Contacts of the helix formed by residues 154 - 170 (chain G) in PDB entry 1O1F
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 HIS 154 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G LEU* 5.0 4.3 - - + +
116G TYR* 2.9 37.2 + + - +
118G TYR* 3.9 6.0 + - - -
123G CYS* 4.4 6.7 - - - -
134G VAL* 3.0 33.4 - - + +
135G TYR* 4.9 1.2 - - - -
139G VAL* 3.9 4.9 - - + +
143G TYR* 2.9 41.1 - - + +
152G PRO 3.1 2.4 + - - -
153G PRO* 1.3 73.8 - - - +
155G ILE* 1.3 73.9 + - + +
156G PHE* 2.9 39.1 - + - +
157G SER* 2.6 35.5 + - - -
158G ILE* 3.5 3.5 + - - +
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Residues in contact with ILE 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G TYR* 4.2 13.1 - - + +
123G CYS* 4.3 11.3 - - - -
125G THR* 4.1 11.7 - - - +
135G TYR* 6.1 0.7 - - + -
154G HIS* 1.3 80.4 - - + +
156G PHE* 1.3 83.7 + - + +
157G SER 2.8 2.0 - - - -
158G ILE* 3.2 8.0 + - + +
159G SER* 3.0 21.6 + - - -
177G ILE* 6.2 0.2 - - + -
188G ASN* 3.3 41.3 - - + +
191G ARG* 5.8 4.5 - - + -
192G VAL* 4.4 23.1 - - + +
672G VAL* 4.5 22.9 - - + -
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Residues in contact with PHE 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G VAL 3.6 10.8 - - - -
135G TYR* 4.3 23.3 - + + -
139G VAL* 4.2 10.8 - - + -
140G VAL* 3.9 18.8 - - + -
143G TYR* 3.7 21.1 - - + -
154G HIS* 2.9 44.3 - + - -
155G ILE* 1.3 87.8 - - + +
157G SER* 1.3 61.2 + - - +
159G SER* 3.5 5.6 + - - -
160G ASP* 2.7 32.6 + - - +
191G ARG* 4.4 15.0 - - + -
192G VAL* 6.0 0.2 - - - -
195G TYR* 2.9 47.6 - + + -
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Residues in contact with SER 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G TYR* 3.2 23.7 + - - -
143G TYR* 4.0 26.1 - - - -
146G LYS 4.3 3.2 + - - -
147G LYS 4.6 0.5 + - - -
148G ARG* 3.4 22.3 + - - +
151G ALA* 4.9 0.7 + - - +
152G PRO 4.7 0.3 + - - -
154G HIS 2.6 20.0 + - - -
156G PHE* 1.3 81.6 - - - +
158G ILE* 1.3 59.8 + - - -
160G ASP* 3.9 1.1 - - - -
161G ASN* 2.7 36.1 + - - +
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Residues in contact with ILE 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G TYR* 3.8 18.4 - - + -
121G LEU 5.0 5.4 - - - +
123G CYS* 3.0 45.1 - - + +
148G ARG* 5.6 2.2 - - - +
154G HIS 3.5 3.2 + - - +
155G ILE* 3.2 9.8 + - + +
157G SER* 1.3 80.5 - - - +
159G SER* 1.3 59.0 + - - +
160G ASP 3.1 0.2 + - - -
161G ASN* 3.2 6.2 + - - +
162G ALA* 2.9 28.8 + - - +
175G ILE* 4.0 25.6 - - + -
192G VAL* 6.5 0.9 - - + -
670G HIS* 4.5 18.4 + - + +
671G PHE 4.4 9.2 - - - +
672G VAL* 4.2 13.9 - - + -
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Residues in contact with SER 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ILE* 3.0 16.9 + - - -
156G PHE* 3.5 5.6 + - - -
158G ILE* 1.3 82.8 - - - +
160G ASP* 1.3 61.9 + - - +
162G ALA* 4.0 2.7 - - - -
163G TYR* 3.8 2.3 + - - +
175G ILE* 4.8 1.6 - - - -
192G VAL* 4.0 26.2 - - - -
195G TYR* 2.8 34.3 - - - -
196G PHE* 3.1 31.6 - - - -
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Residues in contact with ASP 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G TYR 3.4 19.1 - - - +
144G ARG* 2.3 46.0 + - - -
145G GLY* 3.3 6.6 + - - -
146G LYS 4.6 0.6 + - - +
156G PHE 2.7 17.5 + - - +
157G SER 4.0 2.2 - - - +
159G SER* 1.3 76.9 - - - +
161G ASN* 1.3 71.6 + - - +
162G ALA 3.0 1.6 - - - -
163G TYR* 3.0 7.8 + - - +
164G GLN* 2.8 26.7 + - - +
195G TYR* 2.4 33.0 + - - +
199G ILE* 4.1 2.0 - - - +
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Residues in contact with ASN 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G LYS 3.2 22.4 + - - -
147G LYS* 3.6 17.0 - - - +
148G ARG* 4.0 14.2 + - - +
157G SER* 2.7 31.3 + - - +
158G ILE* 3.7 4.9 - - - +
160G ASP* 1.3 81.8 - - - +
162G ALA* 1.3 53.4 + - - +
164G GLN* 2.7 22.9 + - - +
165G PHE* 2.8 60.1 + - + +
670G HIS* 5.2 3.6 - - + -
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Residues in contact with ALA 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G ILE 2.9 16.8 + - - +
159G SER* 3.8 9.2 - - - +
161G ASN* 1.3 77.5 - - - +
163G TYR* 1.3 53.7 + - - +
165G PHE* 3.0 4.7 - - - +
166G MET* 2.6 36.4 + - - +
173G GLN* 3.6 27.4 - - + +
175G ILE* 4.5 9.6 - - + -
196G PHE* 4.3 10.5 - - + -
459G ILE* 4.6 2.5 - - + -
670G HIS* 4.1 11.8 + - + -
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Residues in contact with TYR 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G ARG* 4.1 28.5 - - - -
159G SER 3.8 7.7 + - - +
160G ASP* 3.0 13.4 + - - +
162G ALA* 1.3 78.3 - - - +
164G GLN* 1.3 69.6 + - - +
166G MET* 2.9 31.1 + - - +
167G LEU* 3.0 28.8 + - + +
196G PHE* 4.0 19.3 - + + -
199G ILE* 4.3 13.6 + - + -
200G ALA* 3.1 23.8 - - + +
254G PHE* 4.1 14.6 - + - -
258G GLY* 2.4 38.0 + - - -
259G LYS* 4.4 6.2 + - - -
459G ILE* 4.3 5.1 - - + +
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Residues in contact with GLN 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G ARG* 4.3 8.1 - - - +
145G GLY* 4.2 16.8 - - - +
146G LYS 4.1 4.8 + - - -
147G LYS* 3.0 33.2 - - - +
160G ASP* 2.8 26.0 + - - +
161G ASN* 2.7 46.1 + - - +
163G TYR* 1.3 72.4 - - - +
165G PHE* 1.3 58.1 + - + +
166G MET 2.7 0.5 + - - -
167G LEU* 2.6 35.6 + - - +
168G THR* 2.8 19.9 + - - +
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Residues in contact with PHE 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G LYS* 6.2 4.5 - - + -
161G ASN* 2.8 43.2 + - + +
162G ALA 3.0 5.4 - - - +
164G GLN* 1.3 78.9 - - + +
166G MET* 1.3 65.8 + - - +
168G THR* 3.7 7.6 - - + -
169G ASP* 2.9 52.2 + - - +
170G ARG 3.9 0.2 + - - -
171G GLU 4.6 0.2 + - - -
173G GLN* 3.6 16.4 + - - +
668G HIS* 4.6 12.1 - + - -
670G HIS* 3.9 23.3 - + - -
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Residues in contact with MET 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G ALA 2.6 18.6 + - - +
163G TYR* 3.0 24.5 - - - +
164G GLN 2.7 0.8 + - - -
165G PHE* 1.3 78.4 - - - +
167G LEU* 1.3 60.4 + - - -
170G ARG* 3.0 24.6 + - - -
171G GLU 3.7 13.4 + - - +
173G GLN* 3.6 12.1 - - - +
254G PHE* 3.0 52.9 - - + -
457G TYR* 3.6 41.4 - - + -
458G PHE 3.6 12.3 - - - +
459G ILE* 3.7 12.3 - - + -
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Residues in contact with LEU 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G ARG* 5.5 3.1 - - - +
163G TYR* 3.5 42.6 - - + +
164G GLN* 2.6 14.3 + - - +
166G MET* 1.3 80.1 - - + +
168G THR* 1.3 61.2 + - - +
170G ARG* 4.0 12.2 + - - +
256G ALA 5.0 1.6 - - - +
257G THR 3.7 9.9 - - - +
258G GLY* 3.6 30.5 - - - -
457G TYR* 4.9 19.0 + - + +
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Residues in contact with THR 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G GLN* 2.8 26.6 + - - +
165G PHE* 4.1 7.8 + - + -
167G LEU* 1.3 75.3 - - - +
169G ASP* 1.3 74.6 + - - +
170G ARG* 3.9 4.0 + - - +
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Residues in contact with ASP 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G PHE* 2.9 41.9 + - - +
168G THR* 1.3 94.6 - - - +
170G ARG* 1.3 74.0 + - - +
171G GLU* 3.3 30.1 + - + +
173G GLN* 5.2 0.6 - - - +
668G HIS* 4.7 5.9 + - - -
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Residues in contact with ARG 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G MET 3.0 14.2 + - - -
167G LEU 4.1 11.9 - - - +
168G THR 3.5 4.0 - - - +
169G ASP* 1.3 82.8 - - - +
171G GLU* 1.3 58.9 + - - +
456G GLN* 5.2 9.1 + - - +
457G TYR* 3.9 39.7 + - + +
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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