Contacts of the helix formed by residues 170 - 183 (chain G) in PDB entry 3PUY
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 ILE 170 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71F GLY* 3.5 39.3 - - - +
75F MET* 3.8 18.4 - - + -
99G ILE* 3.7 37.7 - - + +
102G LEU* 4.6 8.1 - - + -
103G SER* 4.0 21.3 - - - +
106G CYS* 5.1 2.2 - - - -
125G MET* 5.7 0.2 - - + -
167G LEU 4.5 11.4 - - - +
168G GLY 3.3 3.7 + - - +
169G GLY* 1.3 73.7 - - - +
171G ALA* 1.3 70.5 + - - +
172G LEU 3.2 2.5 - - - -
173G HIS* 2.8 9.2 + - - -
174G VAL* 2.8 40.1 + - + +
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Residues in contact with ALA 171 (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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75F MET* 3.8 22.0 - - + -
125G MET* 3.5 30.5 - - + +
126G LEU* 5.2 1.6 - - - -
129G GLN* 3.4 23.7 + - + +
169G GLY 3.7 1.0 - - - -
170G ILE* 1.3 79.1 - - - +
172G LEU* 1.3 64.8 + - + +
174G VAL* 3.4 7.3 + - - +
175G TRP* 3.2 27.3 + - - -
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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
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383F TYR* 4.0 19.3 - - - +
428F PRO 3.9 11.7 - - - +
429F LEU* 4.0 15.3 - - + +
432F ALA* 3.3 35.7 - - + -
126G LEU* 5.3 6.5 - - + -
129G GLN* 3.7 18.9 - - + +
169G GLY 6.2 0.2 - - - +
170G ILE 3.2 1.0 - - - -
171G ALA* 1.3 78.5 - - + +
173G HIS* 1.3 64.4 + - + +
175G TRP* 2.8 32.7 + - + +
176G THR* 2.8 16.2 + - - -
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Residues in contact with HIS 173 (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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383F TYR* 6.1 2.0 - + - -
99G ILE* 3.6 22.9 - - + +
103G SER* 3.9 19.5 - - - +
169G GLY 3.7 18.7 + - - -
170G ILE* 2.8 8.4 + - - +
172G LEU* 1.3 77.4 - - + +
174G VAL* 1.3 58.0 + - - +
176G THR* 3.1 9.3 + - - -
177G ILE* 2.9 35.7 + - - +
218G VAL* 3.7 28.6 - - + +
221G LEU* 4.0 31.9 - - + +
222G SER* 4.0 12.5 + - - -
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Residues in contact with VAL 174 (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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103G SER* 3.8 30.7 - - - +
106G CYS* 4.1 13.0 - - - -
107G ALA* 3.9 10.6 - - - +
110G PHE* 3.9 28.5 - - + -
122G LEU* 4.7 5.4 - - + -
125G MET* 4.2 13.0 - - - -
170G ILE* 2.8 38.0 + - + +
171G ALA* 3.5 9.9 - - - +
173G HIS* 1.3 70.7 - - - +
175G TRP* 1.3 56.9 + - - +
178G LYS* 2.8 33.9 + - + +
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Residues in contact with TRP 175 (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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425F PRO 5.6 1.6 - - - +
428F PRO* 3.8 36.7 - - + +
429F LEU* 5.5 2.2 - - + -
122G LEU* 3.2 54.9 + - + +
123G LYS* 4.5 11.2 - - + -
125G MET* 4.7 2.4 - - + +
126G LEU* 3.5 40.2 - - + +
171G ALA 3.2 23.5 + - - -
172G LEU* 2.8 21.4 + - + +
174G VAL* 1.3 75.8 - - + +
176G THR* 1.3 60.5 + - - +
178G LYS* 3.7 39.0 + - - +
179G GLY* 3.1 18.7 + - - -
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Residues in contact with THR 176 (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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387F LEU* 3.8 20.4 - - + +
391F LEU* 5.0 6.7 - - + +
425F PRO* 6.0 1.5 - - - +
429F LEU* 3.3 31.6 - - + +
172G LEU 2.8 16.3 + - - -
173G HIS* 3.1 15.4 + - - +
175G TRP* 1.3 75.6 - - - +
177G ILE* 1.3 61.2 + - - +
179G GLY* 3.4 2.3 + - - -
180G TYR* 3.3 20.4 + - - +
214G ILE* 3.5 28.9 - - + +
217G VAL* 5.0 0.4 - - + -
218G VAL* 4.6 8.7 - - + -
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Residues in contact with ILE 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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100G VAL* 5.4 0.2 - - - -
103G SER* 3.7 19.1 - - - +
104G THR* 3.4 26.9 - - - +
107G ALA* 3.9 9.2 - - + -
173G HIS 2.9 22.3 + - - +
176G THR* 1.3 67.9 - - - +
178G LYS* 1.3 66.1 + - - +
179G GLY 3.1 1.1 - - - -
180G TYR* 4.0 0.6 - - - +
181G PHE* 3.0 51.7 + - + -
214G ILE* 4.0 16.2 - - + -
215G LEU* 3.9 20.2 - - + -
218G VAL* 3.6 32.1 - - + -
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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
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107G ALA* 3.6 12.8 - - + +
110G PHE* 4.0 16.4 - - + +
111G ALA* 3.9 17.2 - - + +
122G LEU* 3.7 40.4 - - + -
174G VAL 2.8 19.6 + - - +
175G TRP* 3.7 28.5 + - + +
177G ILE* 1.3 76.4 - - - +
179G GLY* 1.3 72.1 + - - +
181G PHE* 3.5 8.0 - - - +
182G GLU* 3.4 53.8 + - - +
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Residues in contact with GLY 179 (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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425F PRO* 5.0 17.3 - - - -
175G TRP 3.1 11.6 + - - -
176G THR 3.7 4.0 - - - -
177G ILE 3.1 1.0 - - - -
178G LYS* 1.3 81.8 - - - +
180G TYR* 1.3 65.5 + - - +
182G GLU* 2.9 29.5 + - - +
183G THR* 3.7 9.5 + - - +
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Residues in contact with TYR 180 (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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390F GLY 3.8 19.3 - - - -
391F LEU* 4.6 14.2 - - + +
393F LYS 4.0 10.7 + - - -
394F ALA* 3.4 30.4 - - + -
176G THR 3.3 8.0 + - - +
177G ILE 4.0 1.3 - - - +
179G GLY* 1.3 73.5 - - - +
181G PHE* 1.3 63.6 - - - +
183G THR* 2.8 26.2 + - - -
184G ILE* 3.8 14.5 + - + +
210G LEU 3.2 28.5 + - - -
211G SER* 3.3 18.2 - - - -
213G PRO* 3.5 19.9 - - + +
214G ILE* 3.6 49.6 - - + -
289G LEU* 4.8 2.9 - - - +
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Residues in contact with PHE 181 (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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104G THR* 3.7 22.7 - - + -
107G ALA* 3.8 5.8 - - + -
108G TYR* 3.6 36.3 - - + -
111G ALA* 4.2 10.3 - - + -
112G ARG* 2.6 30.3 + - + +
177G ILE* 3.0 41.3 + - + +
178G LYS* 3.5 7.0 - - - +
179G GLY 3.2 0.2 - - - -
180G TYR* 1.3 76.6 - - - +
182G GLU* 1.3 53.3 + - - +
184G ILE* 3.1 19.8 + - - +
203G PHE* 4.4 1.6 - + - -
207G LEU* 3.6 28.3 - - + -
208G LEU* 4.3 7.0 - - + -
211G SER* 3.0 36.1 - - - -
215G LEU* 5.3 0.2 - - + -
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Residues in contact with GLU 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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424F LYS* 6.0 1.9 - - - -
110G PHE 5.1 0.7 - - - +
111G ALA* 4.2 18.0 - - + +
112G ARG* 4.1 10.5 + - - +
178G LYS* 3.4 47.9 + - - +
179G GLY* 2.9 13.5 + - - +
181G PHE* 1.3 75.8 - - - +
183G THR* 1.3 60.3 + - + +
184G ILE 3.3 6.8 + - - +
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Residues in contact with THR 183 (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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394F ALA* 3.4 38.4 - - + +
421F LEU* 6.0 3.6 - - + +
425F PRO* 5.8 9.6 - - + -
179G GLY 4.1 9.9 - - - +
180G TYR* 2.8 18.2 + - - -
182G GLU* 1.3 77.6 - - + +
184G ILE* 1.3 61.7 + - - +
185G ASP 3.9 1.6 + - - -
290G THR* 5.4 3.6 - - - +
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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
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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