Contacts of the helix formed by residues 170 - 185 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLU* 4.4 0.4 - - - -
112H LYS* 3.3 18.6 - - - +
121H ASP* 3.7 12.1 - - - +
124H MET* 5.2 4.0 - - + -
167H PRO 4.8 0.2 - - - -
169H ASN* 1.3 95.3 + - - +
171H PRO* 1.3 63.3 - - - +
172H LEU 3.4 2.0 - - - -
173H LEU* 3.3 28.3 + - + -
174H MET* 2.8 45.6 + - + +
296H PHE* 3.8 28.9 - + - -
297H ASN* 3.5 27.4 - - + -
300H GLN 3.6 16.6 - - - -
301H CYS* 4.2 20.2 - - - -
302H CYS* 5.3 1.1 - - - -
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Residues in contact with PRO 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLU* 3.3 29.2 - - - +
110H ASN* 4.1 7.0 - - + +
112H LYS* 4.5 2.2 - - - +
166H ILE* 3.5 13.0 - - + +
167H PRO 4.2 10.3 - - - +
168H TRP 3.3 19.3 - - - +
169H ASN 3.5 3.8 - - - +
170H PHE* 1.3 88.4 - - - +
172H LEU* 1.3 60.0 + - - +
175H GLN* 3.3 17.4 + - - +
197H THR* 3.5 35.7 - - + +
200H THR* 3.7 9.9 - - - +
201H ALA* 5.3 5.2 - - + +
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Residues in contact with LEU 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ILE* 6.3 0.9 - - + -
102H LEU* 4.2 17.3 - - + +
106H GLU* 3.0 30.0 + - - +
121H ASP* 5.5 2.5 - - + -
122H LEU* 3.7 33.2 - - + -
125H VAL* 3.6 22.0 - - + +
171H PRO* 1.3 70.7 - - - +
173H LEU* 1.3 66.3 + - - +
175H GLN* 3.2 11.0 + - - +
176H ALA* 3.0 19.4 + - - +
200H THR* 3.5 35.0 - - + +
201H ALA 4.5 0.2 - - - +
204H VAL* 3.6 30.1 - - + -
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Residues in contact with LEU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLU* 4.7 0.4 + - - -
121H ASP* 4.9 9.5 + - - +
124H MET* 3.3 66.4 - - + +
125H VAL* 3.7 11.1 - - + +
128H CYS* 4.8 0.9 - - + -
170H PHE* 3.3 25.4 + - + -
172H LEU* 1.3 80.0 - - - +
174H MET* 1.3 59.6 + - + +
176H ALA* 3.2 1.6 + - + +
177H TRP* 2.9 70.8 + - + +
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Residues in contact with MET 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H ILE* 4.0 24.0 - - + -
167H PRO* 3.8 19.5 - - + +
169H ASN* 4.1 4.3 - - - +
170H PHE* 2.8 42.9 + - + +
173H LEU* 1.3 80.3 - - + +
175H GLN* 1.3 62.8 + - - +
177H TRP* 3.3 55.0 + - + +
178H LYS* 3.2 32.9 + - - +
244H THR* 4.2 24.0 - - - -
302H CYS* 6.5 2.0 - - - -
476H GLU* 5.3 0.2 - - - +
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Residues in contact with GLN 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H ILE* 3.6 13.4 - - + +
171H PRO 3.3 11.9 + - - +
172H LEU* 3.2 15.3 + - - +
173H LEU 3.2 0.8 - - - -
174H MET* 1.3 79.0 - - - +
176H ALA* 1.3 58.0 + - - +
178H LYS* 3.2 3.3 + - - +
179H LEU* 2.8 50.7 + - + +
191H MET* 3.8 14.3 - - - +
201H ALA* 3.3 36.8 - - + +
204H VAL* 3.4 41.1 - - - +
208H ILE* 5.0 0.3 - - - +
220H ILE* 3.6 13.9 - - - +
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Residues in contact with ALA 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H VAL* 4.0 29.4 - - + +
128H CYS* 3.5 18.4 - - + -
129H LEU* 4.1 21.8 - - + +
172H LEU 3.0 15.3 + - - +
173H LEU* 3.2 4.7 + - - +
175H GLN* 1.3 78.2 - - - +
177H TRP* 1.3 55.8 + - - +
179H LEU* 4.4 2.7 - - - +
180H GLY* 2.8 28.2 + - - -
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Residues in contact with TRP 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H CYS* 3.6 23.5 - - - +
132H TYR* 5.1 1.0 - - - -
173H LEU* 2.9 49.6 + - + +
174H MET* 3.3 36.3 - - + +
175H GLN 3.3 0.2 - - - -
176H ALA* 1.3 77.1 - - - +
178H LYS* 1.3 59.0 + - + +
181H PRO* 3.2 22.7 - - - +
302H CYS* 6.2 1.3 - - - -
459H PHE* 4.3 24.0 - + + -
461H ALA* 6.1 0.2 - - - +
465H PHE* 4.0 29.4 - + - -
476H GLU* 3.5 43.8 - - + +
477H LEU* 3.7 36.6 + - + +
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Residues in contact with LYS 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H GLN* 3.0 42.6 - - + +
165H ILE 4.7 0.4 - - - -
166H ILE* 3.6 18.7 - - + +
174H MET* 3.2 21.0 + - - +
175H GLN 3.7 2.9 - - - +
176H ALA 3.2 0.4 - - - -
177H TRP* 1.3 77.1 - - - +
179H LEU* 1.3 64.0 + - - +
180H GLY 3.4 0.4 - - - -
181H PRO* 3.7 4.2 - - - +
182H ALA* 3.3 13.7 + - - +
191H MET* 4.0 3.8 - - + -
242H ALA* 3.8 26.5 - - + -
244H THR* 2.8 31.1 + - - +
268H GLU* 3.3 3.6 + - - -
476H GLU* 3.0 30.1 + - - +
485H TYR* 4.0 17.1 + - + +
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Residues in contact with LEU 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU* 5.0 0.4 - - - -
91H LEU* 5.1 7.0 - - + -
129H LEU* 4.9 5.8 - - + -
164H GLN* 3.8 8.5 - - - +
175H GLN* 2.8 43.6 + - + +
176H ALA* 4.3 4.0 - - - +
178H LYS* 1.3 74.2 - - - +
180H GLY* 1.3 67.2 + - - +
182H ALA* 4.4 2.7 - - - -
183H LEU* 2.9 40.2 + - + +
189H VAL* 4.2 17.5 - - + -
191H MET* 3.8 17.9 - - + -
204H VAL* 4.8 3.8 - - + -
208H ILE* 3.8 26.9 - - + -
218H VAL* 4.2 17.7 - - + -
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Residues in contact with GLY 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU* 4.0 6.2 - - - +
128H CYS* 5.2 0.2 - - - -
129H LEU* 4.4 12.9 - - - +
132H TYR* 3.5 24.2 - - - +
176H ALA 2.8 15.9 + - - -
179H LEU* 1.3 76.9 - - - +
181H PRO* 1.3 61.2 - - - +
184H ALA* 3.0 32.1 + - - +
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Residues in contact with PRO 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H TYR* 3.6 41.1 - - + +
177H TRP 3.2 26.2 - - - +
178H LYS 3.7 5.2 - - - +
180H GLY* 1.3 87.3 - - - +
182H ALA* 1.3 56.9 + - - +
184H ALA* 3.9 0.6 - - + +
185H THR* 2.7 39.3 + - - +
476H GLU* 6.0 1.1 - - + -
477H LEU 5.8 1.6 - - - +
481H GLY* 4.0 12.3 - - - +
482H LEU* 4.1 5.2 - - + -
485H TYR* 3.9 24.4 - - + +
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Residues in contact with ALA 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H CYS* 5.3 0.2 - - + -
164H GLN* 3.5 12.8 - - - +
178H LYS 3.3 17.9 - - - +
179H LEU 3.4 2.2 + - - +
180H GLY 3.4 0.4 - - - -
181H PRO* 1.3 80.9 - - - +
183H LEU* 1.3 59.7 + - - +
185H THR* 3.1 10.3 + - - -
187H ASN* 3.0 30.5 + - + +
189H VAL* 4.0 19.7 - - + -
485H TYR* 3.8 23.0 - - + -
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Residues in contact with LEU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H TRP* 3.5 13.6 - - + -
84H ARG* 3.5 15.6 - - - +
88H LEU* 4.2 18.8 - - + -
91H LEU* 5.6 2.2 - - + -
179H LEU* 2.9 40.1 + - + +
182H ALA* 1.3 70.1 - - + +
184H ALA* 1.3 66.1 + - - +
185H THR 3.1 2.0 - - - -
186H GLY 3.0 10.2 + - - -
187H ASN 3.7 12.1 - - - +
189H VAL* 4.3 9.0 - - + -
208H ILE* 5.5 1.8 - - + -
213H PHE* 3.9 22.2 - - + -
217H VAL* 3.6 28.5 - - + +
218H VAL* 3.8 25.4 - - + -
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Residues in contact with ALA 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ARG* 3.0 23.4 + - - -
88H LEU* 3.9 10.9 - - + +
132H TYR* 3.4 29.6 - - + +
135H TRP* 4.7 1.3 - - + -
136H ALA* 3.4 23.8 - - - +
180H GLY 3.0 22.2 + - - +
181H PRO* 3.9 6.3 - - + +
182H ALA 3.4 0.2 - - - -
183H LEU* 1.3 75.0 - - - +
185H THR* 1.3 59.3 + - - +
186H GLY 3.4 0.2 - - - -
482H LEU* 4.7 6.1 - - + -
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Residues in contact with THR 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500E SER* 5.1 0.7 - - - -
84H ARG* 4.0 9.8 + - - +
135H TRP 6.2 0.2 - - - +
139H TYR* 4.6 9.4 - - + -
156H HIS 5.5 1.2 - - - +
157H GLU 4.9 0.5 - - - -
158H PRO* 3.3 23.2 - - - +
181H PRO 2.7 16.9 + - - -
182H ALA 3.1 0.2 + - - -
183H LEU 3.1 0.2 - - - -
184H ALA* 1.3 79.0 - - - +
186H GLY* 1.3 56.9 + - - +
187H ASN* 2.8 25.1 + - - -
482H LEU* 3.7 33.7 - - + +
485H TYR* 3.4 4.0 - - + +
486H THR* 3.7 29.7 - - + +
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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) + - + + + + + -
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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