Contacts of the helix formed by residues 160 - 177 (chain B) in PDB entry 1ULH
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 160 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 3.8 4.9 - - - -
159B LEU* 1.3 78.9 - - - +
161B LEU* 1.3 65.3 + - - +
162B ASP* 3.4 10.3 + - - +
163B GLN* 3.1 42.5 + - - +
164B ALA* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 3.6 46.9 - - + +
205A VAL* 4.8 4.5 - - + -
206A LYS* 4.2 22.7 - - + -
154B TYR* 3.6 41.9 - - + -
160B THR* 1.3 74.1 - - - +
162B ASP* 1.3 63.0 + - - +
164B ALA* 3.4 3.9 + - - +
165B TYR* 3.0 23.6 + - - +
191B LEU* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B THR* 3.4 10.3 + - - +
161B LEU* 1.3 79.0 - - - +
163B GLN* 1.3 57.6 + - + +
165B TYR* 3.2 9.3 + - - +
166B SER* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASP 4.0 2.1 - - - +
159B LEU* 3.0 33.6 - - + +
160B THR* 3.1 41.6 + - - +
162B ASP* 1.3 78.1 - - + +
164B ALA* 1.3 62.4 + - - +
166B SER* 3.1 11.1 + - - -
167B TYR* 3.0 45.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
117B PRO* 4.1 4.3 - - - +
150B ASP* 3.4 39.7 - - + +
153B LYS* 5.4 0.9 - - + -
154B TYR* 4.1 12.6 - - + -
159B LEU* 4.2 17.6 - - + +
160B THR 3.0 13.9 + - - +
161B LEU* 3.8 5.2 - - - +
163B GLN* 1.3 80.4 - - - +
165B TYR* 1.3 61.6 + - - +
167B TYR* 3.6 5.8 + - - +
168B ALA 3.4 12.5 + - - -
191B LEU* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASP* 3.8 11.4 - - - +
161B LEU 3.0 14.8 + - - +
162B ASP* 3.6 10.1 - - - +
164B ALA* 1.3 74.3 - - - +
166B SER* 1.3 69.4 + - - +
168B ALA* 2.9 15.7 + - + +
169B VAL* 3.0 35.7 + - + +
189B SER* 3.6 30.7 - - - -
191B LEU* 4.7 6.5 - - + +
192B ASP* 3.4 26.9 + - + -
414B MET* 4.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASP* 2.9 21.7 + - - +
163B GLN* 3.2 14.4 - - - -
165B TYR* 1.3 79.0 - - - +
167B TYR* 1.3 64.2 + - - +
169B VAL* 3.1 10.9 + - - +
170B GLU* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 3.3 32.8 - - + +
118B SER 3.8 2.9 - - - -
119B SER* 3.5 27.5 - - - +
120B GLU* 3.6 36.1 + - + -
159B LEU* 3.6 38.2 - - + +
163B GLN* 3.0 28.1 + - + +
164B ALA* 4.0 3.4 - - - +
165B TYR 3.2 0.2 - - - -
166B SER* 1.3 79.8 - - - +
168B ALA* 1.3 57.8 + - - +
170B GLU* 4.4 4.9 - - - +
171B ASN* 2.7 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 3.7 14.1 - - + +
148B MET* 3.2 33.9 - - + +
150B ASP* 4.2 13.5 - - + +
164B ALA 3.4 10.2 + - - +
165B TYR* 2.9 12.9 + - + +
167B TYR* 1.3 77.6 - - - +
169B VAL* 1.3 63.7 + - - +
172B ALA* 3.0 22.3 + - - +
189B SER* 4.4 7.6 - - - -
414B MET* 4.8 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TYR* 3.0 47.2 + - + +
166B SER* 3.4 9.4 - - - +
168B ALA* 1.3 77.4 - - - +
170B GLU* 1.3 73.8 + - - +
172B ALA* 3.2 19.1 + - - +
173B LYS* 3.4 15.6 + - - +
410B VAL* 3.8 20.7 - - + +
414B MET* 4.7 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 4.3 30.1 - - + +
166B SER* 2.9 19.0 + - - +
167B TYR* 4.0 5.2 - - - +
169B VAL* 1.3 81.5 - - - +
171B ASN* 1.3 68.4 + - - +
173B LYS* 2.7 44.6 + - - +
174B ASP* 3.6 3.2 + - - +
402B ARG* 3.0 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 2.6 40.8 + - + +
117B PRO* 3.7 7.0 - - + +
119B SER 3.3 17.6 + - - -
120B GLU* 3.3 21.0 + - - +
122B MET* 3.3 22.4 - - + +
148B MET* 3.6 17.9 - - + -
167B TYR 2.7 25.7 + - - +
170B GLU* 1.3 72.5 - - - +
172B ALA* 1.3 61.3 + - - +
174B ASP 3.4 1.0 + - - -
175B ILE* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 3.7 8.9 - - + +
168B ALA 3.0 18.9 + - - +
169B VAL 3.3 7.2 - - - +
170B GLU 3.1 0.4 - - - -
171B ASN* 1.3 74.0 - - - +
173B LYS* 1.3 57.0 + - - +
175B ILE* 3.6 6.8 - - - +
176B ILE* 2.7 45.2 + - + +
187B ILE* 4.4 12.7 - - + +
410B VAL* 4.8 5.8 - - + -
414B MET* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.6 13.5 - - - +
170B GLU* 2.7 48.6 + - - +
172B ALA* 1.3 76.9 - - - +
174B ASP* 1.3 58.2 + - - +
176B ILE* 3.2 4.2 + - - +
177B ALA* 2.8 27.5 + - - +
402B ARG* 3.6 27.8 - - + +
405B VAL* 3.8 30.9 - - + +
406B THR 5.8 0.2 - - - -
407B ASP* 4.6 15.3 + - - +
410B VAL* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU 4.6 5.4 - - - +
122B MET* 3.4 35.3 + - + +
170B GLU 3.7 2.6 - - - +
171B ASN 3.4 1.0 + - - -
172B ALA 3.3 0.2 - - - -
173B LYS* 1.3 76.5 - - - +
175B ILE* 1.3 66.1 + - - +
177B ALA* 3.2 16.8 + - - +
178B CYS* 3.6 5.4 + - - -
314B LEU* 4.1 14.3 - - + +
398B HIS* 3.1 37.8 + - + -
402B ARG* 2.8 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ARG* 4.1 8.5 - - + -
122B MET* 4.7 6.3 - - - -
130B PHE* 3.7 36.1 - - + -
146B ILE* 3.6 31.6 - - + -
148B MET* 3.6 32.5 - - + -
171B ASN 3.1 16.8 + - - +
172B ALA* 3.6 7.2 - - - +
174B ASP* 1.3 72.9 - - - +
176B ILE* 1.3 66.4 + - - +
178B CYS* 3.0 14.0 + - - +
180B PHE* 3.0 34.3 - - + -
187B ILE* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA* 2.7 27.1 + - + +
173B LYS 3.2 4.2 + - - +
175B ILE* 1.3 72.7 - - - +
177B ALA* 1.3 51.8 + - - +
178B CYS 2.8 4.9 + - - -
179B GLY* 2.7 30.8 + - - -
180B PHE* 3.9 7.4 + - - +
187B ILE* 3.9 17.3 - - + -
405B VAL* 3.6 27.8 - - + -
409B ILE* 4.4 4.7 - - + -
410B VAL* 4.2 18.2 - - + -
413B PHE* 3.5 51.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS 2.8 13.7 + - - +
174B ASP 3.2 12.6 - - - +
175B ILE 3.2 0.6 - - - -
176B ILE* 1.3 76.7 - - - +
178B CYS* 1.3 59.2 + - - +
179B GLY* 3.1 2.6 + - - -
398B HIS* 3.8 35.0 - - + +
401B ARG* 3.3 35.0 + - - +
402B ARG* 3.9 15.7 - - + +
405B VAL* 4.8 2.7 - - - -
----------------------------------------------------------
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