Contacts of the strand formed by residues 206 - 211 (chain D) in PDB entry 1F1H
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D CYS* 3.7 42.8 - - + +
199D MET* 4.3 10.1 - - + -
200D GLU* 3.0 29.9 + - + +
205D VAL* 1.3 74.9 - - - +
207D GLU* 1.3 63.9 + - - +
208D ALA 3.6 14.1 - - - +
221D VAL* 4.2 10.1 - - + -
222D ALA 3.6 10.3 - - - +
223D THR* 4.3 4.7 - - + +
34E PRO* 3.3 17.4 - - + +
36E HIS* 3.2 25.3 - - - -
37E GLN* 4.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D VAL* 3.8 2.1 + - + -
206D VAL* 1.3 76.0 - - - +
208D ALA* 1.3 61.4 + - + +
222D ALA* 2.7 19.7 + - + +
223D THR 3.7 1.1 - - - +
224D ARG* 3.5 39.4 - - + +
225D PHE* 5.2 0.3 - - - -
1474D ADP 3.2 43.5 + - - +
33E ILE* 3.3 20.3 - - - +
34E PRO* 3.4 7.3 - - - +
37E GLN* 3.5 27.5 + - - +
47E LYS* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D VAL* 3.6 7.3 - - - +
207D GLU* 1.3 81.4 - - + +
209D HIS* 1.3 61.2 + - - +
210D HIS* 5.0 5.6 - - + -
221D VAL* 3.6 1.2 - - - -
222D ALA* 2.7 44.0 + - + +
1474D ADP 5.6 2.7 - - - +
31E VAL* 4.8 5.8 - - + -
32E THR 3.3 7.4 - - - +
33E ILE* 3.3 20.4 - - + -
34E PRO* 4.2 4.5 - - - -
47E LYS* 4.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D GLN* 3.2 32.8 + - - -
192D ARG* 2.8 37.5 + - + -
193D SER* 2.8 32.4 + - - -
196D CYS* 3.7 29.4 - - - -
208D ALA* 1.3 77.1 - - - +
210D HIS* 1.3 65.3 + - - +
220D GLU 3.4 11.9 - - - +
221D VAL* 4.0 6.1 - - + -
16E PHE* 4.3 5.2 - + - -
31E VAL* 3.8 0.7 - - - +
32E THR* 2.8 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D TYR* 3.5 11.7 - - - -
180D PHE* 3.5 23.0 - + + -
192D ARG* 3.4 17.3 - - - +
208D ALA* 5.0 6.1 - - + -
209D HIS* 1.3 85.0 + - - +
211D HIS* 1.3 79.8 + - - +
212D GLU* 3.3 26.0 - - - -
220D GLU* 2.9 51.8 + - + +
222D ALA* 5.8 1.3 - - + -
1474D ADP 2.8 25.4 + - - -
30E HIS* 4.7 0.9 - - - +
31E VAL* 3.9 20.6 - - + +
50E ASP* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D GLU* 2.7 36.0 + - - -
173D PRO* 4.5 6.4 - - + +
178D GLY* 2.9 21.1 + - - +
179D TYR* 3.0 12.5 - - - -
180D PHE* 3.4 10.7 - - + +
181D PRO 5.8 0.2 - - - +
186D ASP* 3.5 30.9 + - + +
188D ALA* 5.4 0.2 - - - +
192D ARG* 3.6 12.3 - - - +
210D HIS* 1.3 89.4 + - - +
212D GLU* 1.3 89.8 + - - +
214D ALA 3.4 16.4 + - - -
217D GLY* 4.2 4.7 - - - -
218D GLN 2.9 13.8 + - - -
219D ASN* 3.5 14.4 + - - +
30E HIS* 5.6 1.4 + - + -
----------------------------------------------------------
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