Contacts of the strand formed by residues 199 - 205 (chain F) in PDB entry 1Q57
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 PHE 199 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F TRP* 3.9 18.6 - - + -
149F GLY 2.7 46.4 - - - -
150F GLY* 3.3 13.9 - - - +
152F LYS 4.4 1.8 - - - +
153F ILE* 3.3 53.2 - - + +
174F PRO* 4.0 16.6 - - + -
195F TYR* 3.7 30.7 - + - -
196F PHE* 2.9 20.7 + - - +
197F ASP 4.0 1.1 - - - -
198F GLN* 1.3 80.1 - - + +
200F GLU* 1.3 54.0 + - - +
201F GLN* 3.5 5.1 + - - +
202F ILE* 4.9 1.1 - - + +
227F LYS* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F GLY 3.4 8.1 + - - +
151F LYS* 3.1 54.6 + - - +
199F PHE* 1.3 71.3 - - - +
201F GLN* 1.3 64.1 + - + +
227F LYS* 3.0 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F LYS 3.5 5.2 + - - +
152F LYS* 3.2 47.5 + - + +
153F ILE* 3.1 25.1 + - - +
199F PHE* 4.4 1.0 - - - +
200F GLU* 1.3 82.3 - - - +
202F ILE* 1.3 63.3 + - - +
203F ILE* 4.0 5.1 - - + +
227F LYS* 3.4 15.3 - - - +
229F ARG* 3.3 41.4 + - + +
256F ASN* 4.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ILE* 3.7 14.6 - - + +
155F VAL* 4.4 11.0 - - + -
196F PHE* 3.6 30.3 - - + +
199F PHE 4.9 1.8 - - - +
201F GLN* 1.3 74.4 - - - +
203F ILE* 1.3 61.7 + - - +
204F LEU* 3.5 24.0 + - + -
223F LEU* 3.4 33.4 - - + -
224F PRO* 3.5 24.2 - - + +
227F LYS* 2.8 23.1 + - + +
228F VAL* 3.2 7.9 - - + +
229F ARG 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F LYS* 3.2 29.8 - - + -
153F ILE 3.0 13.0 + - - +
154F VAL* 3.4 16.1 - - + +
155F VAL 3.0 22.7 + - - -
201F GLN* 4.0 9.9 - - + +
202F ILE* 1.3 72.8 - - - +
204F LEU* 1.3 58.5 + - - +
205F MET* 3.1 6.0 + - + +
229F ARG* 3.4 20.6 - - + +
231F ALA* 4.5 12.1 - - + -
253F GLN 3.8 9.0 - - - +
254F VAL* 3.0 31.4 - - - +
257F ALA* 4.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F VAL* 3.8 20.2 - - + -
189F CYS* 5.5 0.9 - - - -
202F ILE* 3.5 27.8 + - + -
203F ILE* 1.3 71.0 - - - +
205F MET* 1.3 58.2 + - - +
206F PHE* 3.5 23.1 + - + -
213F ARG* 5.0 0.2 + - - -
216F VAL* 4.1 24.4 - - + +
219F ALA* 3.3 33.9 - - + -
220F ALA* 4.3 1.6 - - - +
223F LEU* 3.9 13.2 - - + -
228F VAL* 3.9 13.2 - - + -
229F ARG 2.9 12.0 + - - +
230F VAL* 3.8 4.7 - - + +
231F ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F VAL* 3.8 18.2 - - + -
155F VAL 3.0 9.5 + - - +
156F THR* 3.5 20.6 - - + -
157F GLU* 3.8 2.3 + - - +
161F ASP* 5.7 1.2 - - - +
165F VAL* 3.8 13.2 - - + -
203F ILE* 3.1 4.6 + - + +
204F LEU* 1.3 69.4 - - - +
206F PHE* 1.3 62.1 + - - +
231F ALA* 3.3 23.8 - - + -
233F LEU* 3.9 19.6 - - + +
238F ALA* 3.5 30.1 + - + +
250F ILE* 3.7 34.1 - - + +
253F GLN* 4.3 7.9 - - + -
254F VAL* 4.0 15.7 - - + +
----------------------------------------------------------
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