Contacts of the helix formed by residues 200 - 207 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C TRP* 5.7 0.7 - - - -
195C TYR* 3.8 27.1 - - + +
198C ILE 4.1 1.0 + - - -
199C THR* 1.3 77.5 - - - +
201C TRP* 1.3 66.1 + - - +
202C VAL* 3.5 9.9 + - - +
203C TYR* 3.2 29.5 + - - +
204C GLU* 3.1 19.8 + - - +
228C PHE* 4.3 5.7 - - + -
230C ASP* 2.7 37.4 - - - +
255C PRO* 5.1 0.9 - - + +
257C PRO* 5.3 0.5 - - - +
264C PRO* 3.2 21.9 - - - +
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Residues in contact with TRP 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TRP* 3.4 44.8 - + + +
195C TYR* 5.3 1.2 + - - -
200C ASP* 1.3 79.2 + - - +
202C VAL* 1.3 73.9 + - + +
204C GLU* 3.2 5.2 + - - +
205C GLU* 3.1 43.4 + - + +
254C VAL* 3.9 16.2 - - + -
255C PRO 3.8 20.7 + - - +
256C TYR* 3.4 32.3 - + - -
257C PRO* 5.6 0.2 - - + -
663C ASP* 3.8 20.6 - - + -
709C ASP* 2.9 29.4 + - - +
710C ASN* 3.6 44.2 - - - -
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ASP* 3.5 19.0 - - - +
201C TRP* 1.3 89.8 - - + +
203C TYR* 1.3 66.6 + - + +
206C GLU* 2.9 30.6 + - + +
207C VAL* 4.4 1.0 - - - +
257C PRO* 3.9 34.7 - - + +
264C PRO* 4.0 11.4 - - + -
299C TYR* 6.1 0.2 - - + -
663C ASP* 3.8 23.6 - - + +
665C VAL* 3.4 32.1 - - + +
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Residues in contact with TYR 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C THR* 3.7 17.3 - - + -
200C ASP* 3.2 24.3 + - - +
202C VAL* 1.3 90.0 - - + +
204C GLU* 1.3 61.3 + - - +
207C VAL* 3.2 24.0 + - + -
208C PHE* 3.1 47.3 + + - -
228C PHE* 3.4 31.2 - + + -
264C PRO* 4.1 21.1 + - + -
266C VAL* 3.9 9.8 - - + +
298C HIS 4.1 1.2 + - - -
299C TYR* 3.2 42.4 - + + +
300C LEU 3.2 26.4 + - - -
665C VAL* 6.0 0.2 - - + -
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C TRP* 3.3 23.8 - - - +
125C ARG* 3.6 1.4 + - + -
126C HIS* 2.8 21.1 + - + -
127C SER* 2.6 53.4 + - - -
199C THR* 3.2 13.3 + - - +
200C ASP 3.1 19.3 + - - +
201C TRP 3.6 3.8 - - - +
203C TYR* 1.3 77.4 - - - +
205C GLU* 1.3 57.7 + - + +
209C SER* 3.1 28.4 - - - -
210C ALA 3.4 19.9 + - - +
211C TYR* 4.0 7.0 - - - -
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Residues in contact with GLU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 2.9 44.8 + - - +
126C HIS* 5.2 2.6 + - - -
201C TRP* 3.1 40.4 + - + +
202C VAL 4.1 0.9 - - - +
203C TYR 3.3 0.2 - - - -
204C GLU* 1.3 80.4 - - + +
206C GLU* 1.3 78.6 + - + +
207C VAL 3.8 0.2 - - - -
209C SER* 4.1 4.3 + - - -
710C ASN* 3.0 24.6 + - - -
801C 8VU 3.1 38.3 + - - +
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Residues in contact with GLU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 2.9 18.0 + - + +
205C GLU* 1.3 86.0 - - + +
207C VAL* 1.3 63.8 + - - +
209C SER 5.1 0.2 - - - -
357C PHE* 4.4 4.2 - - - +
358C ARG* 5.4 1.0 - - - +
662C TYR* 3.3 1.4 + - - -
663C ASP* 2.5 40.1 - - - +
665C VAL* 3.6 23.6 - - + -
666C TYR* 3.4 19.0 - - - +
669C ARG* 3.4 20.0 + - - +
801C 8VU 2.8 55.4 + - - +
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Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL 4.4 1.3 - - - +
203C TYR* 3.2 37.0 + - + +
205C GLU 3.8 0.2 - - - -
206C GLU* 1.3 83.7 - - - +
208C PHE* 1.3 74.7 + - + +
209C SER* 3.5 3.7 + - - -
299C TYR* 5.3 5.8 - - + -
300C LEU 3.3 25.6 - - - +
301C CYS* 3.6 20.4 - - + +
358C ARG* 3.2 30.5 + - + +
665C VAL* 4.1 22.2 - - + -
801C 8VU 5.2 2.4 - - - -
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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