Contacts of the strand formed by residues 216 - 226 (chain A) in PDB entry 2PG0
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 ALA 216 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 2.9 40.5 + - - +
164A GLY* 4.1 12.8 - - - +
165A ILE* 3.7 29.4 - - + -
201A ARG* 5.3 0.4 - - + -
202A GLY 3.9 11.0 - - - +
203A ARG 4.3 3.8 - - - +
204A LYS* 4.6 0.2 - - - -
205A LEU* 4.0 9.6 - - - -
215A THR* 1.3 78.9 - - - +
217A GLU* 1.3 66.6 + - - +
218A LEU* 4.7 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO* 4.3 2.6 - - - +
157A GLN* 2.9 28.3 + - - -
158A LYS 3.2 9.0 - - - +
159A THR* 3.3 30.7 + - - +
201A ARG* 3.5 3.3 - - - -
202A GLY* 2.9 29.3 + - - +
203A ARG 5.0 0.8 + - - -
205A LEU* 4.3 22.3 - - + +
216A ALA* 1.3 77.5 - - - +
218A LEU* 1.3 62.7 + - - +
219A PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 4.1 6.5 - - + -
156A GLY 4.2 0.2 - - - +
157A GLN* 3.4 7.4 - - - +
158A LYS* 2.9 34.8 + - + +
161A ILE* 3.9 27.4 - - + -
164A GLY* 3.9 20.0 - - - +
170A ILE* 3.8 32.5 - - + -
199A PHE* 3.8 20.6 - - + -
200A THR 3.7 1.8 - - - -
201A ARG* 3.8 26.0 - - + +
216A ALA 4.9 0.2 - - - +
217A GLU* 1.3 82.6 - - - +
219A PHE* 1.3 61.6 + - - +
220A PHE* 4.2 14.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLY 3.8 3.1 - - - +
157A GLN* 3.3 40.6 - - + -
198A GLY 3.4 1.3 - - - +
199A PHE* 3.4 7.4 - - - -
200A THR* 2.9 53.2 + - - +
201A ARG 4.2 1.1 - - - -
202A GLY* 3.7 34.3 - - - -
217A GLU* 3.9 28.3 - - + -
218A LEU* 1.3 74.6 - - - +
220A PHE* 1.3 62.2 + - - +
221A GLN* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 4.6 3.8 - - + -
154A VAL* 3.5 34.5 - - + +
155A ASN* 3.2 5.4 - - - +
156A GLY 2.9 49.8 + - - +
157A GLN 4.7 0.4 - - - -
158A LYS* 3.9 24.0 - - + -
170A ILE* 5.5 0.2 - - + -
172A VAL* 3.8 27.1 - - + -
192A VAL* 4.0 21.8 - - + -
198A GLY 3.5 3.1 - - - -
199A PHE* 3.5 35.9 - + + -
218A LEU* 4.2 16.4 - - + -
219A PHE* 1.3 71.8 - - - +
221A GLN* 1.3 63.2 + - - +
223A ALA* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN* 3.7 4.5 - - - -
198A GLY* 2.9 25.7 + - - +
200A THR* 4.3 7.7 + - - +
219A PHE* 4.1 20.3 - - + +
220A PHE* 1.3 77.4 - - - +
222A ASP* 1.3 72.3 + - - +
223A ALA 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.5 21.3 - - + +
154A VAL 3.2 5.0 + - - -
155A ASN* 2.8 35.1 + - - +
197A PRO* 4.1 3.5 - - - +
198A GLY* 4.4 1.0 - - - -
221A GLN* 1.3 74.3 - - - +
223A ALA* 1.3 65.3 + - - +
224A LYS* 3.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR 2.9 8.7 - - - +
153A ILE* 3.3 2.3 - - - -
154A VAL* 2.7 55.4 + - + +
196A THR* 4.4 4.9 - - + -
197A PRO 3.2 13.0 - - - +
198A GLY* 4.1 9.4 - - - -
199A PHE 4.4 0.2 - - - +
220A PHE* 4.0 22.4 - - + -
221A GLN 3.2 1.2 - - - -
222A ASP* 1.3 71.1 - - - +
224A LYS* 1.3 59.7 + - - +
225A VAL* 3.5 8.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP* 5.3 5.7 + - - -
151A TYR* 3.6 55.3 - - + +
152A TYR 3.8 2.0 - - - -
153A ILE* 4.2 17.3 - - + +
196A THR* 3.4 13.9 - - - +
197A PRO* 3.1 33.8 + - + +
222A ASP 3.3 6.1 + - - +
223A ALA* 1.3 68.3 - - - +
225A VAL* 1.3 60.8 + - - +
226A PRO* 3.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 3.3 3.7 - - - -
152A TYR* 2.6 40.2 + - - +
154A VAL* 3.8 22.7 - - + -
190A LEU* 3.8 22.0 - - + -
191A VAL 3.6 24.2 - - - +
192A VAL* 4.0 17.9 - - + -
196A THR* 4.0 15.7 - - + +
223A ALA* 4.1 5.8 - - + +
224A LYS* 1.3 76.5 - - - +
226A PRO* 1.4 79.1 - - + +
229A ASN* 3.9 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP 3.7 7.6 - - - +
151A TYR* 3.7 16.5 - - + -
190A LEU* 4.2 2.8 - - - +
193A GLU* 5.3 5.4 - - - +
196A THR* 5.8 2.9 - - - +
224A LYS 3.9 6.5 - - - +
225A VAL* 1.4 91.2 - - + +
227A ALA* 1.3 60.0 + - - +
228A TYR* 4.2 12.1 - - + +
229A ASN* 3.0 42.8 + - - +
----------------------------------------------------------
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