Contacts of the helix formed by residues 212 - 219 (chain A) in PDB entry 3MBL
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LSG 2.9 12.9 + - - -
111A ILE* 4.2 5.5 - - - -
114A GLU* 2.7 34.1 + - - +
115A LEU* 4.1 14.8 - - - -
210A GLY 3.4 0.8 - - - -
211A VAL* 1.3 80.4 - - - +
213A GLY* 1.3 64.2 + - - +
214A GLN* 4.2 0.7 - - - +
215A LEU* 2.9 33.7 + - - +
216A ILE* 2.9 19.4 + - - +
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 3.6 8.9 + - - -
211A VAL 3.8 3.6 + - - -
212A SER* 1.3 71.8 + - - +
214A GLN* 1.3 62.4 + - - +
216A ILE* 3.4 15.5 + - - +
217A ASP* 3.2 23.5 + - - +
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Residues in contact with GLN 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 4.0 31.3 - - + +
110A GLN* 3.1 32.3 + - - +
111A ILE* 3.8 20.4 - - + -
114A GLU* 3.1 20.1 + - - +
213A GLY* 1.3 76.5 - - - +
215A LEU* 1.3 56.4 + - - +
217A ASP* 3.2 24.1 + - - +
218A SER* 3.2 23.0 + - - -
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LSG 3.7 36.1 - - + +
99A ILE* 4.3 17.9 - - + -
101A LEU* 3.9 28.0 - - + -
111A ILE* 4.2 22.4 - - + +
115A LEU* 4.3 16.6 - - + -
139A ILE* 5.0 3.6 - - + -
141A ILE* 4.9 0.4 - - + -
212A SER* 2.9 21.7 + - - +
214A GLN* 1.3 72.7 - - - +
216A ILE* 1.3 69.0 + - - +
217A ASP 3.0 1.6 + - - -
218A SER* 3.2 1.6 + - - +
219A MET* 3.1 42.2 + - + +
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Residues in contact with ILE 216 (chain A).
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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7A LSG 3.6 18.0 - - + +
189A ARG* 3.9 46.7 - - - +
210A GLY* 4.4 12.8 - - - +
212A SER 2.9 20.6 + - - +
213A GLY* 3.4 15.9 - - - +
215A LEU* 1.3 76.7 - - - +
217A ASP* 1.3 68.7 + - - +
219A MET* 3.4 5.0 + - - +
220A ALA* 3.3 16.8 + - - +
234A ARG* 6.2 1.1 - - - +
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Residues in contact with ASP 217 (chain A).
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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213A GLY 3.2 14.1 + - - +
214A GLN* 3.3 27.5 - - - +
215A LEU 3.0 1.8 - - - -
216A ILE* 1.3 76.2 - - - +
218A SER* 1.3 58.1 + - - +
219A MET 2.8 10.9 + - - -
220A ALA* 2.9 24.2 + - - +
221A ASN 4.8 0.2 + - - -
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.3 20.6 - - - +
103A ILE* 3.9 20.2 - - - -
107A ILE* 3.6 22.0 - - - +
111A ILE* 4.1 4.1 - - - +
214A GLN* 3.2 17.5 + - - -
215A LEU* 3.2 3.3 + - - -
217A ASP* 1.3 74.9 - - - +
219A MET* 1.3 60.3 + - - +
220A ALA 3.5 0.4 - - - -
221A ASN* 4.9 6.3 + - - +
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Residues in contact with MET 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LSG 3.8 43.1 - - - +
78A ASN* 4.5 11.0 - - + +
99A ILE* 4.4 30.5 - - + -
101A LEU* 5.2 2.2 - - + -
215A LEU* 3.1 44.0 + - + +
216A ILE* 3.7 5.8 - - - +
217A ASP 2.8 1.2 + - - -
218A SER* 1.3 83.4 - - - +
220A ALA* 1.3 62.7 + - - +
221A ASN 3.2 3.8 + - - -
222A SER* 3.9 15.9 + - - +
223A PHE* 4.8 4.4 - - - -
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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