Contacts of the strand formed by residues 206 - 211 (chain G) in PDB entry 1FPY
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 VAL 206 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G CYS* 3.6 44.2 - - + +
199G MET* 4.3 11.2 - - + -
200G GLU* 2.9 34.5 + - + +
205G VAL* 1.3 73.6 - - - +
207G GLU* 1.3 63.0 + - - +
208G ALA 3.6 14.1 - - - +
221G VAL* 3.9 6.7 - - + -
222G ALA 3.6 9.0 - - - +
223G THR* 4.3 7.6 - - + -
34L PRO* 3.1 15.3 - - + +
36L HIS* 3.0 26.3 - - - -
37L GLN* 4.3 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G VAL* 3.7 2.0 + - + -
206G VAL* 1.3 75.5 - - - +
208G ALA* 1.3 66.2 + - + +
222G ALA* 2.8 16.4 + - + +
223G THR 4.1 1.2 - - - +
224G ARG* 3.5 45.4 - - + +
225G PHE* 5.1 0.7 - - - -
4477G ADP 3.5 38.3 + - - +
33L ILE* 3.4 10.4 - - - +
34L PRO* 3.1 14.5 - - - +
37L GLN* 3.5 27.3 + - - +
47L LYS* 5.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G VAL* 3.5 8.4 - - - +
207G GLU* 1.3 84.0 - - + +
209G HIS* 1.4 61.5 + - - +
210G HIS* 5.2 3.5 - - + -
221G VAL* 3.5 1.4 - - - +
222G ALA* 2.6 44.7 + - + +
31L VAL* 5.2 3.6 - - + -
32L THR 3.2 5.6 - - - +
33L ILE* 3.1 25.1 - - + -
34L PRO* 4.0 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLN* 2.7 35.8 + - - -
192G ARG* 2.7 32.1 + - + +
193G SER* 3.0 30.4 + - - -
196G CYS* 3.6 30.5 - - - -
208G ALA* 1.4 75.7 - - - +
210G HIS* 1.3 67.7 + - - +
220G GLU 3.6 12.3 - - - +
221G VAL* 3.9 7.9 - - + -
16L PHE* 4.5 5.4 - + - -
31L VAL* 3.8 0.7 - - - +
32L THR* 2.9 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G TYR* 4.2 11.2 - + - -
180G PHE* 3.4 27.0 - + + -
192G ARG* 3.5 18.1 - - - +
208G ALA* 5.2 4.9 - - + -
209G HIS* 1.3 85.0 + - - +
211G HIS* 1.3 86.9 + - - +
212G GLU* 3.4 25.4 - - - -
220G GLU* 3.2 56.8 + - + +
222G ALA* 5.7 3.6 - - + +
469G MN 4.1 5.5 + - - -
30L HIS* 4.9 1.6 - - - +
31L VAL* 3.9 16.8 - - + +
32L THR 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G GLU* 2.7 36.6 + - - -
173G PRO* 4.6 5.8 - - + +
178G GLY* 2.9 22.2 - - - +
179G TYR* 4.1 0.4 - - - -
180G PHE* 4.0 20.4 - - - +
181G PRO 5.8 0.2 - - - -
186G ASP* 3.3 30.4 + - + +
192G ARG* 3.6 10.7 - - - +
210G HIS* 1.3 106.2 + - - +
212G GLU* 1.3 86.6 + - - +
214G ALA 3.6 12.1 + - - -
217G GLY* 4.0 6.1 - - - -
218G GLN 3.1 12.0 + - - -
219G ASN* 3.7 14.0 + - - +
30L HIS* 5.8 1.8 + - + -
----------------------------------------------------------
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