Contacts of the helix formed by residues 207 - 214 (chain B) in PDB entry 5FW2
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLY 3.3 5.0 + - - +
206B VAL* 1.3 72.8 - - - +
208B ALA* 1.3 63.7 + - - +
209B LYS* 4.0 6.7 + - - +
210B ALA* 2.9 42.4 + - + +
211B ILE* 3.2 31.0 + - + +
228B GLN* 6.0 0.4 - - - -
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Residues in contact with ALA 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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181B VAL* 4.5 6.3 - - + +
182B ASP* 5.3 4.6 - - - +
185B PHE* 3.6 42.0 - - + -
206B VAL 3.1 8.3 + - - +
207B ASP* 1.3 70.5 - - - +
209B LYS* 1.3 59.3 + - - +
211B ILE* 4.6 1.3 - - - -
212B LEU* 2.7 58.4 + - + +
225B LEU* 4.9 3.6 - - + -
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Residues in contact with LYS 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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178B ASN* 3.8 9.1 + - - +
179B SER* 2.4 33.1 + - - +
181B VAL* 3.6 28.7 - - + +
182B ASP* 3.1 45.7 + - + +
207B ASP* 3.5 6.3 - - - +
208B ALA* 1.3 76.7 - - - +
210B ALA* 1.3 53.2 + - - +
212B LEU* 5.2 0.2 - - - -
213B SER* 2.4 44.6 + - - +
309B ASN* 5.8 6.1 + - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASP* 2.9 29.5 + - + +
209B LYS* 1.3 75.5 - - - +
211B ILE* 1.3 61.5 + - + +
213B SER* 3.8 4.0 - - - -
214B ALA* 2.9 33.3 + - - +
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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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206B VAL* 4.2 12.1 - - + -
207B ASP* 3.2 23.2 + - + +
208B ALA* 4.1 2.0 - - - +
210B ALA* 1.3 80.8 - - + +
212B LEU* 1.3 61.1 + - + +
214B ALA* 3.9 5.4 + - - +
216B LEU* 5.3 1.2 - - - +
221B ARG* 3.2 45.6 - - - +
224B ASN* 3.7 36.0 + - + +
225B LEU* 3.8 11.7 - - + +
228B GLN* 4.2 20.0 - - + +
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Residues in contact with LEU 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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181B VAL* 5.3 0.4 - - + -
185B PHE* 4.7 8.1 - - + -
208B ALA* 2.7 52.6 + - + +
211B ILE* 1.3 77.2 - - - +
213B SER* 1.3 54.8 + - - +
214B ALA 3.4 0.4 - - - -
221B ARG* 2.6 49.3 + - + +
225B LEU* 4.1 23.1 - - + -
242B ILE* 4.6 7.6 - - + -
246B LEU* 4.0 26.2 - - + +
296B LEU* 6.0 3.4 - - + -
300B ILE* 3.8 30.3 - - + +
303B SER* 3.6 5.7 + - - -
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Residues in contact with SER 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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178B ASN* 4.7 12.6 - - - -
181B VAL* 6.3 0.7 - - - -
209B LYS* 2.4 33.6 + - - +
210B ALA* 3.9 4.3 + - - -
212B LEU* 1.3 71.0 - - - +
214B ALA* 1.3 67.2 + - - +
215B ARG* 3.8 2.6 + - - +
300B ILE* 5.5 3.6 - - - -
303B SER* 3.6 32.5 + - - +
307B ARG* 5.3 8.5 + - - -
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Residues in contact with ALA 214 (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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210B ALA 2.9 19.3 + - - +
211B ILE* 3.9 10.3 + - - +
212B LEU 3.4 1.8 - - - -
213B SER* 1.3 82.9 - - - +
215B ARG* 1.3 60.7 + - - +
216B LEU* 3.2 26.4 + - + -
221B ARG* 3.3 17.9 + - - -
303B SER* 4.8 1.2 + - - +
304B ASP* 6.0 1.6 - - - -
307B ARG* 6.0 0.4 - - - +
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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