Contacts of the helix formed by residues 170 - 185 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F GLU* 4.5 0.2 - - - -
112F LYS* 3.2 27.8 - - - +
121F ASP* 3.6 11.0 - - - -
124F MET* 5.4 3.4 - - + -
167F PRO 4.7 0.7 - - - -
169F ASN* 1.3 95.0 + - - +
171F PRO* 1.3 59.3 - - - +
172F LEU 3.5 1.8 - - - -
173F LEU* 3.4 29.8 + - + -
174F MET* 2.7 44.6 + - + +
177F TRP* 6.5 1.1 - + - -
296F PHE* 3.7 35.9 - + - -
297F ASN* 3.4 23.8 - - + -
300F GLN 3.8 9.9 - - - -
301F CYS* 4.3 15.9 - - + -
302F CYS* 5.4 1.1 - - - -
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Residues in contact with PRO 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F GLU* 3.4 30.7 - - + +
110F ASN* 4.0 7.4 - - + +
112F LYS* 4.6 1.3 - - - +
166F ILE* 3.5 9.4 - - + +
167F PRO 4.2 9.4 - - - +
168F TRP 3.4 13.2 - - - +
169F ASN 3.6 3.1 - - - +
170F PHE* 1.3 84.9 - - - +
172F LEU* 1.3 61.8 + - - +
175F GLN* 3.1 24.2 + - - +
197F THR* 3.3 43.7 - - + +
200F THR* 3.8 8.1 - - - +
201F ALA* 5.4 4.8 - - + +
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ILE* 6.2 0.4 - - + -
102F LEU* 4.1 16.8 - - + +
106F GLU* 3.0 24.5 + - + +
121F ASP* 5.5 3.1 - - + -
122F LEU* 4.1 32.5 - - + -
125F VAL* 3.6 17.8 - - + +
171F PRO* 1.3 74.6 - - - +
173F LEU* 1.3 66.2 + - - +
175F GLN* 3.2 13.9 + - - +
176F ALA* 3.0 22.9 + - - +
200F THR* 3.5 31.6 - - + +
204F VAL* 3.5 32.1 - - + -
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F GLU* 4.6 0.6 + - - -
121F ASP* 4.8 10.4 + - - +
124F MET* 3.3 65.3 - - + +
125F VAL* 3.7 11.6 - - + +
128F CYS* 4.8 0.9 - - + -
170F PHE* 3.4 27.6 + - + -
172F LEU* 1.3 78.4 - - - +
174F MET* 1.3 58.6 + - - +
176F ALA* 3.2 1.2 + - - +
177F TRP* 2.9 69.7 + - + +
459F PHE* 6.5 0.4 - - + -
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Residues in contact with MET 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F ILE* 4.0 17.3 - - + -
167F PRO* 3.7 24.5 - - + +
169F ASN* 4.1 4.7 - - - +
170F PHE* 2.7 43.7 + - + +
171F PRO* 3.9 3.1 - - + +
173F LEU* 1.3 75.8 - - - +
175F GLN* 1.3 60.9 + - - +
177F TRP* 3.4 31.9 + - + +
178F LYS* 3.2 38.9 + - - +
244F THR* 3.3 38.8 - - + +
476F GLU* 4.9 0.9 - - - +
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Residues in contact with GLN 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ILE* 3.6 13.8 - - + +
171F PRO 3.1 14.6 + - - +
172F LEU* 3.2 15.7 + - - +
174F MET* 1.3 75.0 - - - +
176F ALA* 1.3 53.1 + - - +
178F LYS* 3.2 2.9 + - - +
179F LEU* 2.8 57.2 + - + +
191F MET* 3.7 14.9 - - - +
201F ALA* 3.2 36.0 - - + +
204F VAL* 3.4 40.0 - - - +
208F ILE* 5.1 0.2 - - - +
220F ILE* 3.4 18.2 - - - +
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Residues in contact with ALA 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F VAL* 4.2 26.2 - - + -
128F CYS* 3.5 20.6 - - + -
129F LEU* 4.2 22.7 - - + +
172F LEU 3.0 13.2 + - - +
173F LEU 3.6 7.4 - - - +
175F GLN* 1.3 77.8 - - - +
177F TRP* 1.3 57.6 + - - +
179F LEU* 4.5 2.9 - - - +
180F GLY* 2.8 27.5 + - - -
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Residues in contact with TRP 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F MET* 6.0 1.3 - - - -
128F CYS* 3.5 17.2 - - - +
132F TYR* 5.1 1.2 - - - -
170F PHE* 6.5 1.3 - + - -
173F LEU* 2.9 51.2 + - + +
174F MET* 3.7 32.8 - - + +
175F GLN 3.3 0.2 - - - -
176F ALA* 1.3 76.9 - - - +
178F LYS* 1.3 59.7 + - + +
181F PRO* 3.1 22.5 - - - +
459F PHE* 4.5 31.9 - + + -
461F ALA* 5.8 0.6 - - - +
465F PHE* 4.6 18.4 - + - -
476F GLU* 3.9 31.7 - - + +
477F LEU* 3.4 52.9 + - + +
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Residues in contact with LYS 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F GLN* 3.2 39.0 + - + +
166F ILE* 3.6 17.4 - - + +
174F MET* 3.2 19.5 + - - +
175F GLN 3.2 7.0 + - - +
176F ALA 3.1 0.4 - - - -
177F TRP* 1.3 77.8 - - - +
179F LEU* 1.3 65.2 + - - +
181F PRO* 3.5 5.2 - - - +
182F ALA* 3.4 13.7 + - - +
191F MET* 4.0 5.6 - - + -
242F ALA* 3.8 26.9 - - - -
244F THR* 2.9 28.8 + - - -
268F GLU* 3.1 4.3 + - - -
476F GLU* 2.6 32.6 + - - +
485F TYR* 3.8 15.4 + - - +
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Residues in contact with LEU 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU* 5.1 0.4 - - - -
91F LEU* 4.9 7.9 - - + -
129F LEU* 4.9 7.0 - - + -
164F GLN* 4.1 6.7 - - - +
175F GLN* 2.8 44.1 + - + +
176F ALA* 4.2 3.6 - - - +
178F LYS* 1.3 70.4 - - - +
180F GLY* 1.3 65.8 + - - +
182F ALA* 4.7 1.8 - - - -
183F LEU* 2.9 41.5 + - + +
189F VAL* 4.3 9.0 - - + -
191F MET* 3.9 18.8 - - + -
204F VAL* 5.0 2.2 - - + -
208F ILE* 3.8 26.7 - - + -
218F VAL* 4.1 28.5 - - + -
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Residues in contact with GLY 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU* 4.0 6.7 - - - +
129F LEU* 4.4 12.8 - - - +
132F TYR* 3.5 22.8 - - - +
176F ALA 2.8 19.9 + - - -
179F LEU* 1.3 72.0 - - - +
181F PRO* 1.3 62.6 - - - +
184F ALA* 3.0 30.7 + - - +
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Residues in contact with PRO 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F TYR* 3.7 38.8 - - + +
177F TRP 3.1 29.4 - - - +
178F LYS 3.5 6.3 - - - +
180F GLY* 1.3 85.1 - - - +
182F ALA* 1.3 56.8 + - - +
184F ALA* 4.0 0.4 - - + +
185F THR* 2.8 38.7 + - - +
476F GLU* 6.6 0.2 - - + -
477F LEU 6.0 1.3 - - - +
481F GLY* 3.9 21.1 - - - +
482F LEU* 4.0 4.7 - - + -
485F TYR* 3.9 16.3 - - + +
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F CYS* 5.0 0.2 - - - -
164F GLN* 3.5 17.5 - - - +
178F LYS 3.4 17.0 - - - +
179F LEU 3.5 1.8 + - - +
180F GLY 3.4 0.6 - - - -
181F PRO* 1.3 81.0 - - - +
183F LEU* 1.3 61.0 + - - +
185F THR* 3.3 2.5 + - - -
187F ASN* 3.0 35.7 + - + +
189F VAL* 3.9 19.1 - - + -
485F TYR* 3.7 23.0 - - + -
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Residues in contact with LEU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F TRP* 3.6 13.0 - - + -
84F ARG* 3.4 15.1 - - - +
88F LEU* 4.2 19.7 - - + -
91F LEU* 5.4 2.9 - - + -
179F LEU* 2.9 36.0 + - + +
182F ALA* 1.3 73.1 - - + +
184F ALA* 1.3 66.6 + - - +
185F THR 3.1 2.0 - - - -
186F GLY 3.0 10.7 + - - -
187F ASN 3.7 11.9 - - - +
189F VAL* 4.7 6.1 - - + -
208F ILE* 5.6 0.4 - - + -
213F PHE* 3.9 24.0 - - + -
217F VAL* 3.5 31.6 - - + +
218F VAL* 3.8 25.1 - - + -
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Residues in contact with ALA 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ARG* 2.9 24.3 + - - +
88F LEU* 3.9 10.4 - - + +
132F TYR* 3.4 30.7 - - + +
135F TRP* 4.7 4.0 - - + -
136F ALA* 3.5 24.3 - - - +
180F GLY 3.0 20.4 + - - +
181F PRO* 4.0 6.3 - - + +
182F ALA 3.4 0.2 - - - -
183F LEU* 1.3 75.3 - - - +
185F THR* 1.3 61.7 + - + +
482F LEU* 4.9 0.9 - - + -
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Residues in contact with THR 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ARG* 3.8 9.4 + - - +
135F TRP 6.2 0.4 - - - +
139F TYR* 4.7 6.7 - - + -
156F HIS 5.5 1.2 - - - +
157F GLU 4.9 0.5 - - - -
158F PRO* 3.4 23.6 - - - +
181F PRO 2.8 22.4 + - - +
183F LEU 3.1 0.4 - - - -
184F ALA* 1.3 80.4 - - + +
186F GLY* 1.3 56.3 + - - +
187F ASN* 2.8 22.7 + - - -
482F LEU* 3.9 31.4 - - + +
485F TYR* 3.4 5.0 - - - +
486F THR* 3.8 27.7 - - + +
500G SER* 5.2 0.5 - - - -
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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
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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