Contacts of the helix formed by residues 213 - 224 (chain B) in PDB entry 4D2W
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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211B ASP* 3.7 6.4 + - - +
212B ASP* 1.4 89.7 + - + +
214B ALA* 1.3 58.9 + - - +
215B ALA* 4.4 6.5 - - - +
216B ALA* 3.4 21.8 + - - +
217B LEU* 3.1 27.3 + - - +
79C ALA* 4.0 5.6 - - + -
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Residues in contact with ALA 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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172B LEU* 3.6 20.1 - - + +
213B THR* 1.3 69.6 - - - +
215B ALA* 1.3 59.5 + - - +
217B LEU* 3.4 3.9 + - - +
218B VAL* 3.0 36.4 + - + +
79C ALA* 4.4 6.2 - - + +
80C ASN* 4.6 14.8 - - - +
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Residues in contact with ALA 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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213B THR* 3.4 5.9 + - - +
214B ALA* 1.3 74.4 - - - +
216B ALA* 1.3 63.9 + - - +
218B VAL* 3.7 6.7 + - - +
219B ALA* 3.2 22.9 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP* 3.4 27.8 - - - +
213B THR* 3.4 19.9 + - - +
214B ALA 3.4 0.4 - - - -
215B ALA* 1.3 78.5 - - - +
217B LEU* 1.4 62.1 + - - +
219B ALA* 3.5 6.5 + - - +
220B LYS* 3.2 27.1 + - - +
223B ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 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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172B LEU* 3.8 27.8 - - + -
173B ALA* 3.9 20.2 - - + +
209B PHE* 3.4 35.9 - - + +
210B ASP* 3.8 6.3 - - - +
211B ASP* 3.8 21.6 - - + +
213B THR 3.1 14.3 + - - +
214B ALA* 3.4 9.2 + - - +
216B ALA* 1.4 71.5 - - - +
218B VAL* 1.3 65.3 + - - +
220B LYS* 3.1 5.8 + - + +
221B ILE* 3.0 34.5 + - + +
80C ASN* 5.1 10.1 - - - +
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Residues in contact with VAL 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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172B LEU* 3.7 29.1 - - + +
180B ILE* 3.8 26.5 - - + -
214B ALA* 3.0 22.3 + - + +
215B ALA* 3.9 7.0 - - - +
217B LEU* 1.3 74.1 - - - +
219B ALA* 1.4 63.1 + - - +
221B ILE* 3.3 9.7 + - - +
222B MET* 3.0 32.7 + - + +
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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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215B ALA 3.2 18.4 + - - +
216B ALA* 3.7 7.9 - - - +
217B LEU 3.3 0.2 - - - -
218B VAL* 1.4 76.1 - - - +
220B LYS* 1.4 57.1 + - - +
222B MET* 3.5 7.7 + - - +
223B ARG* 3.0 57.4 + - - +
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Residues in contact with LYS 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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209B PHE* 3.5 25.6 - - + -
210B ASP 2.8 35.7 + - - +
211B ASP* 3.1 22.7 + - + +
216B ALA 3.2 11.7 + - - +
217B LEU* 3.1 9.7 + - - +
219B ALA* 1.4 76.1 - - - +
221B ILE* 1.3 55.9 + - - +
223B ARG* 3.5 15.1 + - - +
224B GLY 2.9 24.1 + - - -
225B LYS 4.1 4.7 + - - +
2C LYS* 6.2 0.4 - - - +
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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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172B LEU* 3.3 30.1 - - + +
173B ALA* 4.3 5.2 - - - +
175B ALA 3.6 19.1 - - - +
177B PRO* 3.9 13.8 - - + +
180B ILE* 3.7 20.4 - - + -
193B TRP* 3.9 16.0 - - + +
209B PHE* 3.8 27.6 - - + -
217B LEU* 3.0 35.6 + - + +
218B VAL 3.3 6.0 + - - +
220B LYS* 1.3 75.8 - - - +
222B MET* 1.3 61.5 + - - +
224B GLY* 3.3 13.9 + - - -
246B VAL* 3.6 9.4 - - - +
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Residues in contact with MET 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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177B PRO* 3.8 32.3 - - + +
180B ILE* 4.8 12.1 - - - -
181B GLN* 3.3 35.0 - - + +
218B VAL* 3.0 31.5 + - + +
219B ALA* 3.7 7.4 - - - +
221B ILE* 1.3 79.0 - - - +
223B ARG* 1.3 61.9 + - + +
246B VAL* 3.7 20.7 - - + +
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Residues in contact with ARG 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 ALA* 3.0 44.2 + - - +
220B LYS* 4.1 13.2 - - - +
222B MET* 1.3 77.6 - - + +
224B GLY* 1.3 63.4 + - - +
225B LYS* 3.3 38.2 + - + +
246B VAL* 4.4 3.3 - - - +
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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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193B TRP* 4.9 0.9 - - - -
209B PHE* 3.6 13.8 - - - -
220B LYS 2.9 10.8 + - - -
221B ILE 3.3 13.3 + - - -
223B ARG* 1.3 77.3 - - - +
225B LYS* 1.3 60.1 + - - +
226B TYR* 3.6 18.2 - - - -
244B LEU 4.9 4.0 - - - +
246B VAL* 3.7 13.7 - - - -
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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