Contacts of the helix formed by residues 147 - 166 (chain N) in PDB entry 3SDI
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 147 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8N PHE* 3.6 2.7 - - - -
9N LYS* 4.9 9.4 - - - +
10N ASP* 5.8 0.7 - - - -
146N MET* 1.3 73.3 - - - +
148N LYS* 1.3 63.0 + - - +
149N GLU* 2.9 28.1 + - - -
150N GLU* 2.9 36.7 + - - +
151N THR* 2.8 27.7 + - - -
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Residues in contact with LYS 148 (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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8N PHE* 3.4 29.7 - - + -
10N ASP* 4.6 8.5 + - - +
13N ILE* 4.2 1.1 - - + +
147N SER* 1.3 73.1 - - - +
149N GLU* 1.3 64.4 + - + +
151N THR* 3.1 4.1 + - - -
152N VAL* 2.9 45.6 + - + +
177N VAL* 4.5 19.1 - - + -
179N THR* 6.2 1.3 - - + -
185N GLU* 2.7 36.2 + - - +
187N LEU* 5.3 3.1 - - - -
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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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147N SER* 2.9 24.7 + - - +
148N LYS* 1.3 80.5 - - + +
150N GLU* 1.3 62.5 + - + +
152N VAL* 3.5 7.3 + - - +
153N ASP* 3.1 31.7 + - - +
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Residues in contact with GLU 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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143N ARG* 3.4 30.1 + - - +
146N MET* 3.3 26.0 - - + +
147N SER* 2.9 43.7 + - - +
149N GLU* 1.3 80.2 - - + +
151N THR* 1.3 58.3 + - - +
153N ASP* 3.2 9.9 + - - +
154N PHE* 2.9 23.9 + - - +
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Residues in contact with THR 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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6N VAL* 4.0 31.9 - - + -
7N THR 4.9 0.2 + - - -
8N PHE* 3.1 25.0 - - + +
13N ILE* 3.6 26.5 - - + -
146N MET* 3.5 16.9 - - - +
147N SER 2.8 21.9 + - - -
148N LYS 3.5 3.6 - - - -
150N GLU* 1.3 73.0 - - - +
152N VAL* 1.3 65.7 + - - +
153N ASP 3.2 0.3 + - - -
154N PHE* 3.2 2.3 + - - +
155N ILE* 3.1 26.8 + - + +
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Residues in contact with VAL 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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13N ILE* 3.9 17.0 - - + -
148N LYS* 2.9 35.1 + - + +
149N GLU* 3.8 8.1 - - - +
151N THR* 1.3 71.3 - - - +
153N ASP* 1.3 62.5 + - - +
156N LYS* 3.1 29.5 + - - +
175N MET* 3.4 14.6 - - + +
187N PHE* 3.7 53.8 - - + +
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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
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149N GLU* 3.1 21.3 + - - +
150N GLU* 3.4 11.0 - - - +
151N THR 3.1 0.2 - - - -
152N VAL* 1.3 75.9 - - - +
154N PHE* 1.3 60.6 + - - +
156N LYS* 3.2 26.1 + - - +
157N HIS* 2.9 47.4 + - + +
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Residues in contact with PHE 154 (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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4N MET* 3.7 15.7 - - + -
6N VAL* 3.8 32.8 - - + -
124N TYR* 4.6 4.7 - + - -
137N TYR* 4.6 5.6 - + - -
138N CYS* 4.0 27.4 - - + -
141N ASN* 4.1 22.0 - - + -
142N PHE* 3.8 37.0 - + + -
146N MET* 3.8 15.7 - - + -
150N GLU 2.9 13.4 + - - +
151N THR 3.5 7.0 - - - +
153N ASP* 1.3 75.4 - - - +
155N ILE* 1.3 63.6 + - + +
157N HIS* 4.0 4.9 - - - +
158N SER* 2.9 42.8 + - - -
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Residues in contact with ILE 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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4N MET* 4.0 15.7 - - + -
6N VAL* 3.6 33.2 - - + -
13N ILE* 3.7 43.3 - - + +
15N GLY* 4.0 13.0 - - - +
151N THR* 3.1 18.7 + - + +
154N PHE* 1.3 71.1 - - - +
156N LYS* 1.3 66.5 + - - +
158N SER* 3.6 0.2 - - - -
159N LEU* 2.9 48.5 + - + +
175N MET* 3.7 22.4 - - + -
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Residues in contact with LYS 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 VAL* 3.1 19.2 + - - +
153N ASP* 3.2 27.1 + - - +
155N ILE* 1.3 78.7 - - - +
157N HIS* 1.3 59.4 + - + +
160N SER* 3.0 30.0 + - - -
173N ILE* 3.8 10.0 - - + +
175N MET* 4.1 8.1 - - + -
187N LEU* 2.9 105.3 + - + +
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Residues in contact with HIS 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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1402 LYS* 3.8 12.4 + - - +
137N TYR* 3.2 30.6 + - + +
153N ASP* 2.9 31.6 + - + +
154N PHE* 4.0 4.1 + - - +
156N LYS* 1.3 77.4 - - + +
158N SER* 1.3 66.5 + - - +
160N SER* 2.7 19.2 + - - -
161N GLN* 3.1 14.7 + - - +
187N LEU* 3.4 47.0 + - - -
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Residues in contact with SER 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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4N MET* 3.6 22.5 - - - +
134N ILE* 3.3 16.2 - - - +
137N TYR* 3.6 18.2 - - - -
138N CYS* 3.3 25.7 - - - -
154N PHE* 2.9 24.3 + - - -
155N ILE 3.6 4.0 - - - -
157N HIS* 1.3 77.7 - - - +
159N LEU* 1.3 57.8 + - - +
161N GLN* 3.3 0.6 + - - -
162N ALA 3.0 22.2 + - - -
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Residues in contact with LEU 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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2N SER* 3.7 36.3 - - - +
3N ILE 4.3 2.0 - - - +
4N MET* 3.8 21.1 - - + -
15N GLY 3.7 2.5 - - - -
16N ALA* 3.5 32.8 - - - +
17N ASP 5.2 0.7 - - - +
134N ILE* 4.7 6.3 - - + -
155N ILE* 2.9 34.6 + - + +
158N SER* 1.3 76.4 - - - +
160N SER* 1.3 58.0 + - - +
162N ALA* 3.7 2.5 - - - +
163N ILE* 2.7 42.1 + - + +
173N ILE* 3.7 26.5 - - + -
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Residues in contact with SER 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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1402 LYS* 4.6 5.5 + - - -
156N LYS 3.0 16.2 + - - -
157N HIS* 2.7 24.1 + - - -
159N LEU* 1.3 74.5 - - - +
161N GLN* 1.3 62.4 + - - +
163N ILE* 3.4 3.5 + - - +
164N LYS* 2.9 29.5 + - - +
173N ILE* 4.0 0.8 - - - +
187N TYR* 3.6 52.1 + - - -
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Residues in contact with GLN 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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1362 GLY* 2.9 41.3 + - - -
1392 ASP* 3.1 24.3 - - - +
1402 LYS* 3.9 28.2 + - + +
134N ILE* 3.8 13.2 - - + -
137N TYR* 5.0 5.2 - - + -
157N HIS 3.1 11.1 + - - +
158N SER* 3.5 8.7 - - - +
160N SER* 1.3 81.3 + - - +
162N ALA* 1.3 66.8 + - - +
164N LYS* 2.9 19.7 + - - +
165N TRP* 3.1 38.7 + - - +
187N LEU 5.4 1.9 - - - +
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Residues in contact with ALA 162 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2N SER* 3.5 26.7 - - - +
130N GLY 3.3 25.8 - - - +
133N PHE* 4.9 3.8 - - - -
134N ILE* 3.6 14.2 - - + +
158N SER 3.0 16.6 + - - +
159N LEU* 3.7 4.3 - - - +
161N GLN* 1.3 73.9 - - - +
163N ILE* 1.3 58.2 + - - +
165N TRP* 4.1 0.2 - - - -
166N ASP* 2.9 35.7 + - - +
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Residues in contact with ILE 163 (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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251 LEU* 4.2 0.3 - - - +
2N SER* 4.8 1.6 - - - +
17N ASP* 3.9 18.6 - - + -
159N LEU* 2.7 25.5 + - + +
160N SER* 3.7 4.7 - - - +
162N ALA* 1.3 72.7 - - - +
164N LYS* 1.3 64.2 - - - +
166N ASP 3.1 5.0 - - - +
169N SER* 4.0 11.7 - - - -
170N GLY* 3.7 28.5 - - - +
172N VAL 4.9 0.7 - - - +
173N ILE* 3.9 19.1 - - + -
187N TYR* 3.6 43.5 - - + +
201N MG 2.6 28.9 - - - -
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Residues in contact with LYS 164 (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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251 LEU* 3.5 22.7 - - - +
281 ASN* 4.9 15.1 + - - +
1392 ASP* 3.1 38.8 + - - +
160N SER 2.9 14.0 + - - +
161N GLN* 2.9 19.7 + - - +
163N ILE* 1.3 79.3 - - - +
165N TRP* 1.3 77.2 + - + +
187N GLU 5.7 4.0 - - - -
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Residues in contact with TRP 165 (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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241 LEU* 3.3 15.6 - - + +
251 LEU* 3.0 53.5 + - - -
261 ARG 4.0 14.4 - - - -
281 ASN* 4.5 11.4 - - - -
1242 TYR* 5.3 4.0 - - - -
1352 TYR* 3.5 48.4 + + + -
1362 GLY 4.1 2.9 - - - -
1392 ASP* 3.7 29.2 - - + -
133N PHE* 3.6 26.5 - - + -
161N GLN* 3.1 48.2 + - - +
164N LYS* 1.3 95.0 - - + +
166N ASP* 1.3 59.4 + - - +
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Residues in contact with ASP 166 (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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231 SER* 3.9 14.4 + - - -
251 LEU* 4.1 1.8 - - - -
129N SER* 2.8 28.7 + - - -
130N GLY* 3.0 17.9 + - - -
133N PHE* 3.8 9.6 - - + -
162N ALA 2.9 16.7 + - - +
163N ILE 3.1 3.6 - - - +
165N TRP* 1.3 77.1 - - - +
167N GLY* 1.3 65.2 + - - +
168N SER* 3.2 18.0 + - - -
169N SER* 2.6 30.3 + - - +
201N MG 2.8 20.6 - - - -
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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