Contacts of the strand formed by residues 217 - 223 (chain A) in PDB entry 3QWR
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 LYS 217 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO 3.5 1.7 + - - +
216A PRO* 1.3 72.6 - - - +
218A ASN* 1.3 85.2 + - - +
219A LEU 3.1 4.4 + - - -
234A TRP* 3.4 3.8 - - - +
235A GLU* 2.8 67.2 + - + -
236A TYR 3.6 16.0 + - - +
237A PRO* 4.7 4.9 - - + -
238A ASP* 2.7 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LYS* 1.3 89.7 - - - +
219A LEU* 1.3 65.8 + - - +
220A GLN* 3.4 14.9 + - + +
233A SER* 3.6 6.6 + - - +
234A TRP* 3.7 4.3 - - - -
235A GLU* 3.1 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 5.3 1.1 - - + +
217A LYS 3.1 6.2 + - - +
218A ASN* 1.3 75.3 - - - +
220A GLN* 1.3 68.9 + - - +
232A VAL* 3.7 23.6 - - + -
233A SER 3.2 17.9 - - - +
234A TRP* 4.1 7.4 - - + -
284A ILE 4.1 3.1 - - - +
286A VAL* 3.9 17.0 - - + -
301A ALA* 3.3 46.0 - - + +
302A SER* 3.8 14.8 - - - +
303A VAL* 3.6 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASN* 3.7 14.2 - - + +
219A LEU* 1.3 83.1 + - - +
221A LEU* 1.3 75.4 + - - +
222A LYS* 4.6 18.5 - - + -
231A GLU 3.6 0.3 - - - +
232A VAL* 3.5 1.2 - - - +
233A SER* 2.9 46.4 + - - +
303A VAL* 5.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLN* 1.3 86.3 + - - +
222A LYS* 1.3 65.7 + - - +
223A PRO* 4.2 4.9 - - - +
230A VAL* 4.0 19.5 - - + -
231A GLU 3.5 0.9 - - - -
232A VAL* 3.9 15.7 - - + -
278A CYS* 3.7 27.1 - - - -
284A ILE* 3.6 22.2 - - + -
303A VAL* 3.6 22.6 - - + +
304A PRO 3.9 19.3 - - - +
305A CYS* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLN* 4.6 16.8 - - + +
221A LEU* 1.3 79.3 - - - +
223A PRO* 1.4 73.8 - - + +
230A VAL* 3.4 3.7 - - - +
231A GLU* 2.7 60.9 + - + +
233A SER* 5.1 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU 4.2 4.5 - - - +
222A LYS* 1.4 94.4 - - + +
224A LEU* 1.3 63.2 + - - +
225A LYS 4.2 0.3 + - - -
228A ARG* 3.9 16.4 - - - +
230A VAL* 3.7 13.0 - - + -
231A GLU* 5.4 0.3 - - - +
----------------------------------------------------------
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