Contacts of the helix formed by residues 213 - 225 (chain B) in PDB entry 6V99
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 THR 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B ILE* 4.5 5.4 - - + -
122B GLU* 6.1 2.2 - - + -
125B ALA* 5.9 0.4 - - - -
126B PRO* 3.0 40.0 + - + +
127B GLU* 2.9 9.5 + - - -
128B TYR 3.1 24.4 + - - -
129B MET* 3.3 20.6 - - + +
211B PHE 3.6 1.6 + - - -
212B HIS* 1.3 70.5 - - - +
214B LYS* 1.3 66.5 + - + +
216B LEU* 3.2 3.1 + - - +
217B MET* 2.9 42.7 + - + +
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Residues in contact with LYS 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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122B GLU* 3.1 28.9 + - - +
127B GLU 4.9 0.2 + - - -
212B HIS* 3.2 2.7 - - + +
213B THR* 1.3 82.5 - - + +
215B PHE* 1.3 66.6 + - - +
217B MET* 3.2 26.5 + - - +
218B GLU* 3.2 23.8 + - - +
221B ARG* 4.6 2.4 - - - +
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Residues in contact with PHE 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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155B ASP* 3.6 44.2 - - + +
211B PHE* 3.9 18.6 - + - -
212B HIS* 3.0 20.7 + - + +
214B LYS* 1.3 78.1 - - - +
216B LEU* 1.3 59.7 + - - +
218B GLU* 3.5 5.4 + - + +
219B ALA* 2.9 33.8 + - + +
222B ARG* 3.5 26.9 + - - -
241B ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 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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114B VAL* 5.0 1.1 - - + -
129B MET* 3.6 33.2 - - + -
131B ILE* 4.0 15.0 - - + -
211B PHE* 3.7 47.1 - - + -
212B HIS 2.9 6.5 + - - +
213B THR* 3.6 9.0 - - - +
215B PHE* 1.3 81.4 - - - +
217B MET* 1.3 68.8 + - + +
219B ALA* 3.2 8.1 + - + -
220B LEU* 2.8 50.1 + - + +
233B PHE* 4.2 9.0 - - + -
237B ILE* 5.4 1.1 - - + -
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Residues in contact with MET 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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114B VAL* 4.8 0.7 - - + -
118B ILE* 3.7 33.3 - - - +
121B ILE* 4.3 28.9 - - + -
122B GLU* 3.7 9.9 - - + +
129B MET* 4.4 3.1 - - + -
213B THR* 2.9 31.7 + - + +
214B LYS* 3.2 31.0 - - - +
215B PHE 3.3 0.2 - - - -
216B LEU* 1.3 96.4 - - + +
218B GLU* 1.3 63.5 + - - +
220B LEU* 3.0 15.3 + - + +
221B ARG* 3.0 38.2 + - - +
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Residues in contact with GLU 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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214B LYS* 3.2 13.8 + - - +
215B PHE* 3.8 4.7 - - - +
217B MET* 1.3 77.6 - - - +
219B ALA* 1.3 57.4 + - - +
221B ARG* 3.1 13.3 + - - +
222B ARG* 2.8 42.3 + - + +
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Residues in contact with ALA 219 (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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211B PHE* 5.6 0.4 - - + -
215B PHE* 2.9 29.2 + - + +
216B LEU* 3.4 13.2 - - + +
218B GLU* 1.3 76.6 - - - +
220B LEU* 1.3 63.2 + - - +
222B ARG* 3.2 28.8 + - - +
223B ASP* 3.0 22.7 + - - +
237B ILE* 4.3 23.3 - - + +
241B ILE* 5.5 0.4 - - + -
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Residues in contact with LEU 220 (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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111B ALA* 3.7 25.8 - - + +
114B VAL* 3.5 33.2 - - + +
115B TYR* 3.6 32.3 - - + +
118B ILE* 4.3 5.8 - - + -
216B LEU* 2.8 32.6 + - + +
217B MET* 3.5 20.9 - - + +
219B ALA* 1.3 72.7 - - - +
221B ARG* 1.3 56.8 + - - +
223B ASP* 3.4 4.8 + - + +
224B ALA* 3.1 22.2 + - - +
231B ARG* 4.4 2.1 + - - +
233B PHE* 4.4 5.2 - - + -
237B ILE* 3.8 21.8 - - + -
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Residues in contact with ARG 221 (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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115B TYR* 4.2 20.9 - - + +
118B ILE* 3.7 19.0 - - + +
122B GLU* 3.3 34.6 + - - -
214B LYS* 4.6 2.2 - - - +
217B MET* 3.0 30.8 + - - +
218B GLU* 3.1 12.3 + - - +
220B LEU* 1.3 75.8 - - - +
222B ARG* 1.3 63.8 + - - +
224B ALA* 3.7 2.0 + - - +
225B ALA* 3.4 23.4 + - - +
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Residues in contact with ARG 222 (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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215B PHE* 3.5 36.4 + - - -
218B GLU* 2.8 22.3 + - + +
219B ALA* 3.3 28.2 - - - +
221B ARG* 1.3 78.1 - - - +
223B ASP* 1.3 61.9 + - - +
225B ALA* 3.6 4.4 + - - +
226B ASP* 3.6 18.4 + - - +
237B ILE* 6.3 0.6 - - - +
240B TYR* 3.9 49.3 - - + -
241B ILE* 5.2 5.3 - - - +
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Residues in contact with ASP 223 (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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111B ALA* 4.1 3.7 - - + +
219B ALA 3.0 15.7 + - - +
220B LEU* 3.8 4.9 - - + +
221B ARG 3.2 0.2 - - - -
222B ARG* 1.3 73.8 - - - +
224B ALA* 1.3 66.2 + - - +
226B ASP* 3.0 24.6 + - - +
229B SER* 2.7 27.3 + - - -
231B ARG* 2.8 40.3 + - - +
236B ASP* 3.6 14.7 - - - +
237B ILE* 3.7 25.8 - - + +
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Residues in contact with ALA 224 (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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115B TYR* 3.8 27.8 - - + +
220B LEU 3.1 14.7 + - - +
221B ARG 4.2 3.4 - - - +
222B ARG 3.5 0.2 - - - -
223B ASP* 1.3 77.3 - - - +
225B ALA* 1.3 56.9 + - - +
226B ASP 3.1 9.0 + - - +
231B ARG* 3.4 35.4 + - - +
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Residues in contact with ALA 225 (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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221B ARG 3.4 15.4 + - - +
222B ARG* 4.1 5.2 - - - +
223B ASP 3.2 1.0 - - - -
224B ALA* 1.3 77.3 - - - +
226B ASP* 1.3 56.0 + - - +
227B PRO* 3.5 11.1 - - - +
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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