Contacts of the helix formed by residues 154 - 170 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17J LEU* 5.0 4.5 - - + +
116J TYR* 2.9 38.7 + + - +
118J TYR* 3.9 5.6 + - - -
123J CYS* 4.4 6.5 - - - -
134J VAL* 3.0 33.7 - - + +
135J TYR* 4.9 1.0 - - - -
139J VAL* 4.0 4.0 - - + -
143J TYR* 2.9 41.9 - - + +
152J PRO 3.1 2.6 + - - -
153J PRO* 1.3 74.2 - - - +
155J ILE* 1.3 74.4 + - + +
156J PHE* 2.9 38.6 + + - +
157J SER* 2.6 34.8 + - - -
158J ILE* 3.5 4.0 + - - +
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Residues in contact with ILE 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J TYR* 4.2 12.5 - - + +
123J CYS* 4.3 10.8 - - - -
125J THR* 4.1 11.2 - - - +
135J TYR* 5.5 0.7 - - + +
154J HIS* 1.3 80.3 - - + +
156J PHE* 1.3 83.7 + - + +
157J SER 2.8 1.8 - - - -
158J ILE* 3.2 7.7 + - + +
159J SER* 2.9 22.0 + - - -
177J ILE* 6.2 0.4 - - + -
188J ASN* 3.3 41.5 - - + +
191J ARG* 5.8 3.8 - - + -
192J VAL* 4.4 23.1 - - + +
672J VAL* 4.5 23.3 - - + -
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Residues in contact with PHE 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J VAL* 3.6 11.2 - - + -
135J TYR* 4.3 22.4 - + + -
139J VAL* 4.2 11.0 - - + -
140J VAL* 3.9 19.5 - - + -
143J TYR* 3.7 21.7 - - + +
154J HIS* 2.9 44.1 - + - -
155J ILE* 1.3 87.6 - - + +
157J SER* 1.3 61.1 + - - +
159J SER* 3.7 5.4 - - - -
160J ASP* 2.7 32.7 + - - +
191J ARG* 4.4 14.4 - - + -
192J VAL* 6.0 0.2 - - - -
195J TYR* 2.9 48.7 - + + -
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Residues in contact with SER 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J TYR* 3.2 23.1 + - - -
143J TYR* 4.0 25.5 - - - -
146J LYS 4.3 3.8 + - - -
147J LYS 4.6 0.2 + - - -
148J ARG* 3.4 22.0 - - - +
151J ALA* 4.9 1.2 + - - +
152J PRO 4.7 0.5 + - - -
154J HIS 2.6 20.2 + - - -
156J PHE* 1.3 80.3 - - - +
158J ILE* 1.3 60.8 - - - -
160J ASP* 3.9 1.3 - - - -
161J ASN* 2.7 35.7 + - - +
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Residues in contact with ILE 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J TYR* 3.8 18.6 - - + -
121J LEU 5.0 5.4 - - - +
123J CYS* 3.0 44.9 - - + +
148J ARG* 5.6 2.0 - - - +
154J HIS 3.5 3.0 + - - +
155J ILE* 3.2 9.6 + - + +
157J SER* 1.3 80.4 - - - +
159J SER* 1.3 60.2 + - - +
161J ASN* 3.2 5.9 + - - +
162J ALA* 2.9 28.2 + - - +
175J ILE* 4.0 26.0 - - + -
192J VAL* 6.5 0.7 - - + -
670J HIS* 4.5 18.2 + - + +
671J PHE 4.4 9.9 - - - +
672J VAL* 4.2 14.4 - - + -
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Residues in contact with SER 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ILE* 2.9 17.9 + - - -
156J PHE* 3.5 6.1 + - - -
158J ILE* 1.3 82.0 - - - +
160J ASP* 1.3 62.0 + - - +
162J ALA* 4.0 2.7 - - - -
163J TYR 3.8 2.3 + - - -
175J ILE* 4.8 2.0 - - - -
192J VAL* 4.0 25.8 - - - -
195J TYR* 2.8 33.6 - - - -
196J PHE* 3.1 32.3 - - - -
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Residues in contact with ASP 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J TYR 3.4 18.8 - - - +
144J ARG* 2.3 46.2 + - - -
145J GLY* 3.3 6.6 + - - -
146J LYS 4.6 0.6 + - - +
156J PHE 2.7 17.9 + - - +
157J SER 4.0 2.0 - - - +
159J SER* 1.3 76.4 - - - +
161J ASN* 1.3 71.3 + - - +
162J ALA 3.0 1.6 - - - -
163J TYR* 2.9 8.2 + - - +
164J GLN* 2.8 26.0 + - - +
195J TYR* 2.4 34.0 + - - +
199J ILE* 4.1 1.8 - - - +
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Residues in contact with ASN 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J LYS 3.2 21.8 + - - -
147J LYS* 3.6 16.8 - - - +
148J ARG* 4.0 13.7 + - - +
157J SER* 2.7 31.9 + - - +
158J ILE* 3.7 5.2 - - - +
160J ASP* 1.3 80.0 - - - +
162J ALA* 1.3 53.4 + - - +
164J GLN* 2.7 24.2 + - - +
165J PHE* 2.8 59.8 + - + +
670J HIS* 5.2 3.8 - - + -
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Residues in contact with ALA 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J ILE 2.9 16.1 + - - +
159J SER* 3.8 9.0 - - - +
161J ASN* 1.3 78.8 - - - +
163J TYR* 1.3 53.4 + - - +
165J PHE* 3.0 4.5 - - - +
166J MET* 2.6 36.4 + - - +
173J GLN* 3.6 28.2 - - + +
175J ILE* 4.5 10.3 - - + -
196J PHE* 4.3 10.5 - - + -
459J ILE* 4.6 2.5 - - + -
670J HIS* 4.1 11.4 + - + -
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Residues in contact with TYR 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J ARG* 4.1 27.8 - - - -
159J SER 3.8 6.9 + - - +
160J ASP* 2.9 13.6 + - - +
162J ALA* 1.3 77.6 - - - +
164J GLN* 1.3 71.1 + - - +
166J MET* 2.9 30.5 + - - +
167J LEU* 3.0 29.0 + - + +
196J PHE* 4.0 18.8 - + + -
199J ILE* 4.3 14.5 + - + -
200J ALA* 3.1 24.9 - - + +
254J PHE* 4.1 14.1 - + - -
258J GLY* 2.4 38.3 + - - -
259J LYS* 4.4 6.3 + - - -
459J ILE* 4.3 5.3 - - + +
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Residues in contact with GLN 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J ARG* 4.3 8.5 - - - +
145J GLY* 4.2 16.7 - - - +
146J LYS 4.1 4.4 + - - -
147J LYS* 3.0 31.0 - - - +
160J ASP* 2.8 27.4 + - - +
161J ASN* 2.7 46.7 + - - +
163J TYR* 1.3 71.5 - - - +
165J PHE* 1.3 58.3 + - + +
166J MET 2.7 0.7 + - - -
167J LEU* 2.6 36.3 + - - +
168J THR* 2.8 20.3 + - - +
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Residues in contact with PHE 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J LYS* 6.2 4.0 - - + -
161J ASN* 2.8 43.7 + - + +
162J ALA 3.0 5.2 - - - +
164J GLN* 1.3 78.5 - - + +
166J MET* 1.3 65.3 + - - +
168J THR* 3.7 8.3 + - + -
169J ASP* 2.9 51.6 + - - +
170J ARG 3.9 0.2 + - - -
171J GLU 4.6 0.2 + - - -
173J GLN* 3.6 17.5 + - - +
668J HIS* 4.5 12.8 - + - -
670J HIS* 3.9 23.3 - + - -
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Residues in contact with MET 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J ALA 2.6 17.8 + - - +
163J TYR* 3.0 24.5 - - - +
164J GLN 2.7 1.0 + - - -
165J PHE* 1.3 79.4 - - - +
167J LEU* 1.3 61.0 + - - -
170J ARG* 3.0 24.8 + - - -
171J GLU 3.7 14.0 + - - +
173J GLN* 3.6 12.1 - - - +
254J PHE* 3.0 52.7 - - + -
457J TYR* 3.6 41.8 - - + -
458J PHE 3.6 12.3 - - - +
459J ILE* 3.7 11.4 - - + -
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Residues in contact with LEU 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J ARG* 5.5 3.4 - - - +
163J TYR* 3.5 40.8 - - + +
164J GLN* 2.6 12.9 + - - +
166J MET* 1.3 80.9 - - + +
168J THR* 1.3 61.8 + - - +
170J ARG* 4.0 12.5 + - - +
256J ALA 5.0 1.3 - - - +
257J THR 3.7 9.9 - - - +
258J GLY* 3.6 31.0 - - - -
457J TYR* 4.9 17.4 + - + +
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Residues in contact with THR 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLN* 2.8 27.0 + - - +
165J PHE* 4.1 8.1 - - + -
167J LEU* 1.3 76.3 - - - +
169J ASP* 1.3 74.1 + - - +
170J ARG* 4.5 3.8 - - - +
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Residues in contact with ASP 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J PHE* 2.9 40.4 + - - +
168J THR* 1.3 94.3 - - - +
170J ARG* 1.3 72.6 + - - +
171J GLU* 3.3 30.1 + - + +
173J GLN* 5.2 0.2 - - - +
668J HIS* 4.7 5.9 + - - -
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Residues in contact with ARG 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J MET 3.0 13.6 + - - -
167J LEU 4.1 11.9 - - - +
168J THR 3.5 4.0 - - - +
169J ASP* 1.3 81.3 - - - +
171J GLU* 1.3 59.5 - - - +
456J GLN* 5.2 9.5 + - - +
457J TYR* 3.9 40.2 + - + +
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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