Contacts of the helix formed by residues 215 - 220 (chain B) in PDB entry 2YYU
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 GLY 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ALA* 4.2 16.8 - - - -
12B ASP* 5.1 1.3 - - - -
185B ILE 5.4 0.4 + - - -
214B ILE* 1.3 77.2 - - - +
216B ARG* 1.3 53.4 + - - -
217B SER* 3.0 5.0 - - - +
218B LEU* 2.8 30.1 + - - +
219B THR* 2.9 17.5 + - - +
2301B C5P 2.8 22.2 + - - -
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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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12B ASP* 6.0 2.2 - - + +
186B ARG* 5.1 11.0 - - - +
215B GLY* 1.3 65.6 - - - -
217B SER* 1.3 57.2 + - - +
218B LEU 2.9 10.5 + - - -
219B THR* 3.1 9.3 + - - +
220B ARG* 3.1 78.0 + - + +
2301B C5P 2.6 25.8 + - - +
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Residues in contact with SER 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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185B ILE* 3.3 10.0 + - - -
186B ARG* 3.0 36.4 + - - +
187B PHE* 3.7 18.6 - - - -
190B ASP* 3.3 12.2 + - - -
214B ILE* 3.9 17.5 - - - -
215B GLY 2.9 1.8 + - - +
216B ARG* 1.3 76.6 - - - +
218B LEU* 1.3 57.2 + - - +
221B ALA* 4.1 6.2 - - - +
227B THR* 3.5 19.1 - - - +
2301B C5P 4.7 0.4 + - - -
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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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9B VAL* 3.9 33.9 - - + -
22B PHE* 3.9 18.1 - - + -
26B PHE* 4.5 4.9 - - + -
187B PHE* 6.0 0.2 - - + -
214B ILE* 3.9 15.7 - - + -
215B GLY 2.8 7.7 + - - +
217B SER* 1.3 80.8 - - - +
219B THR* 1.3 61.5 + - + +
220B ARG 3.1 5.8 + - - -
221B ALA* 3.4 14.2 + - - +
224B PRO* 3.4 33.6 - - + +
227B THR* 3.7 18.4 - - + -
228B TYR* 3.9 26.2 - - + +
231B LEU* 4.9 6.1 - - + -
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Residues in contact with THR 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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9B VAL* 4.4 5.4 - - + -
10B ALA 3.9 18.7 + - - +
11B LEU* 5.5 0.2 - - + -
13B PHE* 3.8 24.4 - - + -
22B PHE* 3.7 34.4 - - + -
215B GLY 2.9 9.1 + - - +
216B ARG* 3.1 18.0 + - - +
218B LEU* 1.3 74.9 - - - +
220B ARG* 1.3 91.7 + - - +
221B ALA 3.6 1.1 - - - +
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Residues in contact with ARG 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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12B ASP* 4.6 9.9 + - - +
13B PHE* 4.1 21.7 - - - -
216B ARG* 3.1 68.7 + - + +
219B THR* 1.3 119.0 + - - +
221B ALA* 1.3 64.7 + - - +
222B ALA 3.8 0.5 + - - -
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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