Contacts of the helix formed by residues 211 - 218 (chain B) in PDB entry 5X6E
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 LEU 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B LEU* 4.2 11.9 - - + -
151B THR* 4.1 27.1 - - + -
152B TYR* 4.2 20.2 - - + +
162B ILE* 5.4 10.3 - - + -
208B VAL* 4.4 9.2 - - + -
209B GLN 3.4 6.7 + - - +
210B ASN* 1.3 68.6 - - - +
212B ASP* 1.3 59.8 + - - +
213B TYR 2.8 5.9 + - - -
214B LEU* 2.5 48.2 + - + +
215B LYS* 3.3 26.8 - - + +
236B LEU* 4.3 17.0 - - + +
237B ASN* 5.4 0.2 - - - +
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Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ASN* 3.5 10.2 + - - +
211B LEU* 1.3 79.3 + - - +
213B TYR* 1.3 60.9 + - - +
214B LEU 3.3 0.2 - - - -
215B LYS* 3.5 20.3 - - + +
216B ARG* 3.1 36.6 + - - +
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 5.5 4.7 - - + +
144B CYS* 4.6 7.2 - - - -
193B LEU* 3.7 20.9 - - + +
196B GLU* 3.5 39.2 + - + +
198B VAL* 4.1 18.6 - - + -
210B ASN* 3.0 28.7 + - - +
211B LEU 2.8 1.0 + - - -
212B ASP* 1.3 77.2 - - - +
214B LEU* 1.3 68.0 + - + +
216B ARG* 3.4 25.2 + - - +
217B TYR* 3.4 47.4 + + - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B CYS* 3.9 39.2 - - + +
147B LEU* 4.4 16.8 - - + -
148B LEU* 3.6 24.9 - - + +
151B THR* 5.5 1.1 - - - +
193B LEU* 5.1 2.7 - - + -
198B VAL* 3.5 18.8 - - + -
199B ILE* 5.2 2.5 - - + -
208B VAL* 3.7 17.3 - - + -
210B ASN 3.5 17.0 - - - +
211B LEU* 2.5 30.6 + - + +
213B TYR* 1.3 76.7 - - + +
215B LYS* 1.3 55.7 + - - +
217B TYR* 3.1 5.0 + - - +
218B ALA* 2.9 29.5 + - - +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LEU* 3.5 11.0 - - + +
152B TYR* 2.8 15.4 + - - -
211B LEU* 3.3 31.7 - - + +
212B ASP* 3.5 25.1 - - + +
214B LEU* 1.3 69.7 - - - +
216B ARG* 1.3 65.9 + - - +
217B TYR 3.0 2.0 - - - -
218B ALA 3.2 2.6 - - - -
219B PRO* 3.1 30.1 - - + +
222B ASP* 2.7 45.9 + - + -
233B TRP* 3.5 15.4 - - - -
237B ASN* 4.1 6.9 + - - -
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ASN* 5.2 1.7 - - - +
210B ASN* 4.8 4.9 + - - +
212B ASP* 3.1 31.4 + - - +
213B TYR* 3.5 26.1 - - - +
215B LYS* 1.3 76.6 - - - +
217B TYR* 1.3 73.8 + - + +
219B PRO* 4.3 7.8 - - - +
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP* 4.3 12.0 - - - +
137B ASN* 3.9 49.2 - - + +
140B LEU* 3.7 36.5 - - + +
141B GLY* 4.4 9.9 - - - -
144B CYS* 4.0 19.7 - - + -
213B TYR* 3.4 41.9 + + - +
214B LEU 3.1 7.6 + - - +
215B LYS 3.0 0.6 - - - -
216B ARG* 1.3 92.6 - - + +
218B ALA* 1.3 59.7 + - - +
219B PRO* 3.5 8.0 - - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP* 3.3 21.4 - - + +
145B GLY* 3.7 30.1 - - - +
148B LEU* 4.2 7.2 - - + +
214B LEU 2.9 13.3 + - - +
215B LYS* 3.2 7.0 - - - +
217B TYR* 1.3 79.4 - - - +
219B PRO* 1.3 65.2 - - - +
221B LEU* 4.1 6.7 - - + -
222B ASP* 3.5 18.5 + - - +
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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