Contacts of the strand formed by residues 243 - 248 (chain A) in PDB entry 3F1O
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 THR 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 2.8 19.3 + - - +
240A ASP* 3.1 10.2 + - - +
241A SER 3.4 0.4 - - - -
242A LYS* 1.3 81.7 - - - +
244A PHE* 1.3 65.6 + - - +
260A ARG* 2.8 38.2 + - - +
264A LEU* 4.8 0.4 - - - -
340A VAL* 3.7 26.5 - - + -
341A ASN 3.2 11.0 - - - +
342A TYR* 3.5 13.7 - - - -
446B PHE* 4.3 8.8 - - + -
448B ASN* 4.7 2.8 + - - -
456B TYR* 4.1 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 2XY 4.2 14.8 - - - -
243A THR* 1.3 78.7 - - - +
245A LEU* 1.3 59.2 + - - +
246A SER* 4.9 0.9 - - - -
254A PHE* 5.5 0.7 - + - -
257A CYS* 3.8 20.9 - - - -
258A ASP* 3.7 6.7 - - + -
260A ARG* 3.6 24.2 - - + +
261A ILE* 3.7 35.2 - - + +
264A LEU* 4.1 14.4 - - + -
265A ILE* 4.4 4.0 - - + -
309A MET* 4.4 4.7 - - - -
319A LEU* 4.2 11.2 - - + -
341A ASN* 2.9 76.5 + - + -
343A VAL* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 1.3 75.1 - - - +
246A SER* 1.3 82.0 + - - +
256A TYR* 3.8 8.1 - - + -
257A CYS* 3.6 3.5 - - - -
258A ASP* 2.9 45.3 + - - +
260A ARG* 3.8 3.3 - - - +
338A MET* 3.4 25.1 - - + -
339A CYS 3.3 14.1 - - - +
340A VAL* 4.3 8.3 - - + +
341A ASN* 4.2 0.4 - - - -
364B ILE* 3.6 32.8 - - + -
458B ILE* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 2XY 3.6 3.3 - - - -
244A PHE* 4.9 0.4 - - - -
245A LEU* 1.3 88.1 - - - +
247A GLU* 1.3 60.3 + - - +
248A HIS* 2.8 26.5 + - - -
254A PHE* 3.6 19.7 - - - -
256A TYR 3.4 7.9 - - - -
257A CYS* 4.1 5.8 - - - -
337A ILE 4.0 0.2 - - - +
338A MET* 3.6 1.2 - - - -
339A CYS* 2.9 35.7 + - - +
341A ASN* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 1.3 73.8 - - - +
248A HIS* 1.3 64.3 + - - +
254A PHE* 3.5 2.1 - - - -
255A THR* 2.6 46.8 + - - +
256A TYR* 2.9 21.1 + - + +
336A CYS* 4.2 14.1 - - + -
337A ILE 3.3 9.9 - - - +
338A MET* 4.2 6.4 - - - +
362B ARG* 3.0 31.1 + - - -
364B ILE* 3.5 17.5 - - + +
379B ARG* 2.9 40.2 + - - -
460B THR* 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A 2XY 3.3 35.4 + - - +
246A SER* 2.8 26.1 + - - -
247A GLU* 1.3 80.8 - - - +
249A SER* 1.3 67.7 + - - +
252A MET* 3.1 23.8 + - - +
253A LYS 3.1 7.4 - - - +
254A PHE* 3.5 42.5 + + - -
255A THR* 3.8 5.2 - - - -
277A ALA* 4.4 0.2 - - + -
336A CYS* 3.2 7.6 - - - +
337A ILE* 2.8 47.0 + - + +
339A CYS* 3.9 13.7 - - - -
----------------------------------------------------------
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