Contacts of the helix formed by residues 147 - 161 (chain F) in PDB entry 3IT8
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 LEU 147 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PHE* 4.2 22.7 - - + +
71F SER* 6.2 0.2 - - - +
72F LEU* 4.3 25.1 - - + -
75F GLU* 5.3 4.5 - - - +
145F ASN* 2.5 18.3 + - - +
146F THR* 1.3 85.4 - - + +
148F TRP* 1.3 63.7 + - - +
149F LYS* 3.1 3.6 - - - -
150F ASP* 2.7 38.4 + - - +
151F VAL* 3.1 11.9 + - - +
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Residues in contact with TRP 148 (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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120F TYR* 4.1 11.2 - + - -
125F LYS 3.6 19.3 + - - -
126F ARG* 4.0 8.3 - - + -
127F PHE* 3.7 24.5 - + - -
140F MET* 3.3 25.6 - - - -
141F LEU 4.5 2.0 - - - -
142F THR 3.5 21.1 - - - +
143F VAL* 3.5 46.1 - - + +
145F ASN* 3.1 20.4 + - + +
146F THR 3.4 0.4 - - - -
147F LEU* 1.3 76.2 - - - +
149F LYS* 1.3 76.9 + - + +
151F VAL* 2.9 33.2 + - + +
152F LYS* 2.9 50.5 + - + +
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Residues in contact with LYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F VAL* 4.8 7.0 - - - +
146F THR 5.2 6.3 - - - +
147F LEU 3.1 1.1 - - - -
148F TRP* 1.3 90.9 - - + +
150F ASP* 1.3 63.5 + - - +
152F LYS* 3.5 33.8 + - + +
153F ALA* 3.2 22.0 + - - +
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Residues in contact with ASP 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE* 3.5 24.7 - - + -
147F LEU* 2.7 39.8 + - - +
149F LYS* 1.3 72.7 - - - +
151F VAL* 1.3 55.1 + - - +
153F ALA* 3.3 5.0 + - - +
154F TYR* 2.7 57.3 + - + +
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Residues in contact with VAL 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE* 4.4 0.4 - - + -
69F TRP* 4.2 22.2 - - + -
72F LEU* 3.6 31.2 - - + -
120F TYR* 5.2 1.8 - - + -
127F PHE* 4.3 10.8 - - + -
140F MET* 4.3 13.0 - - + +
145F ASN* 6.3 0.4 - - - -
147F LEU 3.1 10.2 + - - +
148F TRP* 2.9 41.1 + - + +
150F ASP* 1.3 76.1 - - - +
152F LYS* 1.3 59.1 + - - +
155F LEU* 2.8 44.4 + - + +
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Residues in contact with LYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER 5.5 0.5 - - - +
120F TYR* 3.8 20.8 + - - +
125F LYS* 3.8 29.5 - - + +
143F VAL* 5.3 2.0 - - - +
148F TRP* 2.9 46.4 + - + +
149F LYS* 3.5 36.9 - - + +
151F VAL* 1.3 77.1 - - - +
153F ALA* 1.3 58.2 + - - +
156F GLY* 2.9 28.1 + - - +
157F GLY 3.1 3.1 + - - -
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER 6.0 0.2 - - - -
87A TYR* 5.6 1.2 - - - -
149F LYS 3.2 14.5 + - - +
150F ASP* 3.7 7.0 - - - +
152F LYS* 1.3 78.1 - - - +
154F TYR* 1.3 74.8 + - + +
157F GLY* 3.2 20.4 + - - +
158F PHE 4.2 0.3 + - - -
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Residues in contact with TYR 154 (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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62F ASN* 5.0 4.5 + - - -
65F ASN* 3.5 38.4 + - - +
68F PHE* 3.6 42.8 - + + -
69F TRP* 3.6 18.6 - - + +
150F ASP* 2.7 40.0 + - + +
153F ALA* 1.3 81.7 - - + +
155F LEU* 1.3 58.8 + - - +
158F PHE* 3.3 23.9 + - - +
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F TRP* 3.9 16.4 - - + -
93F LEU* 4.3 22.0 - - + -
95F THR* 3.7 32.1 - - + +
108F GLY* 4.1 11.9 - - - +
120F TYR* 3.9 22.0 - - + -
127F PHE* 3.6 32.5 - - + -
151F VAL* 2.8 23.0 + - + +
154F TYR* 1.3 73.3 - - - +
156F GLY* 1.3 66.7 + - - +
158F PHE* 3.4 3.4 + - + +
159F GLU* 3.0 26.4 + - - +
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Residues in contact with GLY 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 4.6 1.8 - - - -
120F TYR* 3.3 31.2 - - - -
122F THR* 4.1 2.1 + - - -
151F VAL 3.4 1.4 + - - -
152F LYS* 2.9 16.0 + - - +
155F LEU* 1.3 79.2 - - - +
157F GLY* 1.3 51.8 + - - +
159F GLU* 3.3 1.8 + - - +
160F TYR* 2.7 38.2 + - - +
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Residues in contact with GLY 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER 3.4 21.0 + - - -
87A TYR* 3.7 16.9 - - - -
152F LYS 3.1 9.3 + - - -
153F ALA* 3.2 15.5 + - - -
156F GLY* 1.3 76.8 - - - +
158F PHE* 1.3 61.8 + - - +
160F TYR* 3.1 1.6 + - - +
161F MET 3.0 20.3 + - - -
162F GLY 3.1 5.7 + - - -
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Residues in contact with PHE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.9 1.9 - - - -
3F LEU* 4.6 1.6 - - + -
5F TYR* 3.1 50.7 - + - -
58F HIS 4.1 9.6 - - - -
60F PRO* 4.1 22.2 - - + -
95F THR* 3.8 28.7 - - + -
96F GLY* 4.3 4.0 - - - -
153F ALA 4.2 0.4 + - - -
154F TYR 3.3 21.5 + - - +
155F LEU* 3.4 4.4 + - - +
156F GLY 3.4 0.4 - - - -
157F GLY* 1.3 74.1 - - - +
159F GLU* 1.3 62.4 + - - +
161F MET 3.6 0.7 + - - -
162F GLY* 3.3 9.4 + - - +
163F CYS* 2.8 77.2 + - + +
166F ALA* 4.8 2.7 - - + -
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Residues in contact with GLU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F THR* 4.7 2.5 - - - +
96F GLY 5.8 0.2 - - - -
106F SER* 2.7 42.6 + - - +
107F TYR* 3.7 20.5 - - - +
108F GLY* 3.4 29.8 + - - -
120F TYR* 3.1 39.7 - - - +
122F THR* 4.1 14.1 + - - +
155F LEU* 3.0 18.3 + - - +
156F GLY* 3.7 4.0 - - - +
158F PHE* 1.3 79.3 - - - +
160F TYR* 1.3 63.3 + - - +
161F MET 3.6 0.3 + - - -
163F CYS* 5.1 0.7 - - - -
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Residues in contact with TYR 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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82A ARG* 3.4 17.2 + - - -
84A ALA* 4.3 4.5 - - + -
86A SER* 3.8 28.5 - - - +
87A TYR* 4.3 4.0 - - + -
125A GLN 5.6 0.2 + - - -
127A GLU* 3.3 42.0 - - + +
122F THR* 3.3 34.1 - - + +
156F GLY 2.7 22.1 + - - +
157F GLY 3.1 4.2 + - - +
159F GLU* 1.3 75.6 - - - +
161F MET* 1.3 88.8 + - + +
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Residues in contact with MET 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 3.3 33.7 - - - +
84A ALA* 5.0 4.0 - - + -
87A TYR* 4.1 17.7 - - + -
91A VAL* 4.2 17.3 - - + -
33C ALA* 4.8 10.1 - - + +
34C ASN* 3.7 17.5 - - - +
157F GLY 3.0 3.2 + - - -
158F PHE 3.8 0.4 - - - -
159F GLU 3.4 1.8 - - - -
160F TYR* 1.3 97.6 - - + +
162F GLY* 1.3 69.5 + - - +
163F CYS 3.3 2.2 - - - -
164F SER* 2.8 29.9 + - - +
165F LEU* 3.2 33.8 + - + +
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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