Contacts of the strand formed by residues 173 - 183 (chain B) in PDB entry 2D2I
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 ILE 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA* 3.6 32.5 - - + +
167B LEU* 4.3 10.3 - - + +
168B HIS* 2.7 35.6 + - + +
172B GLY* 1.3 71.3 - - - -
174B ILE* 1.3 63.1 + - - +
175B LYS* 3.8 24.5 - - - +
226B LEU* 4.1 22.7 - - + -
229B LYS* 2.8 26.8 + - + +
230B LEU* 4.7 8.3 - - + -
247B LEU* 5.8 0.2 - - + -
249B VAL* 4.1 28.7 - - + -
250B GLN 3.8 3.4 - - - -
251B VAL* 4.7 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASP* 5.1 4.5 - - - +
172B GLY 5.0 0.2 - - - -
173B ILE* 1.3 75.1 - - - +
175B LYS* 1.3 80.1 + - + +
229B LYS* 3.2 32.1 - - - +
250B GLN* 2.9 32.8 + - + +
251B VAL 3.8 18.2 - - - +
252B GLU* 3.6 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A MET* 3.5 26.2 - - + +
306A ASP* 3.1 40.8 + - + -
308A ASP* 3.3 24.6 + - - -
309A LEU* 3.6 18.2 - - + +
173B ILE* 3.7 7.9 - - - +
174B ILE* 1.3 86.9 - - - +
176B GLY* 1.3 61.3 + - - +
229B LYS* 3.2 15.5 - - - +
249B VAL* 3.7 1.2 - - - -
250B GLN* 2.5 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A MET* 3.5 15.3 - - - +
309A LEU* 5.5 4.9 - - - -
175B LYS* 1.3 80.0 - - - +
177B THR* 1.3 62.5 + - - -
229B LYS 2.8 10.3 + - - +
230B LEU* 3.6 15.5 - - - -
231B ASN 3.4 17.2 + - - -
248B VAL 3.2 12.1 - - - -
249B VAL* 4.0 2.7 - - - -
250B GLN 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.4 29.8 - - + -
303A LEU* 4.3 7.9 - - - +
305A MET* 5.5 1.8 - - - -
309A LEU* 4.7 10.3 - - + +
311A LYS* 3.2 39.1 + - + +
176B GLY* 1.3 75.7 + - - -
178B MET* 1.3 61.9 + - - +
230B LEU* 4.3 1.0 - - - +
231B ASN* 3.4 13.8 + - - +
246B ASP 3.8 0.2 - - - +
247B LEU* 3.7 3.1 - - - +
248B VAL* 2.7 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 4.0 3.9 + - - +
156B THR* 3.2 34.8 - - + -
160B LEU* 3.2 35.9 - - + -
177B THR* 1.3 77.5 - - - +
179B THR* 1.3 79.2 + - - +
180B THR* 4.0 5.2 - - - -
213B THR* 5.1 4.0 - - - -
215B ALA* 4.0 8.1 - - + -
216B ALA* 4.1 12.8 - - + +
230B LEU* 6.2 0.7 - - + -
231B ASN 2.9 15.2 + - - +
232B GLY* 2.9 27.3 - - - -
233B ILE 3.2 7.6 + - - +
245B VAL* 4.3 6.5 - - + -
246B ASP 3.1 12.3 - - - +
247B LEU* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASP* 2.6 28.6 + - + +
311A LYS* 3.2 19.3 + - - +
178B MET* 1.3 76.7 + - - +
180B THR* 1.3 66.5 + - - +
181B THR* 4.1 4.9 + - - +
233B ILE* 3.3 22.1 - - + +
235B LEU* 4.1 28.5 - - + -
244B VAL 4.0 0.7 - - - +
245B VAL* 3.9 0.2 - - - -
246B ASP* 2.9 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR* 3.9 24.9 - - + +
178B MET* 4.0 3.1 - - - -
179B THR* 1.3 73.3 - - - +
181B THR* 1.3 57.2 + - - +
182B HIS* 3.4 16.6 + - + +
213B THR* 4.9 4.7 - - - +
233B ILE 3.1 6.9 + - - +
234B ALA* 3.3 25.4 - - + -
235B LEU* 2.8 31.9 + - - +
244B VAL 3.3 9.6 + - - -
245B VAL* 4.4 4.0 - - - +
316B TYR* 2.8 26.5 + - - -
2339B SO4 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 3.9 12.9 + - + -
208A ILE* 3.9 21.0 - - + +
235A LEU* 3.6 21.8 - - + +
237A VAL* 4.2 11.9 - - + -
179B THR* 4.1 4.7 + - - +
180B THR* 1.3 69.7 - - - +
182B HIS* 1.3 58.5 + - - +
235B LEU* 3.4 11.7 - - + +
237B VAL* 3.8 24.9 - - + -
243B SER* 3.4 3.8 - - - -
244B VAL* 2.9 44.9 + - - +
246B ASP* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B CYS* 3.6 24.5 - - - -
156B THR* 3.8 9.4 + - - -
180B THR* 3.4 13.2 + - + +
181B THR* 1.3 73.0 - - - +
183B SER* 1.3 87.8 + - - +
185B THR* 4.0 14.1 - - + -
234B ALA* 5.2 0.9 - - + -
235B LEU 2.9 10.6 + - - +
236B ARG* 3.2 32.6 + - - +
237B VAL* 2.8 32.1 + - - -
243B SER* 3.4 18.8 + - - -
316B TYR* 3.5 20.4 - - - -
318B ASN* 3.8 20.8 - - + +
2340B SO4 5.4 0.7 - - - -
2341B NAP 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B HIS* 1.3 94.5 + - - +
184B TYR* 1.3 65.9 + - - +
236B ARG* 3.4 3.5 - - - -
237B VAL* 3.7 1.3 - - - +
239B THR* 2.7 35.2 + - - -
240B PRO 3.7 2.5 - - - -
241B ASN* 3.0 27.1 + - - -
242B VAL 2.6 26.7 + - - -
243B SER* 3.2 9.5 + - - -
318B ASN* 4.3 4.0 - - - -
----------------------------------------------------------
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