Contacts of the helix formed by residues 196 - 207 (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 ALA 196 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.7 8.3 - - + +
15A PHE* 3.6 29.8 - - + -
20A GLU* 3.2 19.3 - - + +
192E TRP* 2.9 13.9 + - - +
195E TYR* 1.3 80.1 - - + +
197E PRO* 1.3 65.4 - - - +
198E GLN 3.1 3.2 + - - -
199E LEU* 3.1 8.2 + - + -
200E PHE* 2.9 20.1 + - - +
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Residues in contact with PRO 197 (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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20A GLU* 4.0 4.5 - - - +
51A SER* 6.0 6.3 - - - -
53A PHE* 6.2 0.2 - - + -
193E TYR* 3.4 46.1 - - + +
194E ARG 3.8 6.7 - - - +
195E TYR 3.3 9.4 - - - +
196E ALA* 1.3 90.2 - - - +
198E GLN* 1.3 61.6 + - + +
200E PHE* 4.0 0.4 - - + +
201E SER* 3.3 28.1 + - - -
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Residues in contact with GLN 198 (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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20A GLU* 3.3 18.5 + - - +
196E ALA 3.2 1.0 - - - -
197E PRO* 1.3 82.6 - - + +
199E LEU* 1.3 61.9 + - - +
201E SER* 3.7 3.4 + - - -
202E GLU* 3.3 26.7 + - - +
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Residues in contact with LEU 199 (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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10A GLN* 4.2 16.8 - - - +
12A LEU* 4.3 7.6 - - + -
15A PHE* 3.7 30.5 - - + -
20A GLU* 2.9 30.2 + - + +
196E ALA* 3.1 11.1 + - + +
198E GLN* 1.3 73.3 - - - +
200E PHE* 1.3 62.5 + - - +
202E GLU* 3.6 22.8 - - - +
203E TYR* 3.1 63.6 + - + +
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Residues in contact with PHE 200 (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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12A LEU* 4.2 9.2 - - + -
41D TRP* 3.8 23.3 - + - -
166E PHE* 3.8 26.0 - + - -
189E ILE* 3.5 35.2 - - + -
192E TRP* 4.1 27.4 - + + +
193E TYR* 3.7 28.5 - + + -
196E ALA* 2.9 17.4 + - - +
197E PRO 4.0 2.7 - - - +
199E LEU* 1.3 76.4 - - - +
201E SER* 1.3 58.1 + - - +
203E TYR* 3.1 4.4 + - - +
204E LEU* 2.8 65.4 + - + +
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Residues in contact with SER 201 (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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38D LEU 5.3 0.2 - - - +
41D TRP* 5.6 3.9 - - - +
42D ALA* 5.6 4.2 - - - +
193E TYR* 4.4 12.5 - - - -
197E PRO 3.3 16.9 + - - -
198E GLN* 4.0 3.4 - - - -
200E PHE* 1.3 78.3 - - - +
202E GLU* 1.3 67.3 + - - +
204E LEU* 4.5 6.3 - - - +
205E GLY* 2.8 26.5 + - - -
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Residues in contact with GLU 202 (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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7A GLN* 3.4 28.7 + - - +
198E GLN* 3.3 15.1 + - - +
199E LEU* 3.6 30.4 - - - +
201E SER* 1.3 78.0 - - - +
203E TYR* 1.3 66.8 + - + +
205E GLY* 4.1 0.7 - - - -
206E ALA* 3.4 16.3 + - - +
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Residues in contact with TYR 203 (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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7A GLN* 3.8 20.2 - - + +
8A ASN 3.5 9.2 + - - -
9A PHE* 3.5 35.2 - + + -
10A GLN* 2.9 40.6 + - - +
12A LEU* 3.4 37.9 - - + -
166E PHE* 3.6 22.0 - + + -
199E LEU* 3.1 40.0 - - + +
200E PHE 3.1 6.6 + - - +
201E SER 3.1 0.8 - - - -
202E GLU* 1.3 78.5 - - + +
204E LEU* 1.3 67.5 + - - +
205E GLY 3.0 1.2 + - - -
206E ALA* 3.1 19.7 + - - +
207E PHE* 3.4 8.5 - - - -
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Residues in contact with LEU 204 (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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38D LEU* 3.4 42.1 - - + +
41D TRP* 3.4 44.2 - - + +
166E PHE* 3.9 7.0 - - + -
169E MET* 4.7 11.2 - - + -
185E ILE* 6.5 0.2 - - + -
189E ILE* 5.3 4.0 - - + -
200E PHE* 2.8 51.8 + - + +
201E SER* 4.0 4.7 - - - +
203E TYR* 1.3 72.9 - - - +
205E GLY* 1.3 60.5 + - - +
207E PHE* 3.2 23.2 + - + +
229E LEU* 4.2 15.9 - - + -
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Residues in contact with GLY 205 (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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38D LEU 3.8 18.4 - - - -
39D ASP* 4.5 5.6 - - - -
201E SER 2.8 20.9 + - - -
202E GLU 4.1 1.1 - - - -
204E LEU* 1.3 69.0 - - - +
206E ALA* 1.3 63.7 + - - +
207E PHE 3.0 2.2 - - - -
208E ARG* 3.1 32.8 + - - +
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Residues in contact with ALA 206 (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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2A ASN 4.6 3.1 + - - -
3A ASP* 3.9 13.7 + - + -
4A TYR* 3.6 47.1 - - + +
7A GLN* 4.3 5.4 - - - +
9A PHE* 5.0 2.5 - - + -
202E GLU 3.4 10.2 + - - +
203E TYR* 3.1 15.3 + - - +
205E GLY* 1.3 75.9 - - - +
207E PHE* 1.3 61.9 + - + +
208E ARG* 3.2 18.2 + - - +
209E ASP* 4.5 3.3 + - - +
210E VAL* 5.0 0.2 - - - +
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Residues in contact with PHE 207 (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* 4.5 17.0 - + + -
9A PHE* 4.2 17.3 - + - -
38D LEU* 3.9 12.6 - - + -
166E PHE* 4.1 7.2 - + - -
169E MET* 3.4 61.0 - - + -
170E LYS* 4.1 9.0 - - - -
173E VAL* 4.1 6.7 - - + -
203E TYR 3.4 19.3 - - - -
204E LEU 3.4 10.8 - - - +
205E GLY 3.0 1.4 - - - -
206E ALA* 1.3 77.1 - - - +
208E ARG* 1.3 62.3 + - - +
209E ASP 3.1 3.4 - - - -
210E VAL* 2.9 32.2 + - + -
211E LEU* 2.9 33.0 + - + +
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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