Contacts of the strand formed by residues 202 - 209 (chain A) in PDB entry 3N2Q
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 THR 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 5.1 2.5 - - - +
190A PHE* 3.5 12.2 - - - -
191A LYS* 2.7 36.8 + - + +
193A GLU* 5.9 2.7 - - - +
200A ASN 4.3 5.4 - - - +
201A GLY* 1.3 75.7 - - - -
203A TYR* 1.3 66.4 + - - +
204A ILE* 3.7 18.7 + - + -
224A GLU* 5.4 1.7 + - - -
270A LYS* 4.5 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.8 1.8 - - + -
80A TYR* 2.8 44.4 + - - -
83A GLY* 3.7 19.3 - - - -
84A LEU* 3.5 24.9 - - + +
87A ILE* 3.9 14.4 - - + -
126A ILE* 4.2 0.2 - - - +
147A GLY* 3.7 6.0 - - - -
188A ALA* 3.6 34.3 - - + -
189A ILE 3.2 19.3 - - - -
190A PHE* 3.4 35.0 - + + -
202A THR* 1.3 81.2 + - - +
204A ILE* 1.3 61.5 + - - +
205A ALA 4.9 0.4 - - - -
222A ILE* 3.4 23.7 - - + +
224A GLU* 5.0 3.3 - - - +
270A LYS* 5.0 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASN* 3.9 48.7 - - + +
159A ALA* 4.5 2.0 - - + -
160A MSE 5.0 9.0 - - + -
189A ILE* 3.0 38.1 + - + +
191A LYS* 3.8 25.1 - - + -
202A THR* 4.0 14.1 - - + -
203A TYR* 1.3 78.3 - - - +
205A ALA* 1.3 65.7 + - + +
220A SER 4.4 1.0 - - - +
221A THR* 4.5 3.8 - - - +
222A ILE* 3.7 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A MSE 4.7 9.9 - - + -
188A ALA* 3.2 4.2 - - - +
189A ILE* 2.8 35.1 + - + +
204A ILE* 1.3 84.4 - - + +
206A SER* 1.3 63.1 + - - +
219A TRP* 3.7 31.4 - - + -
220A SER 3.2 12.6 - - - +
222A ILE* 3.5 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 4.6 9.5 - - - +
186A THR* 4.1 16.1 - - - +
187A PHE 3.1 11.2 - - - -
188A ALA* 4.4 5.6 - - - -
205A ALA* 1.3 75.0 - - - +
207A ALA* 1.3 59.3 + - - +
208A THR* 5.1 3.1 - - - +
219A TRP* 3.4 5.3 - - - -
220A SER* 2.6 52.2 + - - -
221A THR 4.7 1.7 + - - -
222A ILE* 3.7 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE 4.0 0.5 - - - +
186A THR* 3.4 1.6 - - - -
187A PHE* 2.8 34.5 + - + +
206A SER* 1.3 75.1 - - - +
208A THR* 1.3 63.8 + - - +
216A LEU* 3.7 17.5 - - + -
217A GLY 3.6 22.2 - - - +
218A ASN 3.8 7.6 - - - +
219A TRP* 3.6 23.3 - - + -
220A SER* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 4.0 11.2 - - - +
184A PRO* 5.8 1.3 - - - -
185A ILE 3.2 3.8 - - - -
186A THR* 3.0 34.3 - - + +
206A SER* 5.1 3.8 - - - +
207A ALA* 1.3 81.1 - - - +
209A VAL* 1.3 64.8 + - - +
210A GLN* 3.5 22.5 + - - -
215A ASN 4.2 0.7 - - - +
216A LEU* 4.3 0.2 - - - -
217A GLY* 3.0 27.4 + - - +
218A ASN 4.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 3.6 35.7 - - + -
180A TYR* 6.0 0.4 - - - +
183A SER 6.1 0.2 - - - +
184A PRO* 3.1 23.2 - - - +
185A ILE* 2.7 25.4 + - + +
187A PHE* 4.1 6.7 - - + -
208A THR* 1.3 74.8 - - - +
210A GLN* 1.3 70.8 + - - +
213A ASP* 3.4 32.5 - - + +
214A THR* 3.8 9.0 - - - -
215A ASN 3.8 14.4 - - - +
216A LEU* 3.9 13.0 - - + -
----------------------------------------------------------
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