Contacts of the helix formed by residues 170 - 185 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G GLU* 4.4 0.2 - - - -
112G LYS* 3.2 26.0 - - - +
121G ASP* 3.6 13.0 - - - +
124G MET* 5.4 4.0 - - + -
167G PRO 4.7 0.4 - - - -
169G ASN* 1.3 96.4 + - - +
171G PRO* 1.3 61.0 - - - +
172G LEU 3.5 2.0 - - - -
173G LEU* 3.9 28.3 - - + -
174G MET* 2.8 49.1 + - + +
296G PHE* 3.8 32.5 - + - -
297G ASN* 3.5 20.6 - - + -
300G GLN 3.8 16.4 - - - -
301G CYS* 4.3 17.3 - - + -
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Residues in contact with PRO 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G GLU* 3.3 31.2 - - - +
110G ASN* 4.1 7.9 - - + +
112G LYS* 4.5 2.5 - - - +
166G ILE* 3.6 9.0 - - + +
167G PRO 4.2 10.1 - - - +
168G TRP 3.4 17.4 - - - +
169G ASN 3.6 3.1 - - - +
170G PHE* 1.3 90.1 - - - +
172G LEU* 1.3 61.8 + - - +
175G GLN* 3.2 20.7 + - - +
197G THR* 3.4 35.7 - - + +
200G THR* 3.7 9.6 - - - +
201G ALA* 5.3 4.4 - - + +
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Residues in contact with LEU 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ILE* 6.2 0.9 - - + -
102G LEU* 4.2 16.8 - - + +
106G GLU* 3.1 18.8 + - - +
121G ASP* 5.6 2.2 - - + -
122G LEU* 3.7 33.2 - - + -
125G VAL* 3.7 19.1 - - + +
171G PRO* 1.3 76.8 - - - +
173G LEU* 1.3 65.9 + - - +
175G GLN* 3.2 13.8 + - - +
176G ALA* 3.0 23.2 + - - +
200G THR* 3.5 37.0 - - + +
201G ALA 4.4 0.2 - - - +
204G VAL* 3.6 30.1 - - + -
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Residues in contact with LEU 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G GLU* 4.7 0.6 + - - -
121G ASP* 4.9 8.8 + - - +
124G MET* 3.3 67.1 - - + +
125G VAL* 3.8 10.9 - - + +
128G CYS* 4.8 0.7 - - + -
170G PHE* 3.4 24.8 + - + -
172G LEU* 1.3 78.2 - - - +
174G MET* 1.3 64.0 + - + +
176G ALA* 3.1 3.6 + - + +
177G TRP* 2.8 73.7 + - + +
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Residues in contact with MET 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G ILE* 4.0 20.9 - - + -
167G PRO* 3.8 22.4 - - + +
169G ASN* 4.3 2.5 - - - +
170G PHE* 2.8 46.6 + - + +
171G PRO 4.2 2.0 - - - +
173G LEU* 1.3 75.0 - - + +
175G GLN* 1.3 65.0 + - - +
177G TRP* 3.6 46.3 - - + +
178G LYS* 3.1 35.3 + - + +
244G THR* 4.5 19.3 - - - -
476G GLU* 5.2 0.7 - - - +
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Residues in contact with GLN 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G ILE* 3.6 13.2 - - + +
171G PRO 3.2 13.8 + - - +
172G LEU* 3.4 15.4 + - - +
173G LEU 3.2 0.2 - - - -
174G MET* 1.3 78.5 - - - +
176G ALA* 1.3 58.4 + - - +
178G LYS* 3.1 3.5 + - - +
179G LEU* 2.8 41.7 + - + +
191G MET* 3.7 17.7 - - - +
201G ALA* 3.3 39.7 - - + +
204G VAL* 3.4 39.0 - - + +
208G ILE* 5.1 0.2 - - - +
220G ILE* 3.5 14.7 - - - +
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Residues in contact with ALA 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G VAL* 4.0 26.0 - - + +
128G CYS* 3.5 19.8 - - + -
129G LEU* 4.0 24.1 - - + +
172G LEU 3.0 12.5 + - - +
173G LEU 3.6 6.7 - - - +
175G GLN* 1.3 76.8 - - - +
177G TRP* 1.3 59.5 + - + +
179G LEU* 4.4 2.2 - - - +
180G GLY* 2.9 27.2 + - - -
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Residues in contact with TRP 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G MET* 6.3 0.7 - - - -
128G CYS* 3.7 22.4 - - - +
132G TYR* 5.2 0.5 - - - -
173G LEU* 2.8 58.1 + - + +
174G MET* 3.6 31.4 - - + +
175G GLN 3.3 0.2 - - - -
176G ALA* 1.3 73.1 - - - +
178G LYS* 1.3 60.5 + - + +
181G PRO* 3.1 23.7 - - - +
459G PHE* 4.2 31.2 - + + -
461G ALA* 6.1 0.6 - - - +
465G PHE* 3.9 23.8 - + + -
476G GLU* 3.3 36.2 - - - +
477G LEU* 3.6 45.1 + - + +
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Residues in contact with LYS 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G GLN* 3.0 44.9 + - + +
165G ILE 5.1 0.2 - - - -
166G ILE* 3.6 19.0 - - + +
174G MET* 3.1 25.8 + - - +
175G GLN 3.6 3.1 - - - +
176G ALA 3.1 0.4 - - - -
177G TRP* 1.3 78.5 - - - +
179G LEU* 1.3 64.2 + - - +
181G PRO* 3.6 5.2 - - - +
182G ALA* 3.4 13.2 + - - +
191G MET* 4.0 5.2 - - + -
242G ALA* 4.0 21.5 - - - -
244G THR* 2.9 30.7 + - - +
268G GLU* 3.8 7.6 - - - -
476G GLU* 2.6 33.2 + - - +
485G TYR* 4.0 9.4 + - + +
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Residues in contact with LEU 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 5.0 1.3 - - + -
91G LEU* 5.1 6.5 - - + -
129G LEU* 4.9 6.3 - - + -
164G GLN* 3.8 7.9 - - - +
175G GLN* 2.8 42.0 + - + +
176G ALA* 4.4 3.8 - - - +
178G LYS* 1.3 71.3 - - - +
180G GLY* 1.3 66.9 + - - +
182G ALA* 4.5 2.0 - - - -
183G LEU* 2.8 39.8 + - + +
189G VAL* 4.1 18.4 - - + -
191G MET* 3.8 20.2 - - + -
204G VAL* 5.0 2.9 - - + -
208G ILE* 3.8 28.0 - - + -
218G VAL* 4.2 19.7 - - + -
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Residues in contact with GLY 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 3.9 7.0 - - - +
128G CYS* 5.1 0.4 - - - -
129G LEU* 4.4 12.9 - - - +
132G TYR* 3.5 22.2 - - - +
176G ALA 2.9 15.6 + - - -
179G LEU* 1.3 76.2 - - - +
181G PRO* 1.3 63.4 - - - +
184G ALA* 3.0 31.7 + - - +
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Residues in contact with PRO 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G TYR* 3.7 39.7 - - + +
177G TRP 3.1 29.4 - - - +
178G LYS 3.6 6.1 - - - +
180G GLY* 1.3 86.2 - - - +
182G ALA* 1.3 59.3 + - - +
184G ALA* 3.9 0.5 - - - +
185G THR* 2.9 33.0 + - - +
477G LEU 6.0 1.3 - - - +
481G GLY* 3.9 23.3 - - - +
482G LEU* 4.1 4.2 - - + +
485G TYR* 3.9 16.1 - - + +
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Residues in contact with ALA 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G CYS* 5.2 0.2 - - - -
164G GLN* 3.8 14.4 - - - +
178G LYS 3.4 15.7 - - - +
179G LEU 3.3 2.8 + - - +
181G PRO* 1.3 82.8 - - - +
183G LEU* 1.3 61.2 + - - +
185G THR* 3.3 2.8 + - - -
187G ASN* 3.0 36.6 + - + -
189G VAL* 3.9 20.2 - - + -
485G TYR* 3.8 22.4 - - + -
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Residues in contact with LEU 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G TRP* 3.5 14.4 - - + -
84G ARG* 3.4 14.8 - - - +
88G LEU* 4.2 18.8 - - + -
91G LEU* 5.5 2.7 - - + -
179G LEU* 2.8 40.6 + - + +
182G ALA* 1.3 69.8 - - + +
184G ALA* 1.3 67.4 + - - +
185G THR 3.1 1.8 - - - -
186G GLY 3.0 10.6 + - - -
187G ASN 3.8 11.2 - - - +
189G VAL* 4.6 8.3 - - + -
208G ILE* 5.8 0.7 - - + -
213G PHE* 3.8 23.6 - - + -
217G VAL* 3.5 30.5 - - + +
218G VAL* 3.8 24.9 - - + -
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Residues in contact with ALA 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ARG* 2.9 24.0 + - - -
88G LEU* 3.8 9.5 - - + +
132G TYR* 3.4 31.0 - - + +
135G TRP* 4.8 0.7 - - + -
136G ALA* 3.4 24.3 - - - +
180G GLY 3.0 21.3 + - - +
181G PRO* 3.9 5.8 - - + +
183G LEU* 1.3 76.6 - - - +
185G THR* 1.3 58.2 + - + +
482G LEU* 4.7 6.7 - - + -
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Residues in contact with THR 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500F SER* 5.2 0.3 - - - -
84G ARG* 4.0 9.1 + - - +
139G TYR* 4.6 8.1 - - + -
157G GLU 4.9 0.7 - - - -
158G PRO* 3.2 24.1 - - - +
181G PRO 2.9 19.4 + - - +
182G ALA 3.3 0.3 + - - -
183G LEU 3.1 0.2 - - - -
184G ALA* 1.3 78.5 - - + +
186G GLY* 1.3 55.7 + - - +
187G ASN* 2.7 26.6 + - - -
482G LEU* 3.7 31.0 - - + +
485G TYR* 3.4 5.1 - - + +
486G THR* 3.8 27.3 - - + +
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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