Contacts of the strand formed by residues 209 - 213 (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 ALA 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PRO* 4.2 0.7 - - - -
69B ILE* 2.8 33.9 + - + +
71B GLY 4.0 1.8 - - - +
72B THR 3.3 23.1 - - - +
73B SER* 3.8 9.6 - - - -
76B GLY* 3.7 22.2 - - - +
195B ILE* 4.6 0.7 - - + -
196B GLY 3.6 8.3 - - - +
208B MET* 1.3 75.8 - - - +
210B PRO* 1.4 67.7 - - - +
211B ILE* 3.6 6.9 + - - +
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Residues in contact with PRO 210 (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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55B LEU* 3.9 31.6 - - + -
58B LEU* 5.4 1.6 - - + -
59B PHE* 3.4 10.7 - - + -
67B TYR 3.7 6.1 - - - +
68B PRO* 3.9 5.2 - - + -
179B ILE* 5.6 0.2 - - + -
195B ILE* 3.6 0.9 - - - -
196B GLY* 2.7 49.7 + - - +
197B GLY* 4.1 7.0 - - - +
198B THR* 4.0 13.0 - - + -
202B LEU* 4.5 7.6 - - + -
208B MET* 4.0 6.7 - - + +
209B ALA* 1.4 84.8 - - - +
211B ILE* 1.3 57.9 + - - +
278B LEU* 4.5 16.4 - - + -
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Residues in contact with ILE 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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59B PHE* 4.0 5.1 - - - -
66B ALA* 3.2 3.5 - - - +
67B TYR* 2.8 64.3 + - + +
69B ILE* 3.9 7.0 - - + -
76B GLY* 4.4 9.9 - - - +
80B VAL* 4.2 9.6 - - + -
194B ALA 3.4 7.0 - - - +
195B ILE* 3.8 27.6 - - + -
209B ALA 3.8 9.9 - - - +
210B PRO* 1.3 81.0 - - - +
212B THR* 1.3 63.3 + - - +
213B TYR* 4.0 12.3 - - + -
253B LEU* 3.8 33.9 - - + -
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Residues in contact with THR 212 (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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59B PHE* 3.4 45.5 - - + -
61B THR* 3.8 6.1 - - - +
63B ASN* 3.0 22.1 + - - +
65B TRP 2.7 19.6 + - - -
66B ALA* 3.8 4.6 - - - +
186B VAL* 4.0 14.4 - - + -
193B ALA* 3.1 4.0 - - - +
194B ALA* 2.8 38.5 + - + +
211B ILE* 1.3 78.4 - - - +
213B TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 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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63B ASN* 3.1 20.8 + - - +
65B TRP* 3.0 40.0 + + + +
67B TYR* 2.9 40.3 + + - -
80B VAL* 5.3 2.0 - - + -
192B ASP 3.2 14.8 - - - +
193B ALA* 3.6 13.0 - - + +
211B ILE* 4.0 17.0 - - + -
212B THR* 1.3 78.1 + - - +
214B ASN* 1.3 67.1 + - - +
217B VAL* 3.7 18.8 - - + -
218B ALA* 3.9 15.9 - - + -
221B ILE* 4.0 10.8 - - + +
253B LEU* 4.1 13.6 + - + -
257B GLU* 2.8 20.9 + - - +
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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