Contacts of the strand formed by residues 210 - 216 (chain F) in PDB entry 2HU4
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 210 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F LYS* 4.1 1.1 - - - -
207F TYR 3.1 32.7 + - - +
208F ASN* 3.3 10.1 - - + +
209F GLY* 1.3 83.5 - - - +
211F ILE* 1.3 70.0 + - - +
212F THR* 3.2 9.5 + - + +
100G TYR* 4.1 10.8 - - - +
129G CYS* 5.7 1.1 - - - -
412G GLN* 3.5 63.3 - - + +
413G THR* 3.8 24.9 - - + +
419G ARG* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F VAL* 3.7 19.7 - - + -
205F LEU 3.1 13.2 - - - +
206F LYS* 3.9 6.3 - - - +
209F GLY 4.1 0.4 + - - -
210F ILE* 1.3 72.2 - - - +
212F THR* 1.3 62.6 + - - +
213F ASP 3.8 15.5 - - - +
214F THR* 4.9 1.8 - - - +
98G ALA* 3.9 20.0 - - + +
99G VAL 3.9 16.8 - - - +
100G TYR* 3.7 29.6 - - + -
413G THR* 5.9 1.4 - - - +
419G ARG* 2.9 35.6 + - - +
447G CYS* 4.2 12.8 - - + -
449G VAL* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F LEU 2.8 8.3 + - - -
207F TYR* 3.7 15.5 + - + -
210F ILE* 3.4 19.5 - - + +
211F ILE* 1.3 75.0 - - - +
213F ASP* 1.3 60.6 + - - +
259F LYS 3.4 18.8 - - - +
260F GLY* 2.7 30.6 + - - -
261F LYS* 2.6 35.2 + - - +
413G THR 6.1 0.7 - - - +
415G LEU* 6.3 2.9 - - + -
419G ARG* 5.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F LEU* 3.0 32.9 + - + +
211F ILE* 3.8 7.9 - - - +
212F THR* 1.3 82.0 + - - +
214F THR* 1.3 80.6 + - - +
260F GLY 3.3 16.6 + - - +
261F LYS* 3.9 11.4 - - - +
262F VAL* 2.9 40.6 + - - +
449G VAL* 6.0 0.9 - - - -
451G SER* 4.2 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL* 4.1 12.9 - - + +
203F ALA 3.5 9.6 + - - -
204F VAL* 4.5 2.8 - - - -
205F LEU* 5.0 0.2 - - - -
211F ILE* 4.9 1.6 - - - +
213F ASP* 1.3 90.7 + - - +
215F ILE* 1.3 76.4 + - - +
216F LYS* 4.6 2.0 - - - +
98G ALA* 4.4 12.0 - - - +
449G VAL* 4.3 7.3 - - - +
451G SER* 2.7 31.4 + - - +
452G ASP* 2.7 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F VAL* 3.3 1.4 - - - -
203F ALA* 2.7 45.7 + - + +
205F LEU* 4.8 13.0 - - + -
214F THR* 1.3 84.5 - - - +
216F LYS* 1.3 70.1 + - - +
218F TRP* 4.7 6.7 - - + -
223F LEU* 3.7 10.1 - - + +
239F THR* 6.3 0.4 - - + -
241F MET* 4.2 17.3 - - + -
255F PHE* 3.5 49.1 - - + -
257F MET* 5.7 1.3 - - - -
262F VAL* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F GLY 5.4 0.4 - - - +
201F ALA 3.6 6.3 - - - +
202F VAL* 4.2 8.3 - - + +
214F THR* 4.6 2.2 - - + +
215F ILE* 1.3 84.6 - - - +
217F SER* 1.3 74.7 + - - +
218F TRP* 3.4 7.6 + - - +
223F LEU* 3.9 2.5 - - - -
451G SER* 5.1 1.8 - - - +
452G ASP* 2.7 59.4 - - + +
454G VAL* 5.3 7.4 - - + -
----------------------------------------------------------
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