Contacts of the helix formed by residues 210 - 224 (chain B) in PDB entry 2Z9I
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 VAL 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B LEU* 6.0 0.2 - - + -
105B LEU* 4.2 13.5 - - + -
106B GLY 3.5 22.9 - - - +
108B SER* 3.6 18.5 + - - +
180B LEU* 3.3 48.7 - - + +
181B VAL* 3.0 24.7 + - - +
182B GLY* 4.2 1.3 - - - +
208B ILE 3.5 1.3 + - - -
209B PRO* 1.3 70.7 - - - +
211B ASP* 1.3 59.3 + - - +
213B ALA* 4.2 7.9 - - + -
214B LYS* 2.8 38.2 + - + +
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Residues in contact with ASP 211 (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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106B GLY 4.2 1.9 - - - +
107B SER* 3.5 12.5 - - - -
108B SER* 3.0 43.4 + - - +
109B SER* 3.7 14.7 + - - -
209B PRO* 5.3 0.4 - - + -
210B VAL* 1.3 77.2 - - - +
212B GLN* 1.3 63.6 + - + +
214B LYS* 4.1 5.4 - - - +
215B ARG* 3.1 23.4 + - - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.2 39.7 + - - +
208B ILE* 4.0 11.3 - - + +
209B PRO* 3.1 35.3 + - - +
211B ASP* 1.3 75.7 - - + +
213B ALA* 1.3 66.3 + - - +
215B ARG* 3.1 12.2 + - - +
216B ILE* 3.1 37.3 + - + +
285B ARG 4.8 3.3 - - - +
286B SER* 3.6 36.2 + - - +
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Residues in contact with ALA 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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45B LEU* 4.2 9.6 - - + +
89B ILE* 3.9 28.9 - - + +
183B VAL* 3.7 29.6 - - + -
208B ILE* 3.9 4.6 - - + +
209B PRO 3.0 15.0 + - - +
210B VAL* 3.9 8.3 - - + +
212B GLN* 1.3 75.6 - - - +
214B LYS* 1.3 56.7 + - - +
216B ILE 3.6 0.2 + - - -
217B ALA* 2.9 30.4 + - - +
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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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45B LEU* 5.4 2.7 - - + +
105B LEU* 3.8 34.2 - - + +
106B GLY 5.8 2.0 - - - +
210B VAL* 2.8 26.2 + - + +
211B ASP* 4.1 4.7 - - - +
213B ALA* 1.3 71.4 - - - +
215B ARG* 1.3 66.6 + - - +
217B ALA* 3.8 6.3 - - - +
218B ASP* 3.0 44.5 + - - +
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Residues in contact with ARG 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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211B ASP 3.1 17.5 + - - +
212B GLN* 3.1 11.8 + - - +
214B LYS* 1.3 78.9 - - - +
216B ILE* 1.3 81.8 + - - +
218B ASP* 3.4 5.6 + - - +
219B GLU* 3.2 43.6 + - + +
227B SER 3.3 24.0 + - - -
228B HIS* 5.3 4.4 + - - +
285B ARG 3.8 13.9 + - - -
286B SER 4.9 3.0 + - - -
287B LYS 3.3 23.5 + - - +
288B ALA* 3.8 27.1 - - - +
289B PRO* 3.8 9.9 - - - +
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Residues in contact with ILE 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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84B ASP* 3.6 13.7 - - + +
87B SER* 2.9 46.2 - - - +
89B ILE* 3.8 18.2 - - + -
208B ILE* 6.2 0.9 - - + -
212B GLN* 3.1 24.7 + - + +
213B ALA 4.0 2.2 - - - +
215B ARG* 1.3 98.8 - - - +
217B ALA* 1.3 60.9 + - - +
219B GLU* 3.2 8.2 + - - +
220B LEU* 2.9 37.1 + - + +
226B ALA* 3.8 13.5 - - + -
227B SER 5.3 1.6 - - - +
228B HIS* 5.5 2.7 - - - +
285B ARG 5.8 0.9 - - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.3 12.8 - - + -
45B LEU* 3.9 14.8 - - + -
89B ILE* 4.4 1.3 - - - +
91B VAL* 3.8 23.6 - - + -
213B ALA 2.9 20.5 + - - +
214B LYS* 3.8 7.2 - - - +
216B ILE* 1.3 75.9 - - - +
218B ASP* 1.3 58.0 + - - +
220B LEU* 3.3 4.8 + - - +
221B ILE* 2.8 36.6 + - + +
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 6.1 0.2 - - - +
214B LYS* 3.0 47.9 + - - +
215B ARG* 3.7 5.9 - - - +
217B ALA* 1.3 77.8 - - - +
219B GLU* 1.3 58.8 + - + +
221B ILE* 3.9 14.0 - - - +
222B SER* 3.1 30.1 + - - -
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Residues in contact with GLU 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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215B ARG* 3.2 39.7 + - + +
216B ILE* 3.2 7.8 + - - +
218B ASP* 1.3 75.9 - - + +
220B LEU* 1.3 56.8 + - - +
222B SER* 4.1 4.9 - - - -
223B THR* 2.8 41.2 + - + +
224B GLY 3.3 1.0 + - - -
225B LYS 3.7 11.9 - - - +
226B ALA* 3.2 7.2 - - - +
227B SER* 2.8 43.6 + - - +
289B PRO* 5.1 2.3 - - - +
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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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81B VAL* 3.9 11.8 - - - +
82B GLY* 3.7 23.1 - - - +
83B ALA* 3.7 25.1 - - - +
89B ILE* 3.9 9.2 - - + +
90B ALA* 3.8 22.7 - - - -
91B VAL* 4.3 8.5 - - + -
216B ILE* 2.9 33.5 + - + +
217B ALA* 3.6 5.2 - - - +
219B GLU* 1.3 75.7 - - - +
221B ILE* 1.3 58.3 + - - +
224B GLY* 3.0 43.0 + - - +
226B ALA* 3.8 20.6 - - + +
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Residues in contact with ILE 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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38B LEU* 4.1 22.4 - - + -
43B LEU* 3.7 35.7 - - + -
81B VAL* 4.1 11.3 - - + +
91B VAL* 4.0 16.4 - - + -
217B ALA 2.8 30.0 + - - +
218B ASP* 3.9 15.0 - - - +
220B LEU* 1.3 75.4 - - - +
222B SER* 1.3 63.4 + - - +
224B GLY 4.8 0.3 + - - -
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Residues in contact with SER 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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218B ASP 3.1 18.9 + - - -
219B GLU* 3.7 4.0 + - - -
221B ILE* 1.3 80.1 - - - +
223B THR* 1.3 75.3 + - - +
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Residues in contact with THR 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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219B GLU* 2.8 18.2 + - + +
222B SER* 1.3 90.1 - - - +
224B GLY* 1.3 55.6 + - - +
225B LYS* 3.1 25.8 + - - +
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Residues in contact with GLY 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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81B VAL 4.4 9.8 - - - +
82B GLY* 4.1 9.4 - - - -
83B ALA 4.7 2.8 + - - +
219B GLU 3.3 1.8 + - - -
220B LEU* 3.0 34.2 + - - +
221B ILE 4.7 0.4 + - - -
223B THR* 1.3 76.3 - - - +
225B LYS* 1.3 59.4 + - - +
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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