Contacts of the helix formed by residues 205 - 213 (chain B) in PDB entry 4WGK
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 TYR 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLN* 3.8 24.4 + - + -
203B PHE* 4.5 1.2 - + - +
204B GLN* 1.3 102.6 + - + +
206B THR* 1.3 66.0 + - - +
207B VAL 3.2 2.7 + - - -
208B PHE* 3.3 27.5 + + + +
209B VAL* 3.2 13.6 + - - +
516B PRO* 3.2 23.8 - - + -
517B TRP 3.3 12.6 - - - +
518B HIS 3.8 10.1 - - - -
519B PRO* 3.5 42.9 - - + +
520B ASP 4.8 2.8 + - - -
521B ILE 4.8 1.9 + - - -
575B VAL* 4.9 1.3 - - + -
632B PRO* 3.6 24.5 - - + +
634B PHE* 3.5 22.2 - + - -
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Residues in contact with THR 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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204B GLN 3.7 2.3 + - - -
205B TYR* 1.3 72.0 - - - +
207B VAL* 1.3 62.8 + - - +
209B VAL* 3.1 9.2 + - + +
210B ILE* 2.9 42.2 + - + +
513B LYS 4.4 0.4 - - - +
514B PRO* 3.9 18.0 - - + +
515B HIS* 2.5 36.4 + - - +
516B PRO 3.3 6.1 + - - -
517B TRP* 3.5 31.2 + - + +
638B ILE* 5.9 4.3 - - + -
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR 3.2 0.6 + - - -
206B THR* 1.3 78.1 - - - +
208B PHE* 1.3 71.0 + - + +
210B ILE* 3.5 6.7 + - - +
211B ALA* 3.2 23.5 + - + +
452B LEU* 4.9 8.5 - - + -
456B PHE* 5.7 4.3 - - + -
506B LEU* 5.7 3.6 - - + -
508B THR* 3.6 20.0 - - + -
517B TRP* 3.2 46.9 - - + +
518B HIS* 3.7 20.9 - - + +
578B HIS* 4.7 4.0 - - + +
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Residues in contact with PHE 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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121B MET* 4.8 8.0 - - + +
162B MET* 6.0 1.6 - - + -
203B PHE* 3.3 46.0 - + + -
205B TYR* 3.3 27.9 + + + -
207B VAL* 1.3 78.3 - - + +
209B VAL* 1.3 57.6 + - - +
210B ILE 3.3 0.2 - - - -
211B ALA* 3.7 9.7 - - + +
212B SER* 2.7 36.4 + - - -
518B HIS* 3.8 20.9 - + - -
519B PRO* 4.6 3.4 - - + -
576B TYR* 3.5 44.2 - + + -
578B HIS* 3.3 32.3 - + - -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 3.5 26.2 - - + +
204B GLN* 3.9 11.4 - - - +
205B TYR 3.2 17.0 - - - +
206B THR* 3.1 11.1 + - + +
208B PHE* 1.3 76.3 - - - +
210B ILE* 1.3 59.8 + - - +
212B SER* 3.4 4.4 + - - -
213B GLU* 2.9 6.8 + - - -
214B GLY* 2.9 45.8 + - - +
215B PHE* 4.6 2.7 - - + +
637B LEU* 5.0 5.8 - - + -
638B ILE* 3.7 37.1 - - + +
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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 THR* 2.9 36.9 + - + +
207B VAL* 3.6 9.2 - - - +
209B VAL* 1.3 74.5 - - + +
211B ALA* 1.3 66.6 + - - +
213B GLU* 3.0 19.4 + - - +
517B TRP* 3.9 28.7 - - + -
638B ILE* 5.6 8.5 - - + -
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Residues in contact with ALA 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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119B ASN* 4.5 6.9 + - - +
121B MET* 4.0 21.5 - - + -
124B GLY* 5.4 12.9 - - - -
125B LYS 5.8 0.2 - - - +
207B VAL* 3.2 12.6 + - + +
208B PHE* 3.7 10.5 - - + +
209B VAL 3.3 0.2 - - - -
210B ILE* 1.3 81.4 - - - +
212B SER* 1.3 60.1 + - - +
213B GLU* 3.2 8.1 + - - +
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Residues in contact with SER 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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118B ILE* 5.8 2.1 - - - +
119B ASN* 4.2 10.1 + - - +
121B MET* 3.6 9.5 - - - -
200B ALA* 3.4 17.7 - - - +
201B GLY* 3.1 29.2 + - - -
203B PHE* 4.0 4.4 - - - -
208B PHE 2.7 22.2 + - - -
209B VAL* 3.9 1.6 - - - -
211B ALA* 1.3 73.5 - - - +
213B GLU* 1.3 70.0 + - - +
214B GLY 3.3 20.1 + - - +
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Residues in contact with GLU 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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119B ASN* 3.1 27.1 + - - +
126B SER* 3.8 21.5 + - - +
209B VAL 2.9 6.3 + - - -
210B ILE* 3.0 17.8 + - - +
211B ALA 3.1 4.5 - - - +
212B SER* 1.3 79.9 - - - +
214B GLY* 1.3 56.8 + - - +
638B ILE* 6.4 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