Contacts of the helix formed by residues 164 - 176 (chain E) in PDB entry 2BM9
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 ASN 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PHE 5.3 3.4 + - - -
11A ASP* 3.9 20.5 + - - +
13A ASN* 4.5 0.2 - - - +
139E CYS 3.1 25.6 - - - +
140E SER* 4.1 21.8 + - - +
142E LEU* 4.5 6.9 - - - +
162E HIS 4.4 0.2 + - - -
163E ALA* 1.3 72.8 - - + +
165E THR* 1.3 62.3 + - - +
166E PHE 3.4 2.9 + - - -
167E ASN* 3.4 34.6 - - - +
168E ILE* 3.2 19.4 + - - +
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Residues in contact with THR 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 5.4 0.2 + - - -
159E ASP* 3.1 32.7 + - - +
162E HIS* 3.4 4.7 - - - -
163E ALA 3.3 19.7 + - - -
164E ASN* 1.3 76.5 - - - +
166E PHE* 1.3 62.4 + - + +
168E ILE* 3.3 10.0 + - + +
169E MET* 3.0 25.7 + - + +
183E PHE* 4.4 7.1 - - + -
185E ILE* 3.8 20.9 - - + -
192E TRP* 3.7 26.5 - - + -
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Residues in contact with PHE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.5 34.5 - + + -
10A GLN 5.6 1.8 - - - -
12A LEU* 3.4 28.3 - - + -
164E ASN 3.4 0.6 - - - -
165E THR* 1.3 77.6 - - + +
167E ASN* 1.3 66.1 + - - +
169E MET* 3.2 35.9 + - + +
170E LYS* 3.1 19.8 + - - +
185E ILE* 5.5 2.7 - - + -
192E TRP* 3.8 22.0 - + - -
200E PHE* 3.8 28.3 - + - -
203E TYR* 3.6 31.0 - + + -
204E LEU* 3.9 11.4 - - + -
207E PHE* 4.1 6.7 - + - -
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Residues in contact with ASN 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.5 35.4 + - - +
142E LEU* 4.6 21.4 - - + +
164E ASN* 3.4 33.2 + - - +
166E PHE* 1.3 78.1 - - - +
168E ILE* 1.3 56.8 + - - +
170E LYS* 3.1 17.9 + - - +
171E TRP* 3.0 26.7 + - - +
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.5 5.6 - - + -
139E CYS* 3.6 26.9 - - + +
142E LEU* 4.8 2.9 - - + -
145E PHE* 3.6 39.0 - - + -
157E PHE* 4.1 22.4 - - + -
159E ASP* 5.8 1.3 - - - +
163E ALA 3.3 17.5 - - - +
164E ASN* 3.2 25.3 + - - +
165E THR* 3.3 11.6 + - - +
166E PHE 3.2 0.8 - - - -
167E ASN* 1.3 76.4 - - - +
169E MET* 1.3 60.8 + - - +
171E TRP* 3.9 8.3 - - + +
172E ALA* 3.1 23.9 + - - +
183E PHE* 4.4 5.2 - - + -
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Residues in contact with MET 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E THR 3.0 11.5 + - - +
166E PHE* 3.3 46.0 - - + +
167E ASN 3.2 0.2 - - - -
168E ILE* 1.3 74.8 - - - +
170E LYS* 1.3 63.4 + - - +
172E ALA* 3.9 1.3 - - - +
173E VAL* 3.0 30.0 + - - +
183E PHE* 3.2 43.1 - - + -
185E ILE* 4.6 8.7 - - + -
204E LEU* 4.7 9.2 - - + -
207E PHE* 3.4 26.2 - - + -
211E LEU* 3.7 27.4 - - + -
229E LEU* 4.1 8.3 - - - -
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Residues in contact with LYS 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.6 44.0 - - + +
5A SER* 4.8 9.4 + - - +
9A PHE* 4.9 8.3 - - + -
142E LEU* 6.3 2.7 - - - -
166E PHE 3.1 12.3 + - - +
167E ASN* 3.1 18.8 + - - +
169E MET* 1.3 76.8 - - - +
171E TRP* 1.3 69.0 + - - +
173E VAL* 3.6 0.9 + - - +
174E ASP* 2.9 54.3 + - - +
175E HIS* 6.0 2.8 - - - -
207E PHE* 4.1 4.0 - - + -
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Residues in contact with TRP 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 4.7 15.0 - - + -
145E PHE* 3.3 55.8 - + + +
146E GLU* 3.4 24.2 + - - +
148E LEU* 4.6 11.7 - - + -
157E PHE* 4.7 7.2 - + - -
167E ASN 3.0 14.1 + - - +
168E ILE* 3.9 11.0 - - + +
169E MET 3.3 0.2 - - - -
170E LYS* 1.3 84.9 - - - +
172E ALA* 1.3 81.6 - - + +
174E ASP* 3.0 5.4 + - - -
175E HIS* 2.9 78.0 + + + +
176E LEU* 3.9 38.8 - - + -
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Residues in contact with ALA 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E PHE* 5.4 2.7 - - + -
168E ILE* 3.1 16.6 + - + +
169E MET 3.9 2.9 - - - +
170E LYS 3.3 0.2 - - - -
171E TRP* 1.3 99.0 - - + +
173E VAL* 1.3 62.5 + - - +
176E LEU* 2.9 12.0 + - + -
177E LEU* 2.8 49.0 + - + -
183E PHE* 4.3 13.0 - - + -
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Residues in contact with VAL 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.6 27.6 - - + +
169E MET 3.0 20.5 + - - +
170E LYS* 3.8 4.5 - - - +
172E ALA* 1.3 78.5 - - - +
174E ASP* 1.3 64.1 + - - +
175E HIS 3.3 0.3 + - - -
176E LEU 4.4 0.2 + - - -
177E LEU* 4.0 21.5 - - + +
207E PHE* 4.1 17.0 - - + -
210E VAL* 4.2 23.8 - - + +
211E LEU* 4.5 10.1 - - + -
231E ARG* 3.2 36.6 + - - +
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Residues in contact with ASP 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.2 31.4 + - - -
5A SER* 5.6 1.2 + - - -
170E LYS* 2.9 46.4 + - - +
171E TRP 3.0 6.7 + - - +
173E VAL* 1.3 79.4 - - - +
175E HIS* 1.3 74.1 + - + +
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Residues in contact with HIS 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E GLU* 4.3 8.7 - - - -
170E LYS* 6.0 2.7 + - - -
171E TRP* 2.9 59.4 + + + +
173E VAL 3.2 0.2 - - - -
174E ASP* 1.3 89.9 - - + +
176E LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E MET* 3.7 41.7 - - + +
153E HIS* 3.0 29.2 + - - +
155E LEU* 3.9 16.6 - - + -
157E PHE* 3.9 21.8 - - + -
171E TRP* 3.9 33.0 - - + -
172E ALA* 2.9 10.6 + - + +
173E VAL 4.4 1.0 + - - -
174E ASP 4.0 0.2 - - - -
175E HIS* 1.3 80.2 - - - +
177E LEU* 1.3 81.6 + - + +
178E GLU* 4.3 4.3 - - - +
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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