Contacts of the helix formed by residues 212 - 219 (chain A) in PDB entry 4FBJ
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 LYS 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLU* 3.6 36.1 + - + +
121A PRO 5.8 0.2 - - - -
210A PRO 6.1 0.2 - - - -
211A LEU* 1.3 76.4 - - - +
213A ILE* 1.3 67.8 - - - +
214A ALA* 4.5 1.3 - - + +
215A ASP* 2.9 36.0 + - - +
216A TRP* 2.9 21.7 + - - +
73B LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 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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60A ILE* 5.5 0.4 - - + -
64A HIS* 3.7 35.9 - - + +
74A TRP* 4.0 17.9 - - + -
120A GLU* 3.9 1.8 + - - +
121A PRO* 3.9 17.7 + - + -
126A SER* 4.0 13.7 - - - -
130A ILE* 4.1 10.8 - - + -
200A GLN* 3.2 32.5 - - - +
201A SER* 3.8 16.4 - - - -
212A LYS* 1.3 70.4 - - - +
214A ALA* 1.4 61.8 + - - +
216A TRP* 3.4 1.4 + - - +
217A LEU* 2.9 58.3 + - + +
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Residues in contact with ALA 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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61A ILE* 3.9 35.0 - - + +
64A HIS* 3.9 25.3 - - + +
65A ASN* 4.4 6.3 - - - +
212A LYS* 3.3 2.2 - - + +
213A ILE* 1.4 79.3 - - - +
215A ASP* 1.3 69.3 + - - +
217A LEU* 5.1 0.4 - - - -
218A ASN* 3.1 24.1 + - - +
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Residues in contact with ASP 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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211A LEU* 4.7 1.3 - - + -
212A LYS* 2.9 42.4 + - + +
214A ALA* 1.3 81.6 - - - +
216A TRP* 1.3 63.4 + - - +
218A ASN* 3.6 11.3 + - - +
219A SER* 4.5 1.9 + - - -
220A ARG 5.1 0.5 + - - -
256A ILE* 3.5 25.2 - - + +
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Residues in contact with TRP 216 (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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198A ILE* 2.7 37.4 + - + -
200A GLN* 3.4 59.5 - - + +
211A LEU* 3.5 26.8 - - + +
212A LYS 2.9 9.4 + - - +
213A ILE 3.6 4.0 - - - +
215A ASP* 1.3 78.9 - - - +
217A LEU* 1.3 71.4 + - + +
218A ASN 3.2 0.3 + - - -
220A ARG* 3.1 52.7 + - + +
221A GLY* 3.0 26.0 + - - -
253A THR 3.4 25.6 - - - -
254A LEU 3.7 9.0 - - - -
255A ASP 3.7 15.9 - - - -
256A ILE* 3.7 6.5 - - - -
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Residues in contact with LEU 217 (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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57A ILE* 3.6 25.7 - - + +
60A ILE* 3.9 27.8 - - + -
61A ILE* 3.8 16.6 - - + -
130A ILE* 4.7 3.8 - - + -
199A TYR* 3.6 39.9 - - + -
213A ILE* 2.9 43.5 + - + +
214A ALA* 3.4 0.8 + - - -
216A TRP* 1.3 84.5 - - + +
218A ASN* 1.3 66.8 + - - +
219A SER* 3.2 0.7 + - - -
221A GLY* 4.1 5.6 + - - +
222A LYS* 3.6 19.9 - - - +
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Residues in contact with ASN 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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58A ASP* 4.5 5.0 - - - +
61A ILE* 3.7 20.1 - - - +
214A ALA 3.1 16.2 + - - +
215A ASP* 4.0 7.2 - - - +
216A TRP 3.2 1.4 + - - -
217A LEU* 1.3 77.2 - - - +
219A SER* 1.3 62.5 + - - +
222A LYS* 2.8 27.0 + - - +
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Residues in contact with SER 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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215A ASP 4.5 2.5 + - - -
216A TRP 3.6 0.8 + - - -
218A ASN* 1.3 86.2 - - - +
220A ARG* 1.3 71.1 + - - +
221A GLY 3.3 1.6 - - - -
222A LYS* 3.0 23.2 + - - +
223A ASP* 3.6 13.1 + - - +
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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