Contacts of the strand formed by residues 220 - 227 (chain E) in PDB entry 4QRR
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 HIS 220 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E TRP 3.9 0.2 - - - +
174E VAL* 3.5 6.8 - - - +
175E ASN* 2.7 65.7 + - - +
218E ARG 3.9 0.6 + - - -
219E ASN* 1.3 70.8 - - - +
221E PHE* 1.3 63.5 + - - +
222E ARG* 3.6 34.5 - - + +
251E GLU* 3.2 31.8 + - + +
252E ALA 4.0 4.7 - - - -
253E TRP* 3.4 47.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E VAL* 5.0 3.6 - - - +
156E LEU* 3.9 19.5 - - + -
172E TRP* 5.1 4.0 - - + -
173E TRP 4.1 2.7 - - - -
174E VAL* 4.1 9.9 - - + +
207E LEU* 4.0 21.1 - - + -
209E VAL* 4.3 15.0 - - + -
213E PHE* 3.6 45.8 - + - -
214E TRP* 3.6 42.4 - + - -
219E ASN* 3.7 28.0 - - + -
220E HIS* 1.3 73.9 - - - +
222E ARG* 1.3 59.3 + - - +
223E CYS 4.1 0.3 + - - -
250E ALA 4.3 0.9 - - - +
251E GLU* 3.5 2.7 - - - -
252E ALA* 2.8 42.0 + - - +
254E GLY 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E TRP* 3.8 5.9 - - - -
173E TRP* 2.8 64.7 + - + +
175E ASN 5.5 1.1 + - - +
220E HIS* 3.6 24.4 - - + +
221E PHE* 1.3 73.6 - - - +
223E CYS* 1.3 61.4 + - - +
224E GLN* 2.7 44.1 + - - +
247E ILE* 4.8 4.9 - - - +
249E SER* 3.4 34.0 + - - -
251E GLU* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 4.0 7.9 - - + +
140E VAL* 4.7 4.3 - - + -
158E CYS* 3.1 41.7 - - + -
170E LEU* 4.0 17.0 - - - -
171E SER 3.9 3.6 - - - -
172E TRP* 4.0 21.5 - - + -
221E PHE 4.1 0.2 + - - -
222E ARG* 1.3 72.5 - - - +
224E GLN* 1.3 58.4 + - - +
225E VAL* 4.0 3.2 + - - -
249E SER* 3.2 8.5 - - - -
250E ALA 3.1 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E GLU 4.0 0.6 + - - +
170E LEU* 3.6 0.5 - - - +
171E SER* 2.8 56.2 + - - +
173E TRP* 3.6 24.8 + - + +
222E ARG* 2.7 38.2 + - - +
223E CYS* 1.3 71.0 - - - +
225E VAL* 1.3 66.1 + - - +
226E GLN* 4.1 13.3 - - - +
247E ILE* 3.7 32.4 - - + +
249E SER* 4.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E PRO* 4.4 6.5 - - + +
138E VAL* 3.6 35.9 - - + -
158E CYS* 4.5 0.9 - - - -
160E ALA* 4.3 11.2 - - + -
168E VAL* 4.3 28.7 - - + -
169E GLU 3.7 5.6 - - - +
170E LEU* 3.6 29.6 - - + -
203E LEU* 6.3 0.2 - - + -
223E CYS* 4.2 3.6 - - - -
224E GLN* 1.3 79.8 - - - +
226E GLN* 1.3 58.9 + - - +
227E PHE* 3.5 2.1 + - - +
246E GLN 3.9 0.2 - - - +
247E ILE* 4.6 1.3 - - - -
248E VAL* 3.0 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E HIS 3.8 0.7 - - - +
168E VAL* 3.4 3.7 - - - -
169E GLU* 2.9 49.2 + - + +
224E GLN* 4.1 11.6 - - - +
225E VAL* 1.3 69.8 - - - +
227E PHE* 1.3 66.4 + - - +
228E TYR* 3.6 34.5 + - + +
245E THR* 3.8 12.2 - - - +
246E GLN 3.3 23.3 - - - +
247E ILE* 3.4 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E VAL* 4.5 2.2 - - + -
134E PHE 3.3 24.9 - - - -
135E PRO* 4.0 18.8 - - + -
136E PRO* 3.6 30.5 - - + -
163E PHE* 4.1 5.8 - - + -
164E TYR 3.5 12.1 - - - -
165E PRO* 3.8 27.1 - - + -
167E HIS* 3.5 13.9 - - + -
168E VAL* 3.8 11.2 - - + -
225E VAL 3.5 1.2 + - - +
226E GLN* 1.3 73.4 - - - +
228E TYR* 1.3 60.7 + - - +
229E GLY* 3.7 24.9 - - - -
243E PRO* 4.2 10.3 - - + -
244E VAL 3.9 9.6 - - - -
245E THR* 3.3 8.0 - - - +
246E GLN* 2.9 38.2 + - + +
----------------------------------------------------------
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