Contacts of the helix formed by residues 204 - 213 (chain B) in PDB entry 5YL4
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 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B VAL* 3.4 12.6 - - - +
170B MET 3.2 15.3 + - - +
171B PRO* 5.4 0.2 - - - +
172B SER* 4.2 8.5 - - - +
175B VAL* 3.7 21.7 + - + +
202B ILE 3.8 1.0 + - - -
203B ASP* 1.3 70.7 + - - +
205B GLU* 1.3 66.4 + - - +
207B LEU* 3.6 12.7 - - - +
208B TYR* 3.1 24.3 + - - +
225B LEU* 3.8 7.5 - - - +
501B GDP 2.8 72.0 + - - -
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Residues in contact with GLU 205 (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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172B SER* 2.7 34.2 + - - +
173B PRO* 4.4 5.0 - - - +
174B LYS* 3.7 35.4 + - + +
203B ASP* 3.0 20.3 + - - +
204B ASN* 1.3 79.8 - - - +
206B ALA* 1.3 61.6 + - - +
208B TYR* 3.2 5.3 + - - +
209B ASP* 3.0 29.5 + - - +
302B ALA* 4.2 10.7 - - + +
380B ARG* 3.9 28.7 + - - +
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Residues in contact with ALA 206 (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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203B ASP 3.2 2.7 + - - +
205B GLU* 1.3 80.3 - - - +
207B LEU* 1.3 57.3 + - - +
208B TYR 3.3 0.2 + - - -
209B ASP* 3.3 7.4 + - - +
210B ILE* 2.9 35.5 + - - +
299B MET 3.5 12.1 - - - +
300B MET* 3.5 33.9 - - - +
302B ALA* 3.7 23.5 - - + +
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Residues in contact with LEU 207 (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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202B ILE* 3.7 8.7 - - + -
203B ASP 3.0 20.6 + - - +
204B ASN* 3.6 23.8 - - - +
205B GLU 3.4 0.2 - - - -
206B ALA* 1.3 74.6 - - - +
208B TYR* 1.3 62.8 + - - +
210B ILE* 3.7 1.5 + - + -
211B CYS* 3.1 29.1 + - - -
225B LEU* 3.6 28.7 - - + +
228B LEU* 3.9 18.7 - - + +
229B VAL* 3.4 29.8 - - + -
300B MET* 3.8 39.0 - - + +
501B GDP 4.0 2.0 - - - +
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Residues in contact with TYR 208 (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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174B LYS* 4.1 27.4 - - + -
175B VAL* 3.8 22.7 - - + -
204B ASN 3.1 18.1 + - - +
205B GLU* 3.4 4.7 - - - +
207B LEU* 1.3 74.5 - - - +
209B ASP* 1.3 66.9 + - - +
211B CYS* 3.0 5.3 + - - +
212B PHE* 2.7 59.6 + + + +
218B THR 4.5 6.6 + - - -
220B PRO* 3.7 40.2 - - + +
225B LEU* 3.7 8.2 - - + +
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Residues in contact with ASP 209 (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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174B LYS* 2.9 32.7 + - - +
205B GLU* 3.0 22.6 + - - +
206B ALA* 3.7 9.2 - - - +
208B TYR* 1.3 86.5 - - - +
210B ILE* 1.3 56.6 + - + +
212B PHE* 4.4 5.1 - - - +
213B ARG* 2.8 69.9 + - - +
214B THR* 4.6 0.2 + - - -
302B ALA* 5.3 2.8 - - - +
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Residues in contact with ILE 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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206B ALA 2.9 22.5 + - - +
207B LEU* 4.5 1.6 - - - -
209B ASP* 1.3 75.3 - - + +
211B CYS* 1.3 59.8 + - - +
214B THR* 3.3 11.3 + - - -
215B LEU* 3.0 34.2 + - + +
228B LEU* 3.6 27.8 - - + -
273B LEU* 3.5 31.4 - - + -
297B LYS 3.3 22.2 - - - +
298B ASN* 4.4 7.2 - - - +
299B MET 3.4 29.2 - - - +
300B MET* 4.6 8.7 - - - -
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Residues in contact with CYS 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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207B LEU 3.1 21.3 + - - +
208B TYR* 3.0 8.8 + - - +
210B ILE* 1.3 77.0 - - - +
212B PHE* 1.3 58.3 + - - +
215B LEU* 3.6 12.1 - - - +
216B LYS 3.5 5.4 + - - -
217B LEU* 3.0 36.8 + - + +
220B PRO* 3.8 19.5 - - + -
224B ASP* 3.5 41.1 - - - -
225B LEU* 3.9 5.2 - - - -
228B LEU* 3.9 10.8 - - - -
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Residues in contact with PHE 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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208B TYR* 2.7 46.4 + + + +
209B ASP* 4.1 4.0 - - - +
211B CYS* 1.3 78.4 - - - +
213B ARG* 1.3 77.6 + - + +
216B LYS* 3.4 18.0 + - - +
217B LEU 3.4 17.5 - - - +
218B THR* 3.9 28.0 - - + -
220B PRO* 4.9 0.9 - - + -
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Residues in contact with ARG 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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174B LYS* 4.0 9.3 - - - +
209B ASP* 2.8 56.5 + - - +
212B PHE* 1.3 86.7 - - + +
214B THR* 1.3 63.0 + - - +
216B LYS* 2.9 33.0 + - - +
297B LYS* 6.4 0.7 - - + -
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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