Contacts of the strand formed by residues 216 - 220 (chain B) in PDB entry 2N5T
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 ASP 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LYS* 3.3 2.1 - - - -
16B ALA* 2.6 33.2 + - + +
211B GLN 4.5 2.3 - - - +
212B VAL* 3.5 18.2 - - + -
213B LYS* 2.6 50.3 + - - +
214B ASN 3.1 4.0 - - - +
215B ASP* 1.3 81.7 - - - +
217B TYR* 1.3 62.0 + - - +
218B LEU* 3.9 8.5 - - + -
229B VAL* 5.2 10.0 - - + +
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Residues in contact with TYR 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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13B PHE* 3.3 26.1 - - + +
14B GLY* 3.6 29.4 - - - -
15B LYS* 4.4 11.4 - - + +
215B ASP 3.7 3.0 + - - +
216B ASP* 1.3 72.9 - - - +
218B LEU* 1.3 67.4 + - - +
219B ILE* 3.3 28.0 - - + +
229B VAL* 4.7 0.5 - - - +
230B ASN* 3.3 26.7 + - + +
231B PRO* 4.7 6.5 - - + -
236B ILE* 4.0 24.1 - - + +
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Residues in contact with LEU 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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14B GLY 3.1 30.9 + - - +
16B ALA* 3.4 30.3 - - + -
157B ILE* 3.6 18.4 - - + +
159B VAL* 4.9 8.3 - - + -
180B ILE* 5.5 4.0 - - + -
208B VAL* 5.7 0.2 - - + -
212B VAL* 3.7 21.5 - - + -
216B ASP* 3.6 6.9 + - + +
217B TYR* 1.3 85.4 - - - +
219B ILE* 1.3 65.6 + - - +
227B VAL* 4.3 15.5 - - + -
228B TYR 3.5 3.8 - - - +
229B VAL* 3.4 40.2 - - + -
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Residues in contact with ILE 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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11B ILE* 3.9 3.1 - - + -
12B ALA 3.5 11.0 - - - +
13B PHE* 3.7 13.0 - - + -
217B TYR* 3.3 36.1 - - + +
218B LEU* 1.3 82.4 - - - +
220B LEU* 1.3 63.4 + - - +
221B ASP 3.7 0.7 + - - -
226B GLN 4.0 0.3 - - - +
227B VAL* 3.6 9.0 - - - +
228B TYR* 3.2 35.8 + - + +
231B PRO* 3.4 28.3 - - + -
236B ILE* 4.1 13.7 - - + -
239B MET* 3.6 35.7 - - + -
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Residues in contact with LEU 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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6B LEU* 6.3 1.8 - - + -
11B ILE* 3.2 8.5 - - - +
12B ALA* 2.9 40.5 + - + +
157B ILE* 5.4 11.8 - - + +
178B GLY* 5.6 3.8 - - - -
179B PHE 5.4 1.3 - - - +
180B ILE* 5.9 5.2 - - + -
200B PRO* 3.9 38.6 - - + +
201B ALA* 4.1 8.7 - - - +
202B ILE* 4.1 22.2 - - + -
218B LEU 4.2 0.6 + - - -
219B ILE* 1.3 70.3 - - - +
221B ASP* 1.3 66.1 + - - +
222B ALA* 3.9 16.8 - - + +
225B ASN 6.4 0.2 - - - -
226B GLN 4.5 1.3 - - - +
227B VAL* 4.1 19.7 - - + -
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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