Contacts of the helix formed by residues 214 - 223 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASN* 3.3 21.3 - - - +
65A TRP* 3.9 6.5 - - - -
165A ARG* 3.5 18.0 - - - +
191A ILE 4.2 2.9 + - - +
192A ASP* 2.9 38.6 + - - +
213A TYR* 1.3 79.9 - - - +
215A GLU* 1.3 59.1 + - - +
216A ARG* 3.4 12.5 + - - +
217A VAL* 3.1 21.8 + - - +
218A ALA* 2.9 22.9 + - - +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 3.7 23.0 - - + -
214A ASN* 1.3 72.5 - - - +
216A ARG* 1.3 63.3 + - + +
218A ALA* 4.1 2.7 - - - -
219A ASP* 2.8 55.2 + - - +
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Residues in contact with ARG 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 3.4 36.3 + - - +
168A ASP* 2.9 37.8 + - - +
169A ALA 2.7 22.8 + - - -
170A LEU* 4.0 17.5 - - + +
192A ASP* 2.7 39.0 + - - -
214A ASN* 3.3 16.0 + - - +
215A GLU* 1.3 82.8 - - + +
217A VAL* 1.3 61.7 + - - +
219A ASP* 3.7 4.5 + - - +
220A VAL* 3.6 22.7 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 5.3 5.2 - - + -
83A SER* 5.4 0.2 - - - +
84A VAL* 3.9 20.2 - - + -
170A LEU* 4.4 14.4 - - + -
172A ILE* 5.4 1.6 - - + -
192A ASP* 3.3 39.9 - - + +
193A ALA* 4.1 9.2 - - + -
213A TYR* 3.8 24.9 - - + -
214A ASN* 3.1 14.3 + - - +
216A ARG* 1.3 71.4 - - - +
218A ALA* 1.3 65.6 + - - +
220A VAL* 3.3 7.2 + - - +
221A ILE* 3.2 28.2 + - + +
253A LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 3.7 38.6 - - + -
213A TYR* 4.0 13.9 - - + -
214A ASN 2.9 16.7 + - - +
215A GLU* 3.2 3.3 + - - +
217A VAL* 1.3 75.5 - - - +
219A ASP* 1.3 61.3 + - - +
221A ILE* 3.1 7.6 + - - +
222A ALA* 2.8 29.7 + - - +
257A GLU* 4.5 9.3 - - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 5.9 0.9 - - - -
215A GLU* 2.8 46.3 + - - +
216A ARG* 4.1 5.0 - - - +
218A ALA* 1.3 77.1 - - - +
220A VAL* 1.3 61.0 + - + +
222A ALA* 3.4 9.3 + - - +
223A ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER 4.5 1.6 - - - +
84A VAL* 3.9 27.4 - - + -
86A GLU* 6.0 0.4 - - - +
140A LYS* 3.9 29.8 - - - +
170A LEU* 4.3 16.8 - - + -
216A ARG 3.6 13.6 + - - +
217A VAL 3.3 9.8 + - - +
219A ASP* 1.3 77.2 - - + +
221A ILE* 1.3 61.3 + - - +
223A ALA* 3.4 14.4 + - - +
224A ARG* 3.7 16.6 - - + +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A SER* 3.7 35.4 - - - +
84A VAL* 4.5 2.5 - - + -
213A TYR* 4.0 16.6 - - + +
217A VAL* 3.2 28.7 + - + +
218A ALA* 3.1 7.6 + - - +
220A VAL* 1.3 72.5 - - - +
222A ALA* 1.3 66.8 + - - +
224A ARG* 3.0 24.3 + - - +
246A ILE* 4.5 6.7 - - + -
253A LEU* 3.7 23.6 - - + -
254A SER* 3.6 36.9 + - - +
257A GLU* 4.5 7.4 - - - +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA 2.8 16.0 + - - +
219A ASP* 3.7 10.3 - - - +
220A VAL 3.3 0.2 - - - -
221A ILE* 1.3 72.7 - - - +
223A ALA* 1.3 57.2 + - - +
224A ARG 2.7 18.1 + - - +
254A SER* 5.0 5.2 - - - -
257A GLU* 5.5 5.1 + - - +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLU* 5.9 0.9 - - - +
219A ASP 3.1 16.3 + - - +
220A VAL* 3.7 9.4 - - - +
221A ILE 3.2 1.0 - - - -
222A ALA* 1.3 74.1 - - - +
224A ARG* 1.3 59.7 + - + +
243A ASN* 3.2 39.2 + - - +
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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