Contacts of the helix formed by residues 200 - 207 (chain B) in PDB entry 5Y7K
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 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 5.6 1.3 - - - -
195B TYR* 3.8 23.5 - - + +
198B ILE 4.2 0.6 + - - -
199B THR* 1.3 77.0 - - - +
201B TRP* 1.3 65.2 + - - +
202B VAL* 3.4 7.7 - - - +
203B TYR* 2.9 31.2 + - - +
204B GLU* 3.1 21.8 + - - +
228B PHE* 4.3 7.6 - - + +
230B ASP* 2.8 38.9 - - - +
255B PRO* 5.4 2.7 - - + +
264B PRO* 3.0 21.8 - - - +
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Residues in contact with TRP 201 (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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124B TRP* 3.6 42.9 - + + +
195B TYR* 5.4 0.6 + - - -
200B ASP* 1.3 75.8 - - - +
202B VAL* 1.3 75.6 + - + +
204B GLU* 3.4 4.3 + - - +
205B GLU* 3.1 38.5 + - + +
254B VAL* 4.1 14.1 - - + -
255B PRO 3.8 18.9 + - - +
256B TYR* 3.3 31.4 - + - -
663B ASP* 3.5 28.5 - - - -
709B ASP* 2.7 30.5 + - + -
710B ASN* 3.4 44.4 - - - -
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Residues in contact with VAL 202 (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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200B ASP* 3.4 26.0 - - - +
201B TRP* 1.3 82.8 - - + +
203B TYR* 1.3 55.9 + - + +
205B GLU 3.1 0.7 + - - -
206B GLU* 2.7 38.3 + - - +
207B VAL* 4.9 0.2 - - - -
230B ASP* 4.9 0.7 - - - +
255B PRO 5.2 0.9 - - - +
257B PRO* 3.5 43.3 - - + +
263B ASN* 5.4 0.2 - - - +
264B PRO* 4.0 10.8 - - + -
663B ASP* 3.8 20.0 - - + +
664B SER* 4.6 0.4 - - - +
665B VAL* 3.5 28.7 - - + -
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Residues in contact with TYR 203 (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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199B THR* 3.7 18.8 - - + -
200B ASP* 2.9 26.5 + - - +
202B VAL* 1.3 79.5 - - + +
204B GLU* 1.3 61.5 + - - +
207B VAL* 3.2 23.4 + - + -
208B PHE* 2.8 50.8 + + - +
228B PHE* 3.4 35.0 - + + -
264B PRO* 4.1 23.1 + - + -
266B VAL* 3.9 11.6 - - - +
298B HIS 4.2 1.4 + - - -
299B TYR* 3.4 27.0 - + + -
300B LEU* 3.3 39.6 + - - -
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Residues in contact with GLU 204 (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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124B TRP* 3.0 33.6 - - - +
125B ARG* 4.6 1.1 - - + +
126B HIS* 2.8 21.2 + - + -
127B SER* 2.5 43.3 + - - -
199B THR* 3.2 18.5 + - - +
200B ASP 3.1 15.0 + - - +
201B TRP 3.8 2.9 - - - +
203B TYR* 1.3 77.8 - - - +
205B GLU* 1.3 58.7 + - + +
209B SER* 3.1 29.5 - - - -
210B ALA 3.4 18.6 - - - +
211B TYR* 4.0 7.8 - - - -
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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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125B ARG* 2.8 43.4 + - - +
126B HIS* 5.1 2.6 + - - -
201B TRP* 3.1 38.2 + - + +
202B VAL 4.0 0.9 - - - +
204B GLU* 1.3 81.4 - - + +
206B GLU* 1.3 80.1 + - + +
207B VAL 3.7 0.2 - - - -
209B SER* 4.4 2.6 + - - -
710B ASN* 2.9 25.5 + - - -
801B 8VU 3.1 47.2 + - - +
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Residues in contact with GLU 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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202B VAL* 2.7 20.1 + - - +
205B GLU* 1.3 86.5 - - + +
207B VAL* 1.3 59.6 + - - +
357B PHE 4.3 5.0 - - - +
358B ARG* 5.3 1.6 - - - +
662B TYR* 3.3 0.7 + - - -
663B ASP* 2.7 42.6 - - - +
665B VAL* 3.5 27.1 - - + -
666B TYR* 3.5 13.8 - - + +
669B ARG* 3.3 21.1 + - - +
801B 8VU 2.8 52.3 + - - +
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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
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202B VAL 4.5 1.1 - - - +
203B TYR* 3.2 41.0 + - + +
205B GLU 3.7 0.4 - - - -
206B GLU* 1.3 84.1 - - - +
208B PHE* 1.3 70.4 + - + +
209B SER* 3.6 2.9 + - - -
299B TYR* 5.1 8.3 - - + -
300B LEU 3.5 25.4 - - - +
301B CYS* 3.8 17.9 - - + -
358B ARG* 3.1 33.4 + - + +
665B VAL* 4.0 21.3 - - + -
801B 8VU 5.5 1.0 - - - -
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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