Contacts of the helix formed by residues 214 - 223 (chain B) in PDB entry 3ISL
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 ASN 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASN* 3.3 21.9 - - - +
65B TRP* 3.9 5.6 - - - -
165B ARG* 3.5 19.0 - - - +
191B ILE 4.3 2.3 + - - +
192B ASP* 2.7 44.4 + - - +
213B TYR* 1.3 77.9 - - - +
215B GLU* 1.3 59.2 + - - +
216B ARG* 3.0 11.4 + - - +
217B VAL* 2.9 21.3 + - - +
218B ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 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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65B TRP* 3.7 32.2 - - + -
214B ASN* 1.3 71.0 - - - +
216B ARG* 1.3 62.5 + - + +
218B ALA* 4.2 2.2 - - + +
219B ASP* 2.8 57.9 + - - +
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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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165B ARG* 3.5 33.5 + - - +
168B ASP* 2.7 43.5 + - - +
169B ALA 2.7 30.9 + - - -
170B LEU* 3.9 16.8 - - + +
192B ASP* 2.8 30.2 + - - +
214B ASN* 3.0 12.9 + - - +
215B GLU* 1.3 80.4 - - + +
217B VAL* 1.3 63.2 + - - +
219B ASP* 3.5 8.3 + - - +
220B VAL* 3.5 21.7 + - - +
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Residues in contact with VAL 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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80B VAL* 5.4 3.6 - - + -
84B VAL* 4.0 13.5 - - + -
170B LEU* 4.1 21.5 - - + -
172B ILE* 4.9 3.4 - - + -
192B ASP* 3.4 37.0 - - + +
193B ALA* 4.0 9.4 - - + -
213B TYR* 3.7 24.2 - - + -
214B ASN* 2.9 9.1 + - - +
216B ARG* 1.3 76.1 - - - +
218B ALA* 1.3 62.3 + - - +
220B VAL* 3.1 6.2 + - - +
221B ILE* 3.1 39.0 + - + +
253B LEU* 5.8 0.2 - - + -
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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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65B TRP* 3.9 31.0 - - + -
213B TYR* 3.9 20.4 - - + -
214B ASN 3.0 15.5 + - - +
215B GLU* 3.2 4.9 + - + +
217B VAL* 1.3 77.3 - - - +
219B ASP* 1.3 59.4 + - - +
221B ILE* 3.3 7.5 + - - +
222B ALA* 2.9 30.8 + - - +
257B GLU* 4.5 7.4 - - - +
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Residues in contact with ASP 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 GLU* 2.8 47.4 + - - +
216B ARG* 3.7 8.8 - - - +
218B ALA* 1.3 78.3 - - - +
220B VAL* 1.3 61.6 + - + +
222B ALA* 3.4 8.4 + - - +
223B ALA* 3.3 19.9 + - - +
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Residues in contact with VAL 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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83B SER 4.5 0.7 - - - +
84B VAL* 4.0 26.5 - - + -
140B LYS* 3.9 29.6 - - - +
170B LEU* 4.2 15.9 - - + -
216B ARG 3.5 12.3 + - - +
217B VAL 3.1 8.9 + - - +
219B ASP* 1.3 76.2 - - + +
221B ILE* 1.3 65.3 + - - +
223B ALA* 3.3 18.7 + - - +
224B ARG* 3.9 12.4 - - - +
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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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83B SER* 3.5 40.2 - - - +
84B VAL* 4.3 3.8 - - + -
213B TYR* 4.0 16.2 - - + -
217B VAL* 3.1 31.9 + - + +
218B ALA* 3.6 7.6 - - - +
220B VAL* 1.3 77.4 - - - +
222B ALA* 1.3 58.5 + - - +
224B ARG* 3.0 30.0 + - - +
246B ILE* 5.1 2.3 - - + +
253B LEU* 3.8 21.5 - - + -
254B SER* 3.7 35.7 - - - +
257B GLU* 4.1 11.7 - - - +
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Residues in contact with ALA 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 ALA 2.9 20.0 + - - +
219B ASP* 3.4 8.9 + - - +
221B ILE* 1.3 70.5 - - - +
223B ALA* 1.3 56.5 + - - +
224B ARG 3.0 16.5 + - - +
254B SER* 5.4 2.7 - - - -
257B GLU* 5.2 6.5 - - - +
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Residues in contact with ALA 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 ASP 3.3 11.9 + - - +
220B VAL* 3.6 13.5 - - - +
221B ILE 3.1 1.4 - - - -
222B ALA* 1.3 75.9 - - - +
224B ARG* 1.4 53.8 + - + +
243B ASN* 2.8 41.0 + - - +
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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