
271B LEU* 1.3 62.2 + - - +
272B ILE* 3.5 16.5 + - + +
303B SER* 3.3 23.8 - - - +
304B SER 4.7 2.2 - - - +
305B ALA* 3.7 28.0 - - + -
307B PHE* 4.6 2.2 - - + -
314B LEU* 4.5 12.1 - - + -
318B VAL* 3.7 32.3 - - + -
325B LEU* 4.1 12.1 - - + -
326B PHE 2.9 12.5 + - - +
327B GLU* 3.3 12.7 - - + +
328B THR 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLU 3.9 0.8 + - - -
270B MSE 1.3 70.7 - - - +
272B ILE* 1.3 60.0 + - - +
273B ASN* 5.4 0.9 + - - -
281B PHE* 4.7 3.1 - - + -
282B ALA* 3.8 22.4 - - + +
285B TRP* 3.6 64.0 - - + +
303B SER 2.9 8.2 + - - +
304B SER* 3.3 7.3 - - - -
305B ALA 3.1 22.3 + - - +
328B THR* 3.4 31.9 - - + +
330B LEU* 4.0 35.9 - - + -
401B PHE* 4.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B MSE 3.7 21.5 - - + +
271B LEU* 1.3 77.9 - - - +
273B ASN* 1.3 66.7 - - - +
274B TYR* 4.0 12.3 - - + -
305B ALA* 3.4 21.8 - - + +
307B PHE* 3.3 40.8 - - + -
327B GLU* 3.6 35.0 - - + +
328B THR 2.8 12.5 + - - +
329B VAL* 4.1 12.8 - - + -
330B LEU* 2.8 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU 5.4 0.6 + - - -
272B ILE* 1.3 74.6 - - - +
274B TYR* 1.3 61.1 + - - +
275B GLU 3.0 28.6 + - - +
276B PRO* 5.3 0.2 - - - +
278B LEU* 3.9 39.3 + - + -
279B GLN* 4.1 1.4 - - - +
282B ALA* 5.1 6.7 - - - +
305B ALA 3.2 6.7 + - - -
306B ASN* 2.8 36.1 + - - +
307B PHE* 2.7 35.5 + - - +
330B LEU* 4.1 11.2 - - + -
----------------------------------------------------------
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