Contacts of the helix formed by residues 148 - 162 (chain N) in PDB entry 3V3K
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 SER 148 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M GLY* 3.4 31.6 - - - -
177M ARG* 5.1 0.7 - - - -
144N PRO* 3.6 11.9 - - - +
145N HIS* 2.7 28.5 + - - -
146N HIS 3.4 0.2 - - - -
147N SER* 1.3 83.2 + - - +
149N GLU* 1.3 64.1 + - - +
150N LEU* 3.8 3.8 + - - -
151N TYR* 3.2 18.5 + - - +
152N GLY 3.6 11.6 + - - -
181N TYR* 3.7 11.0 - - - -
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Residues in contact with GLU 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M GLY 4.4 3.6 - - - -
177M ARG* 5.5 7.1 - - + +
77N MET* 4.3 17.7 - - + +
80N ARG* 3.6 44.6 + - - +
81N ASN* 3.8 19.8 + - - +
148N SER* 1.3 72.2 - - - +
150N LEU* 1.3 64.8 + - - +
152N GLY* 3.2 12.3 + - - -
153N ASP* 3.4 8.5 + - - -
178N ASP 5.0 0.9 - - - +
181N TYR* 5.2 4.6 - - - +
183N LYS* 2.8 37.0 + - - +
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Residues in contact with LEU 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N VAL* 3.8 29.6 - - + -
76N LEU* 4.0 20.4 - - + -
77N MET* 6.5 1.3 - - + -
110N TYR* 4.7 2.2 - - - +
114N LEU* 3.8 25.4 - - + -
117N LEU* 4.1 12.1 - - + -
141N LEU 4.6 9.0 - - - +
142N LEU* 6.1 1.1 - - + -
144N PRO* 4.2 14.8 - - + -
148N SER* 3.4 3.9 + - - +
149N GLU* 1.3 78.4 - - - +
151N TYR* 1.3 57.5 + - - +
153N ASP* 3.4 4.3 + - - -
154N LEU* 2.9 47.5 + - + +
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Residues in contact with TYR 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288M GLU* 3.2 49.5 + - - +
290M LYS* 5.8 0.9 - - - -
144N PRO* 3.6 30.6 - - + +
145N HIS 3.3 5.6 - - - +
146N HIS* 3.7 23.6 - - + -
148N SER* 3.2 23.8 + - - +
150N LEU* 1.3 77.4 - - - +
152N GLY* 1.3 58.1 + - - +
154N LEU* 4.0 4.2 - - + +
155N ARG* 2.9 64.0 + - + +
181N TYR* 3.3 28.7 - + - -
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Residues in contact with GLY 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N SER 3.6 4.2 + - - -
149N GLU 3.2 7.5 + - - -
151N TYR* 1.3 79.8 - - - +
153N ASP* 1.3 60.9 + - - +
155N ARG* 4.0 4.8 + - - +
156N ALA* 3.1 26.3 + - - +
178N ASP* 3.4 10.9 - - - +
181N TYR* 3.6 34.3 - - - -
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Residues in contact with ASP 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N ARG* 2.7 29.0 + - - -
110N TYR* 2.6 28.9 + - - -
114N LEU* 3.6 25.5 - - + +
149N GLU 3.4 5.5 + - - +
150N LEU* 3.7 6.2 - - - +
151N TYR 3.2 0.6 - - - -
152N GLY* 1.3 74.4 - - - +
154N LEU* 1.3 55.5 + - - +
156N ALA* 3.2 6.1 + - - +
157N MET* 2.7 37.1 + - - +
176N VAL 4.2 0.6 - - - +
177N PRO* 3.4 8.1 - - - +
178N ASP 2.8 32.1 + - - +
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Residues in contact with LEU 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N LEU* 4.3 13.9 - - + +
117N LEU* 4.0 28.0 - - + +
118N HIS* 4.2 23.8 - - + +
121N LYS* 5.6 11.0 - - + +
142N LEU* 4.2 15.5 - - + +
144N PRO* 4.1 21.3 - - + -
150N LEU* 2.9 43.2 + - + +
151N TYR* 4.0 4.3 - - + +
153N ASP* 1.3 76.7 - - - +
155N ARG* 1.3 58.3 + - - +
157N MET* 3.6 3.6 - - + +
158N LYS* 2.9 29.8 + - - +
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Residues in contact with ARG 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290M LYS* 4.7 9.2 - - - +
151N TYR* 2.9 48.2 + - + +
152N GLY 4.1 4.1 + - - +
154N LEU* 1.3 75.4 - - - +
156N ALA* 1.3 62.2 + - - +
158N LYS* 3.8 8.6 + - + +
159N CYS* 3.3 32.4 + - - -
167N ASP* 3.5 25.0 + - - +
168N PHE* 3.8 26.1 - - - -
178N ASP* 4.8 7.7 + - - -
181N TYR* 3.7 35.7 + - - -
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Residues in contact with ALA 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N GLY 3.1 21.8 + - - +
153N ASP* 3.2 7.4 + - - +
155N ARG* 1.3 74.7 - - - +
157N MET* 1.3 64.3 + - - +
159N CYS* 3.3 13.0 + - - +
160N LEU* 3.4 19.0 + - - +
174N ILE* 4.0 15.3 - - + +
175N ARG 3.1 28.3 - - - +
176N VAL* 4.4 4.0 - - - +
178N ASP* 4.1 8.7 - - + +
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Residues in contact with MET 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N LEU* 4.4 8.1 - - - -
111N ILE* 4.8 4.0 - - - -
114N LEU* 3.4 35.4 - - + +
115N PHE* 3.4 42.4 - - + -
118N HIS* 3.8 19.1 - - + -
153N ASP 2.7 15.1 + - - +
154N LEU* 3.6 7.9 - - - +
156N ALA* 1.3 73.4 - - - +
158N LYS* 1.3 56.2 + - - +
160N LEU* 3.2 2.8 + - - +
161N VAL* 2.9 63.6 + - + +
176N VAL* 3.9 24.4 + - + -
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Residues in contact with LYS 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118N HIS* 3.8 20.3 - - + +
121N LYS* 5.7 8.5 - - - +
125N GLU* 5.6 5.4 + - - -
154N LEU 2.9 18.3 + - - +
155N ARG* 4.0 11.0 - - + +
156N ALA 3.3 0.2 - - - -
157N MET* 1.3 74.7 - - - +
159N CYS* 1.3 58.4 + - - +
162N GLU* 3.0 60.7 + - + +
165N SER* 5.3 11.7 - - - +
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Residues in contact with CYS 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N ARG* 3.3 26.0 - - - -
156N ALA* 3.3 10.0 + - - +
157N MET 3.2 0.6 - - - -
158N LYS* 1.3 79.1 - - - +
160N LEU* 1.3 62.6 + - - +
163N GLY 3.3 2.4 + - - -
164N CYS* 2.7 52.0 + - - +
165N SER* 4.0 11.4 - - - -
167N ASP* 4.7 11.0 - - - -
174N ILE* 3.4 31.9 - - + -
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Residues in contact with LEU 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N VAL 4.2 1.3 - - - +
30N SER 3.2 32.1 - - - +
31N GLU* 4.9 0.4 - - - -
32N LEU* 4.4 22.0 - - + +
156N ALA 3.4 10.3 + - - +
157N MET 3.2 5.9 + - - +
159N CYS* 1.3 77.0 - - + +
161N VAL* 1.3 66.3 + - - +
163N GLY* 4.1 4.0 + - - -
174N ILE* 4.1 26.0 - - + +
176N VAL* 3.4 44.2 - - + +
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Residues in contact with VAL 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N LEU* 3.9 17.0 - - + -
115N PHE* 4.1 13.2 - - + -
118N HIS* 3.5 26.5 - - + +
157N MET* 2.9 48.2 + - + +
160N LEU* 1.3 79.3 - - - +
162N GLU* 1.3 60.5 + - + +
163N GLY* 3.3 4.5 + - - -
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Residues in contact with GLU 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N HIS* 3.8 23.7 + - + -
122N VAL* 4.0 14.2 - - - +
125N GLU* 5.8 0.2 - - - +
158N LYS* 3.0 50.2 + - + +
161N VAL* 1.3 78.4 - - + +
163N GLY* 1.3 63.7 + - - +
165N SER* 4.9 2.6 + - - -
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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