Contacts of the helix formed by residues 145 - 163 (chain F) in PDB entry 6F0X
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 VAL 145 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F TYR* 4.6 17.6 - - + +
143F VAL 2.8 30.6 + - - +
144F GLU* 1.3 77.1 - - - +
146F LYS* 1.3 55.0 + - - +
148F HIS* 3.7 12.3 - - + +
149F LEU* 2.8 43.9 + - + +
177F LEU* 5.3 7.6 - - + -
188F LEU* 4.6 17.6 - - + +
317F GLN* 5.2 9.9 - - + +
319F ILE* 3.9 27.8 - - + -
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Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F TRP* 4.1 41.7 - - + +
137F ASP* 4.0 25.4 + - - +
139F LEU 4.6 16.8 - - - +
140F VAL* 4.3 27.9 - - - +
141F TYR* 5.5 8.7 - - + +
144F GLU* 2.9 9.2 - - - +
145F VAL* 1.3 79.1 - - - +
147F SER* 1.3 65.0 + - - +
149F LEU* 3.9 0.7 - - - +
150F LEU* 3.0 23.0 + - - +
188F LEU* 5.7 7.2 - - + -
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Residues in contact with SER 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E GLN* 2.9 24.0 + - - -
144F GLU* 3.1 9.3 + - - +
146F LYS* 1.3 75.8 - - - +
148F HIS* 1.3 72.9 - - - +
150F LEU* 3.3 10.9 - - - +
199F ARG* 5.5 6.4 + - - +
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Residues in contact with HIS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398E LEU* 4.6 21.5 - - + +
401E GLN* 4.9 0.4 - - - +
143F VAL* 3.7 16.0 + - + -
144F GLU* 2.7 62.6 + - + +
145F VAL* 3.7 11.7 + - + +
147F SER* 1.3 74.3 - - - +
149F LEU* 1.3 52.3 + - + +
150F LEU 3.0 0.2 - - - -
151F ASP* 2.5 51.6 + - - +
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Residues in contact with LEU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F TRP* 6.1 0.4 - - + -
145F VAL* 2.8 31.7 + - + +
146F LYS* 4.2 0.9 - - - +
148F HIS* 1.3 72.0 - - - +
150F LEU* 1.3 62.8 + - - +
151F ASP* 3.2 3.6 - - - +
152F TYR* 3.2 33.7 + - + +
153F VAL* 4.1 1.6 + - - +
175F VAL* 4.8 15.5 - - + -
177F LEU* 4.9 17.9 - - + -
188F LEU* 3.8 29.4 - - + -
192F LEU* 3.8 35.0 - - + +
315F ILE* 6.0 2.2 - - + -
317F GLN* 6.1 2.5 - - + -
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E GLN* 3.0 25.8 - - + +
136F TRP* 5.6 4.5 - - + -
146F LYS 3.0 13.4 + - - +
147F SER* 3.3 15.3 - - - +
148F HIS 2.8 0.2 + - - -
149F LEU* 1.3 77.6 - - - +
151F ASP* 1.3 62.8 + - - +
152F TYR 2.8 1.9 + - - -
153F VAL* 3.2 2.8 + - - +
154F MET* 2.9 43.9 + - + +
192F LEU* 5.0 7.9 - - + +
195F LYS* 5.6 4.0 - - + -
196F LEU* 4.2 17.7 - - + +
199F ARG* 2.9 53.4 - - + +
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Residues in contact with ASP 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394E LEU* 4.7 7.7 - - - +
397E ALA* 2.9 39.9 - - + +
398E LEU* 4.6 8.1 + - - +
401E GLN* 3.1 25.2 - - - +
148F HIS* 2.5 33.3 + - - +
149F LEU* 3.9 1.2 - - - -
150F LEU* 1.3 74.1 - - - +
152F TYR* 1.3 95.9 + - - +
154F MET* 4.1 1.8 - - - -
155F THR* 2.9 26.0 + - - -
315F ILE* 5.9 2.6 - - - +
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Residues in contact with TYR 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F LEU* 3.2 26.9 - - + +
150F LEU 2.8 1.6 + - - -
151F ASP* 1.3 95.0 + - - +
153F VAL* 1.3 71.1 + - + +
155F THR* 3.8 1.0 - - - -
156F THR* 2.1 42.3 + - + -
172F ASN* 3.4 9.4 + - - -
173F ARG* 3.0 10.9 - - - -
174F VAL 2.4 43.4 + - - -
175F VAL* 3.4 29.6 - - + -
294F VAL* 5.3 0.4 - - + -
315F ILE* 3.3 57.6 - - + +
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Residues in contact with VAL 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F LEU 4.1 1.1 + - - +
150F LEU 3.2 2.2 + - - -
152F TYR* 1.3 100.4 - - + +
154F MET* 1.3 63.8 + - - +
155F THR 2.9 5.2 - - - -
156F THR* 3.5 6.5 - - - +
157F LEU* 2.9 53.9 + - + +
175F VAL* 4.6 4.3 - - + -
192F LEU* 5.1 3.8 - - + -
196F LEU* 3.6 44.0 - - + -
200F LEU* 5.3 0.4 - - + -
246F LEU* 5.4 0.4 - - + -
248F PHE* 5.3 0.2 - - + -
294F VAL* 4.1 23.3 - - + -
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Residues in contact with MET 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E HIS* 4.4 2.9 - - - -
401E GLN* 3.5 39.0 - - + +
402E ALA* 4.3 0.2 - - - -
403E PRO* 3.6 30.2 - - + +
150F LEU* 2.9 42.0 + - + +
151F ASP* 4.0 4.5 - - - +
153F VAL* 1.3 76.9 - - - +
155F THR* 1.3 58.6 + - - +
157F LEU* 5.2 0.9 - - - +
158F LEU* 3.8 13.0 + - - +
196F LEU* 4.5 1.6 - - - +
199F ARG* 5.2 3.8 - - - -
200F LEU* 3.6 42.9 - - + +
203F ARG* 5.3 0.9 + - - -
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E PHE* 4.2 15.0 - - + +
396E HIS* 2.7 39.8 + - + +
397E ALA* 4.2 8.9 - - - -
401E GLN* 4.6 1.0 - - - -
151F ASP* 2.9 19.6 + - - -
152F TYR 4.2 0.9 - - - -
154F MET* 1.3 75.5 - - - +
156F THR* 1.3 66.6 + - - +
157F LEU 3.2 1.6 - - - -
158F LEU* 3.0 9.1 - - + +
159F PHE* 2.9 55.4 + - + -
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Residues in contact with THR 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E PHE* 5.9 2.9 - - - -
152F TYR* 2.1 44.6 + - + -
153F VAL* 2.9 13.1 + - + -
155F THR* 1.3 78.0 - - - +
157F LEU* 1.3 59.0 + - + +
159F PHE* 3.4 5.9 + - - +
160F SER* 2.8 28.1 + - - -
171F TRP* 5.4 5.8 - - + -
172F ASN 3.4 24.9 + - - +
173F ARG* 3.6 26.9 - - + -
293F VAL 5.8 0.2 - - - +
294F VAL* 6.1 2.0 - - + -
315F ILE* 5.3 2.4 - - - +
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F VAL* 2.9 35.0 + - + +
154F MET 5.2 0.9 - - - +
156F THR* 1.3 77.5 - - + +
158F LEU* 1.3 67.0 + - - +
160F SER* 3.7 4.7 - - - -
161F ASP* 2.9 21.5 + - - +
200F LEU* 4.5 16.2 - - + -
203F ARG* 2.8 27.1 + - - +
204F TYR* 3.6 31.9 - - + +
246F LEU* 3.6 11.9 - - + -
291F SER 3.7 23.1 - - - +
293F VAL 4.4 1.6 - - - +
294F VAL* 4.0 20.2 - - + -
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Residues in contact with LEU 158 (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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343E ILE* 3.5 45.3 - - + +
396E HIS* 3.5 37.0 - - + +
403E PRO* 3.7 33.4 - - + +
154F MET 3.8 7.8 + - - +
155F THR* 3.0 27.7 - - + +
157F LEU* 1.3 77.9 - - - +
159F PHE* 1.3 72.7 + - + +
161F ASP* 3.4 13.7 - - - +
162F LYS* 4.4 0.2 - - - +
203F ARG* 3.0 14.2 - - - +
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Residues in contact with PHE 159 (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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338E LEU* 3.6 33.9 - - + -
343E ILE* 4.2 4.7 - - + -
392E PRO* 4.7 5.8 - - + -
393E PHE* 3.3 57.4 - + + -
396E HIS* 5.1 2.2 - - + -
410E PHE* 6.3 1.1 - + - -
155F THR* 2.9 48.6 + - + +
156F THR* 3.9 4.0 - - - +
158F LEU* 1.3 87.4 - - + +
160F SER* 1.3 64.4 + - - +
161F ASP 3.4 0.5 + - - -
162F LYS 3.7 0.3 + - - -
163F ASN* 3.6 8.7 + - - -
164F VAL* 3.3 44.8 + - + +
169F ILE* 4.5 5.2 - - + -
171F TRP* 4.5 14.1 + - + -
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Residues in contact with SER 160 (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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156F THR 2.8 23.2 + - - -
157F LEU* 3.1 9.8 + - - -
159F PHE* 1.3 72.2 - - - +
161F ASP* 1.3 60.0 + - - +
163F ASN* 4.0 5.8 + - - +
171F TRP* 5.5 2.2 - - - -
173F ARG* 2.5 47.4 + - - +
291F SER* 2.5 51.9 + - - -
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Residues in contact with ASP 161 (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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157F LEU 2.9 11.7 + - - +
158F LEU 3.4 13.0 - - - +
159F PHE 3.2 0.4 - - - -
160F SER* 1.3 80.6 - - - +
162F LYS* 1.3 95.2 + - + +
163F ASN* 3.4 2.3 + - - +
203F ARG* 4.7 21.6 + - - +
291F SER* 3.9 11.0 + - - -
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Residues in contact with LYS 162 (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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341E CYS* 3.0 49.1 - - + +
342E GLN* 4.0 21.0 + - - +
343E ILE* 3.8 18.4 - - + -
158F LEU 4.1 0.4 + - - -
159F PHE 3.7 2.6 + - - -
160F SER 3.5 0.2 - - - -
161F ASP* 1.3 106.0 + - + +
163F ASN* 1.3 73.0 + - - +
164F VAL 3.5 0.4 - - - -
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Residues in contact with ASN 163 (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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337E GLU* 3.8 5.0 - - - +
340E LYS* 5.6 2.6 + - - -
159F PHE 3.6 6.2 + - - -
160F SER* 4.0 4.6 + - - +
161F ASP 3.4 6.2 - - - +
162F LYS* 1.3 81.4 - - - +
164F VAL* 1.3 75.2 + - - +
166F SER* 4.9 8.3 + - - -
171F TRP* 5.2 7.4 - - - -
173F ARG* 6.3 0.4 - - - +
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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