Contacts of the helix formed by residues 212 - 223 (chain B) in PDB entry 1DWQ
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 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B SER* 3.9 24.3 + - - +
125B PHE* 3.9 21.8 - - + -
208B ASP 3.6 17.7 - - - +
209B LYS* 3.7 25.4 - - + +
210B ILE 3.3 9.3 + - - +
211B PHE* 1.3 76.9 - - - +
213B PRO* 1.4 77.2 - - + +
214B ASP* 3.3 2.9 - - + +
215B PHE* 3.0 19.4 + - + +
216B GLN* 3.0 10.4 + - - +
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Residues in contact with PRO 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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204B TRP* 3.8 16.1 - - + -
206B ASP* 3.4 31.6 - - + +
208B ASP 4.4 4.0 - - - +
211B PHE 4.7 0.2 - - - +
212B LEU* 1.4 91.0 - - + +
214B ASP* 1.3 59.9 + - - +
216B GLN* 3.4 2.1 + - - +
217B ARG* 2.8 60.7 + - - +
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Residues in contact with ASP 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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212B LEU* 3.3 1.4 - - + +
213B PRO* 1.3 80.9 - - - +
215B PHE* 1.3 59.1 + - - +
217B ARG* 3.4 22.5 + - - +
218B TRP* 3.0 26.7 + - - +
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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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106B LEU* 4.1 4.0 - - + -
117B THR 3.9 7.0 - - - -
120B LYS* 3.8 7.9 - - + -
121B LEU* 3.3 60.3 - - + -
124B SER* 3.5 26.2 - - - +
211B PHE* 3.7 23.3 - + + -
212B LEU* 3.0 10.3 + - - +
214B ASP* 1.3 74.5 - - - +
216B GLN* 1.3 68.4 + - - +
218B TRP* 3.2 29.5 + + - +
219B GLN* 2.9 58.5 + - + +
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Residues in contact with GLN 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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104B ASN* 2.9 33.0 + - - +
105B SER 4.7 0.2 - - - +
202B TYR* 2.7 31.1 + - + +
204B TRP* 3.2 42.0 - - + +
205B THR 3.9 7.3 + - - -
208B ASP* 3.4 6.5 + - - -
211B PHE* 3.2 32.7 + - + +
212B LEU 3.0 13.0 + - - +
213B PRO 3.7 2.9 - - - +
215B PHE* 1.3 77.3 - - + +
217B ARG* 1.3 65.0 + - - +
219B GLN* 3.0 13.4 + - - +
220B ILE* 3.1 19.3 + - - +
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Residues in contact with ARG 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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204B TRP* 3.6 34.4 - - + -
206B ASP* 4.7 6.7 - - - +
213B PRO* 2.8 39.5 + - - +
214B ASP* 3.4 22.9 + - - +
216B GLN* 1.3 75.8 - - - +
218B TRP* 1.3 61.3 + - - +
220B ILE* 3.4 11.2 + - + +
221B ALA* 3.0 22.9 + - - +
230B GLN* 5.2 3.2 + - - +
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Residues in contact with TRP 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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116B TYR* 3.4 40.8 + + - -
117B THR* 3.9 11.9 - - + -
120B LYS* 3.3 43.3 - - + +
214B ASP 3.0 19.7 + - - +
215B PHE* 3.3 20.6 - + - +
217B ARG* 1.3 75.5 - - - +
219B GLN* 1.3 82.4 + - + +
221B ALA* 3.0 9.8 + - + +
222B ASN* 2.7 52.8 + - + +
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Residues in contact with GLN 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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105B SER 2.9 16.6 + - - -
106B LEU* 3.2 7.3 - - - -
107B LEU* 2.9 38.5 + - + +
117B THR* 3.7 11.6 - - + +
202B TYR* 2.9 29.5 + - + +
211B PHE* 4.6 1.0 - - - -
215B PHE* 2.9 47.5 + - + +
216B GLN* 3.0 6.2 + - - +
218B TRP* 1.3 97.5 - - + +
220B ILE* 1.3 63.5 + - - +
222B ASN* 3.0 6.8 + - - +
223B TYR* 3.0 24.3 + - - +
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Residues in contact with ILE 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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107B LEU* 4.5 0.7 - - - -
202B TYR* 3.9 30.3 - - + -
204B TRP* 4.1 13.7 - - + +
216B GLN 3.1 15.0 + - - +
217B ARG* 3.6 15.0 - - + +
218B TRP 3.2 0.2 - - - -
219B GLN* 1.3 76.2 - - - +
221B ALA* 1.3 63.2 + - - +
224B LYS* 3.2 28.6 + - + +
225B PRO* 4.0 20.6 - - + -
228B VAL* 3.9 34.3 - - + -
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Residues in contact with ALA 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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217B ARG 3.0 14.1 + - - +
218B TRP* 3.5 11.0 - - + +
220B ILE* 1.3 80.1 - - - +
222B ASN* 1.3 59.5 + - - +
224B LYS* 3.3 19.3 - - - +
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Residues in contact with ASN 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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107B LEU 4.6 2.2 + - - -
109B ASP* 3.4 30.0 + - - +
112B HIS* 3.6 17.3 - - - -
116B TYR* 3.8 6.2 + - - -
117B THR* 4.5 6.9 - - - +
218B TRP* 2.7 55.6 + - + +
219B GLN* 3.0 6.7 + - - +
221B ALA* 1.3 75.3 - - - +
223B TYR* 1.3 68.3 + - - +
224B LYS* 3.7 7.8 + - - -
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Residues in contact with TYR 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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107B LEU* 3.1 28.1 - - + +
108B PRO 3.4 23.8 - - - +
109B ASP* 3.7 24.0 - - + -
110B THR* 4.2 16.7 + - - +
192B GLU* 5.1 1.1 + - - -
195B TYR* 3.8 3.6 - + - -
196B GLY* 3.6 28.1 + - - -
200B LYS* 3.6 32.2 + - + -
219B GLN 3.0 7.8 + - - +
220B ILE 3.5 1.7 - - - +
222B ASN* 1.3 93.2 - - - +
224B LYS* 1.3 74.9 + - - +
225B PRO* 3.1 10.6 - - - +
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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