Contacts of the strand formed by residues 205 - 211 (chain A) in PDB entry 2FPL
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 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 3.6 23.1 - - + +
146A VAL* 3.7 34.8 - - + -
178A PHE* 3.9 17.9 - - + -
195A ILE* 3.9 14.6 - - + -
198A LEU* 4.2 8.5 - - + -
199A ILE* 3.6 33.8 - - + +
203A ASN* 2.8 18.6 + - + +
204A ASN* 1.3 68.9 - - - +
206A LYS* 1.3 74.0 + - - +
207A LEU 4.0 4.5 - - - +
208A VAL* 4.0 15.9 - - + -
248A PHE 4.1 2.6 - - - +
250A CYS* 3.6 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TRP* 3.4 34.8 - - + +
122A LEU* 4.4 3.4 - - + -
128A LEU* 5.8 0.7 - - + -
139A GLU* 3.3 33.6 + - - +
140A VAL* 4.8 5.8 - - + -
143A PRO* 4.2 16.8 - - + -
144A LYS 2.8 8.4 + - - +
204A ASN* 2.8 38.7 + - - +
205A ILE* 1.3 78.7 + - - +
207A LEU* 1.3 61.3 + - - +
248A PHE* 3.3 17.8 + - - +
249A ASN* 3.3 25.1 - - - +
250A CYS* 3.1 8.1 - - - +
251A VAL* 2.9 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TRP* 5.7 0.2 - - + -
80A LEU* 4.3 9.2 - - + -
118A SER* 3.5 37.0 - - - +
119A CYS* 3.8 22.2 - - - +
122A LEU* 4.0 13.5 - - + -
144A LYS 3.3 3.3 + - - +
145A ALA* 3.3 13.1 - - + -
146A VAL* 2.7 30.7 + - - +
205A ILE* 3.8 1.8 - - - +
206A LYS* 1.3 80.7 - - - +
208A VAL* 1.3 64.3 + - - +
209A VAL* 4.1 6.7 - - + -
251A VAL* 3.4 34.1 - - + +
253A LEU* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.3 9.0 - - + +
148A ILE* 5.2 0.2 - - + -
195A ILE* 3.7 33.2 - - + -
205A ILE* 4.0 16.8 - - + -
207A LEU* 1.3 81.0 - - - +
209A VAL* 1.3 61.3 + - - +
210A ILE* 4.3 20.9 - - + -
241A LEU* 4.7 5.2 - - + -
244A LEU* 4.3 7.6 - - + -
250A CYS* 4.2 13.9 - - - -
251A VAL 2.8 12.2 + - - +
252A VAL* 3.3 13.9 - - + +
253A LEU* 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A MET* 3.5 54.7 - - + +
119A CYS* 4.3 6.3 - - - -
146A VAL 2.7 14.6 + - - +
147A TYR* 3.9 22.0 - - + -
148A ILE* 2.8 31.2 + - - +
207A LEU* 4.1 22.9 - - + -
208A VAL* 1.3 78.4 - - - +
210A ILE* 1.3 65.9 + - - +
211A ASP 4.2 5.8 - - - +
253A LEU* 3.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.5 37.7 - - + +
188A GLN* 3.7 27.4 - - + +
192A ALA* 4.8 0.2 - - + -
208A VAL* 4.3 7.9 - - + -
209A VAL* 1.3 78.5 - - - +
211A ASP* 1.3 59.9 + - - +
212A SER 3.8 11.2 - - - +
213A LEU* 3.7 13.1 + - + -
237A HIS* 4.4 8.5 - - + +
241A LEU* 4.3 26.2 - - + -
252A VAL* 5.0 0.4 - - + -
253A LEU 2.8 9.2 + - - +
254A VAL* 3.3 23.5 - - + -
255A THR* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 4.8 1.7 - - - +
112A THR* 2.8 30.2 + - - +
115A MET* 4.1 14.4 - - + -
147A TYR* 3.2 27.2 + - + +
148A ILE 3.0 11.8 + - - +
149A ASP* 3.3 7.8 - - - +
150A THR* 2.6 27.5 + - - -
151A GLU* 3.6 7.1 + - - +
153A THR* 3.9 6.9 + - - -
209A VAL* 4.0 3.6 - - + -
210A ILE* 1.3 74.4 - - - +
212A SER* 1.3 53.5 + - - +
255A THR* 2.6 30.1 + - - +
501A MG 4.2 3.6 - - - -
----------------------------------------------------------
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