Contacts of the helix formed by residues 154 - 172 (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 SER 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 5.0 0.2 - - - +
124B PRO* 3.5 20.7 - - - +
153B ALA* 1.3 80.4 - - - +
155B CYS* 1.3 65.4 + - - +
156B THR 3.6 2.0 + - - -
157B THR* 3.2 22.5 + - - -
158B ASN* 3.0 23.7 + - - +
322B TYR* 3.8 4.3 - - - -
2339B SO4 2.8 41.6 + - - -
2341B NAP 4.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 1.3 74.1 - - - +
156B THR* 1.3 70.3 + - - +
158B ASN* 3.1 12.8 + - - +
159B CYS* 3.1 10.7 + - - +
182B HIS* 3.6 25.6 - - - -
294B SER 5.2 0.2 - - - +
316B TYR* 3.7 13.5 - - + -
318B ASN* 3.7 30.3 - - + +
322B TYR* 3.7 17.6 - - + -
2339B SO4 5.1 3.1 - - - -
2340B SO4 5.9 1.3 - - - -
2341B NAP 3.3 29.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.2 4.3 + - - -
155B CYS* 1.3 81.0 - - - +
157B THR* 1.3 58.0 + - - +
159B CYS* 3.0 3.1 + - - +
160B LEU* 2.8 30.4 + - - +
178B MET* 3.2 33.0 - - + -
180B THR* 3.9 19.0 + - + +
182B HIS* 3.8 14.0 + - - -
215B ALA* 3.5 13.7 - - + -
245B VAL* 4.0 3.8 - - + -
316B TYR* 2.9 27.3 + - - +
2339B SO4 4.1 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 5.7 0.7 - - - +
132B THR* 6.3 0.2 - - + -
134B VAL* 4.4 9.0 - - + -
153B ALA* 3.9 21.8 - - + -
154B SER* 3.2 19.0 + - - -
156B THR* 1.3 76.9 - - - +
158B ASN* 1.3 58.7 + - - +
160B LEU* 4.3 4.0 - - - -
161B ALA* 2.8 30.7 + - + +
215B ALA* 3.2 35.6 + - - +
218B ALA* 3.7 12.8 - - + +
219B VAL* 4.3 19.7 - - + +
222B VAL* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.9 31.0 - - - +
135B ILE 4.5 2.2 + - - +
152B ASN* 2.8 33.4 + - - +
153B ALA* 4.2 0.2 - - - +
154B SER 3.0 13.1 + - - +
155B CYS* 3.1 11.6 + - - +
157B THR* 1.3 77.6 - - - +
159B CYS* 1.3 58.8 + - - +
162B PRO* 2.8 24.7 - - - +
294B SER* 3.4 20.6 + - - +
322B TYR* 3.9 6.6 - - + -
325B ARG* 3.4 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B CYS 3.1 5.6 + - - +
156B THR 3.0 7.4 + - - +
158B ASN* 1.3 76.1 - - - +
160B LEU* 1.3 67.8 + - - +
162B PRO* 3.6 1.7 - - - +
163B VAL* 3.9 6.6 - - - +
245B VAL* 4.0 9.2 - - + -
294B SER 3.3 14.8 + - - +
295B SER* 2.5 26.4 + - - -
314B ALA* 3.7 31.2 - - - -
315B TRP 3.9 3.8 - - - -
316B TYR* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR 2.8 15.4 + - - +
157B THR 4.0 2.0 - - - +
159B CYS* 1.3 80.0 - - - +
161B ALA* 1.3 63.7 + - - +
163B VAL* 3.2 8.3 + - + +
164B ALA* 3.0 21.1 + - + +
178B MET* 3.2 35.2 - - + -
215B ALA* 3.6 11.2 - - + +
216B ALA* 3.7 8.7 - - + -
219B VAL* 3.3 28.5 - - + -
230B LEU* 4.9 7.4 - - + -
245B VAL* 4.4 10.7 - - + +
247B LEU* 3.9 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 4.0 4.9 - - + -
137B VAL* 3.8 16.6 - - + -
157B THR* 2.8 23.5 + - + +
160B LEU* 1.3 74.1 - - - +
162B PRO* 1.3 66.8 - - + +
164B ALA* 3.1 7.7 + - - +
165B LYS* 2.9 24.3 + - - +
219B VAL* 4.5 11.6 - - + +
222B VAL* 4.0 22.4 - - + -
223B ILE* 3.6 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 4.5 4.0 - - + -
135B ILE 4.7 0.2 - - - +
137B VAL* 3.9 17.3 - - + -
158B ASN* 2.8 30.3 - - - +
159B CYS 3.6 6.3 - - - +
161B ALA* 1.3 90.1 - - + +
163B VAL* 1.3 59.1 + - - +
165B LYS* 3.5 3.7 + - + +
166B VAL* 3.2 28.8 + - - +
272B MET* 4.3 6.5 - - - +
275B ILE* 3.5 34.3 - - + -
276B ILE* 3.7 16.1 - - + +
294B SER* 4.6 0.2 - - - -
295B SER* 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B CYS 3.9 13.0 - - - +
160B LEU* 3.2 8.6 + - + +
161B ALA 3.2 0.2 - - - -
162B PRO* 1.3 75.0 - - - +
164B ALA* 1.3 61.1 + - - +
166B VAL* 3.6 1.8 + - - +
167B LEU* 3.0 47.1 + - + +
245B VAL* 6.5 1.3 - - + -
247B LEU* 3.8 9.4 - - + -
264B LEU* 4.6 8.1 - - + -
276B ILE* 4.3 7.9 - - + -
295B SER* 4.0 16.8 - - - -
297B VAL* 4.1 20.9 - - + -
312B VAL* 3.7 19.5 - - + -
314B ALA* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 3.0 18.8 + - + +
161B ALA* 3.6 9.9 - - - +
163B VAL* 1.3 75.0 - - - +
165B LYS* 1.3 56.9 + - - +
167B LEU* 4.5 1.3 - - - -
168B HIS* 2.6 40.1 + - - +
173B ILE* 3.6 10.0 - - + +
219B VAL* 4.8 1.8 - - + -
223B ILE* 4.0 5.6 - - + -
226B LEU* 4.0 22.0 - - + -
230B LEU* 4.7 10.8 - - + -
247B LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY 3.9 9.9 - - - +
137B VAL* 4.1 25.1 - - + -
161B ALA 2.9 15.3 + - - +
162B PRO* 3.6 6.5 - - + +
164B ALA* 1.3 77.0 - - - +
166B VAL* 1.3 58.3 + - + +
168B HIS* 3.8 2.9 - - - -
169B ASP* 2.8 65.7 + - - +
223B ILE* 3.7 19.7 - - + +
272B MET* 3.7 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO 3.2 18.2 + - - +
163B VAL 4.0 3.8 - - - +
164B ALA 3.3 0.2 - - - -
165B LYS* 1.3 76.9 - - + +
167B LEU* 1.3 63.4 + - - +
169B ASP* 4.6 3.4 - - - -
170B ASN* 2.8 44.6 + - - +
263B VAL* 3.9 28.4 - - + +
264B LEU* 4.0 15.7 - - + -
267B ALA* 3.9 22.2 - - + -
271B THR* 5.5 1.1 - - - +
272B MET* 3.9 16.6 - - + -
276B ILE* 3.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.0 38.9 + - + +
164B ALA 3.8 2.2 - - - +
166B VAL* 1.3 76.7 - - - +
168B HIS* 1.3 63.9 + - - +
171B PHE* 2.9 46.5 + - + +
172B GLY 3.5 2.8 + - - -
173B ILE* 4.3 12.8 - - + +
247B LEU* 3.7 18.6 - - + -
249B VAL* 4.5 11.2 - - + -
251B VAL* 4.9 1.9 - - + +
260B VAL* 4.7 7.6 - - + -
263B VAL* 5.0 1.3 - - + -
264B LEU* 4.2 27.6 - - + -
310B VAL* 4.6 9.4 - - + -
312B VAL* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA 2.6 24.6 + - - +
165B LYS* 3.9 4.5 - - - +
167B LEU* 1.3 74.7 - - - +
169B ASP* 1.3 68.0 + - - +
172B GLY* 2.8 32.5 + - - +
173B ILE* 2.7 53.7 + - + +
223B ILE* 4.8 6.7 - - + -
225B GLU* 3.2 37.7 + - + +
226B LEU* 3.8 19.9 - - + +
229B LYS* 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS* 2.8 59.9 + - - +
166B VAL* 3.9 5.5 + - - +
168B HIS* 1.3 82.5 - - - +
170B ASN* 1.3 67.9 + - - +
172B GLY 4.9 0.3 + - - -
253B LYS* 5.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 2.8 42.3 + - - +
169B ASP* 1.3 86.7 - - - +
171B PHE* 1.3 90.1 + - + +
253B LYS* 3.6 17.7 - - - +
263B VAL* 3.9 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 2.9 26.3 + - + +
170B ASN* 1.3 104.1 - - + +
172B GLY* 1.3 67.9 + - - +
251B VAL* 3.0 29.8 - - + -
252B GLU* 3.1 3.3 + - - +
253B LYS* 2.9 45.6 + - + +
254B PRO 5.1 0.2 - - - -
255B THR* 3.2 41.1 - - + -
259B GLN* 3.6 12.8 - - + -
260B VAL* 4.0 26.9 - - + -
263B VAL* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU 3.5 1.6 + - - -
168B HIS* 2.8 25.4 + - - -
169B ASP 4.9 0.2 + - - -
170B ASN 3.9 0.2 - - - -
171B PHE* 1.3 76.6 - - - +
173B ILE* 1.3 64.5 + - - -
251B VAL* 3.3 4.2 - - - -
252B GLU* 2.8 37.5 + - - +
----------------------------------------------------------
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