Contacts of the helix formed by residues 170 - 185 (chain K) in PDB entry 1ZUM
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 PHE 170 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K GLU* 4.6 0.2 - - - -
112K LYS* 3.4 19.7 - - - +
121K ASP* 3.7 11.7 - - - +
124K MET* 5.5 4.0 - - + -
167K PRO 4.7 1.1 - - - -
169K ASN* 1.3 96.7 + - - +
171K PRO* 1.3 58.7 - - - +
172K LEU 3.6 1.6 - - - -
173K LEU* 4.0 24.2 - - + -
174K MET* 2.8 56.7 + - + +
177K TRP* 6.2 0.7 - + - -
296K PHE* 3.8 35.4 - + - -
297K ASN* 3.4 26.0 - - + -
300K GLN 3.7 9.4 - - - -
301K CYS* 4.4 15.5 - - + -
302K CYS* 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 171 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K GLU* 3.3 31.4 - - - +
110K ASN* 4.1 7.0 - - + +
112K LYS* 4.5 2.7 - - - +
166K ILE* 3.7 10.5 - - + +
167K PRO 4.3 9.2 - - - +
168K TRP 3.4 17.9 - - - +
169K ASN 3.6 3.8 - - - +
170K PHE* 1.3 88.8 - - - +
172K LEU* 1.3 61.8 + - - +
175K GLN* 3.2 20.1 + - - +
197K THR* 3.4 33.7 - - + +
200K THR* 3.6 11.4 - - - +
201K ALA* 5.5 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ILE* 6.2 1.3 - - + -
102K LEU* 4.2 17.7 - - + +
106K GLU* 3.0 24.6 + - - +
121K ASP* 5.6 1.3 - - + -
122K LEU* 3.4 31.0 - - + -
125K VAL* 3.8 20.0 - - + +
171K PRO* 1.3 75.1 - - - +
173K LEU* 1.3 60.9 + - - +
175K GLN* 3.2 16.6 + - - +
176K ALA* 3.0 26.9 + - - +
200K THR* 3.4 31.6 - - + +
201K ALA 4.4 0.2 - - - +
204K VAL* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K GLU* 4.7 0.4 + - - -
121K ASP* 4.7 9.9 + - - +
124K MET* 3.6 62.4 - - + +
125K VAL* 3.8 11.6 - - + +
170K PHE* 3.6 26.3 + - + -
171K PRO 3.5 0.2 - - - -
172K LEU* 1.3 78.6 - - - +
174K MET* 1.3 59.8 + - + +
176K ALA* 3.2 2.8 + - + +
177K TRP* 2.8 75.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ILE* 3.9 19.7 - - + -
167K PRO* 3.7 28.9 - - + +
169K ASN* 4.4 2.9 - - - +
170K PHE* 2.8 58.2 + - + +
171K PRO 4.0 1.8 - - - +
173K LEU* 1.3 75.3 - - + +
175K GLN* 1.3 62.8 + - - +
177K TRP* 3.0 48.1 + - + +
178K LYS* 3.2 33.9 + - - +
244K THR* 4.6 14.8 - - - -
302K CYS* 6.5 0.4 - - - -
476K GLU* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ILE* 3.8 13.4 - - + +
171K PRO 3.2 10.7 + - - +
172K LEU* 3.2 17.9 + - - +
173K LEU 3.1 0.2 - - - -
174K MET* 1.3 78.2 - - - +
176K ALA* 1.3 57.9 + - - +
178K LYS* 3.0 5.0 + - - +
179K LEU* 2.9 48.7 + - + +
191K MET* 3.9 15.0 - - - +
201K ALA* 3.4 36.0 - - + +
204K VAL* 3.4 40.4 - - - +
220K ILE* 3.9 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125K VAL* 4.2 28.9 - - + +
128K CYS* 3.6 13.4 - - + -
129K LEU* 4.1 24.2 - - + +
172K LEU 3.0 12.6 + - - +
173K LEU* 3.5 8.1 - - + +
175K GLN* 1.3 77.8 - - - +
177K TRP* 1.3 56.0 + - - +
179K LEU* 4.5 2.9 - - - +
180K GLY* 2.9 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 177 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K MET* 5.3 3.3 - - - -
128K CYS* 3.4 19.8 - - - +
132K TYR* 5.0 1.2 - - - -
170K PHE* 6.2 0.7 - + - -
173K LEU* 2.8 48.2 + - + +
174K MET* 3.0 46.4 - - + +
175K GLN 3.3 0.2 - - - -
176K ALA* 1.3 76.0 - - - +
178K LYS* 1.3 64.0 - - - +
181K PRO* 3.1 22.2 - - - +
302K CYS* 6.2 2.7 - - - -
459K PHE* 4.9 28.9 - + + -
461K ALA* 5.7 1.0 - - - +
465K PHE* 5.3 6.5 - + - -
476K GLU* 3.0 38.5 - - + +
477K LEU* 3.3 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K GLN* 2.9 42.5 + - + +
165K ILE 4.7 0.4 - - - -
166K ILE* 3.6 20.2 - - + +
174K MET* 3.2 21.8 + - - +
175K GLN 3.0 7.4 + - - +
177K TRP* 1.3 83.2 - - - +
179K LEU* 1.3 61.5 + - - +
180K GLY 3.4 0.2 - - - -
181K PRO* 3.6 4.3 - - - +
182K ALA* 3.2 15.9 + - - +
191K MET* 3.9 4.0 - - + -
242K ALA* 4.3 22.0 - - + -
244K THR* 2.9 32.3 + - - +
476K GLU* 4.4 15.4 + - - +
485K TYR* 4.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K LEU* 5.0 0.7 - - - -
91K LEU* 5.0 7.6 - - + -
129K LEU* 4.8 6.5 - - + -
164K GLN* 3.9 6.7 - - - +
175K GLN* 2.9 45.4 + - + +
176K ALA* 4.2 4.5 - - - +
178K LYS* 1.3 69.7 - - - +
180K GLY* 1.3 68.3 + - - +
182K ALA* 4.5 2.0 - - - -
183K LEU* 2.9 43.5 + - + +
189K VAL* 4.2 15.5 - - + -
191K MET* 3.8 19.3 - - + -
204K VAL* 4.8 3.6 - - + -
208K ILE* 4.0 23.6 - - + -
218K VAL* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K LEU* 4.0 6.5 - - - +
128K CYS* 5.1 0.7 - - - -
129K LEU* 4.5 11.6 - - - +
132K TYR* 3.5 23.0 - - - +
176K ALA 2.9 16.1 + - - -
179K LEU* 1.3 80.5 - - - +
181K PRO* 1.3 61.0 - - - +
184K ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 181 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132K TYR* 3.6 41.9 - - + +
177K TRP 3.1 27.8 - - - +
178K LYS 3.6 5.6 - - - +
180K GLY* 1.3 84.9 - - - +
182K ALA* 1.3 57.2 + - - +
184K ALA* 4.1 0.4 - - + +
185K THR* 2.6 38.8 + - - +
477K LEU 6.0 0.9 - - - +
481K GLY* 4.0 19.7 - - - +
482K LEU* 4.3 4.9 - - + -
485K TYR* 4.0 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162K CYS* 5.2 0.2 - - + -
164K GLN* 3.5 16.4 - - - +
178K LYS 3.2 18.8 - - - +
179K LEU 3.4 2.0 + - - +
180K GLY 3.4 0.8 - - - -
181K PRO* 1.3 81.6 - - - +
183K LEU* 1.3 60.3 + - - +
185K THR* 3.1 9.7 + - - -
187K ASN* 2.9 31.1 + - + -
189K VAL* 3.9 16.8 - - + -
485K TYR* 3.7 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K TRP* 3.5 23.8 - - + -
84K ARG* 3.6 6.0 + - - +
88K LEU* 3.9 26.0 - - + -
91K LEU* 5.3 3.4 - - + -
179K LEU* 2.9 38.4 + - + +
182K ALA* 1.3 73.2 - - + +
184K ALA* 1.3 61.4 + - - +
185K THR 3.0 1.8 - - - -
186K GLY 2.8 17.8 + - - -
187K ASN 3.8 10.3 - - - +
189K VAL* 4.8 7.0 - - + -
208K ILE* 5.6 0.9 - - + -
213K PHE* 4.0 15.5 - - + -
217K VAL* 3.6 33.7 - - + +
218K VAL* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K ARG* 2.9 23.0 + - - +
88K LEU* 3.9 12.0 - - + +
132K TYR* 3.3 31.9 - - + +
135K TRP* 4.8 4.0 - - + +
136K ALA* 3.4 22.9 - - - +
180K GLY 3.0 20.6 + - - +
181K PRO* 4.1 5.2 - - + +
183K LEU* 1.3 76.6 - - - +
185K THR* 1.3 58.7 + - - +
482K LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500J SER* 5.2 0.2 - - - -
84K ARG* 3.9 9.3 + - - +
135K TRP 6.2 0.2 - - - +
139K TYR* 4.6 8.3 - - + -
156K HIS 5.6 0.7 - - - +
157K GLU 5.0 0.7 - - - -
158K PRO* 3.2 23.2 - - - +
181K PRO 2.6 23.7 + - - +
182K ALA 3.1 0.2 + - - -
183K LEU 3.0 0.4 - - - -
184K ALA* 1.3 79.2 - - - +
186K GLY* 1.3 59.3 + - - +
187K ASN* 2.9 24.3 + - - -
482K LEU* 3.6 29.6 - - + +
485K TYR* 3.4 4.4 - - + +
486K THR* 3.9 27.7 - - + +
----------------------------------------------------------
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