Contacts of the strand formed by residues 200 - 205 (chain C) in PDB entry 2ZUQ
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 THR 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C TRP* 3.6 9.2 - - - -
161C ASN* 2.7 53.1 + - - +
198C SER* 3.6 15.9 - - - +
199C ILE* 1.3 78.3 - - - +
201C CYS* 1.3 59.4 + - - +
202C ASN* 3.4 17.8 + - - -
213C ASP* 4.9 4.7 + - - -
214C LYS 3.5 14.9 + - - -
215C LYS* 3.6 20.4 - - + -
216C ILE* 4.0 0.9 - - - -
238E GLU* 4.0 10.3 + - - +
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Residues in contact with CYS 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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127C VAL* 4.4 2.5 - - - -
129C PRO* 6.0 0.2 - - + -
146C CYS* 2.0 53.2 - - + -
158C LEU* 3.7 9.2 - - - -
159C THR 3.9 2.9 - - - -
160C TRP* 3.8 13.7 - - + -
200C THR* 1.3 72.5 + - - +
202C ASN* 1.3 61.3 + - - +
203C VAL* 3.5 20.0 - - - -
212C VAL 4.1 0.9 - - - +
213C ASP* 3.7 1.4 - - - -
214C LYS* 2.8 44.4 + - + +
216C ILE* 3.7 4.9 - - + +
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Residues in contact with ASN 202 (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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158C LEU* 3.3 3.8 - - - +
159C THR* 2.7 72.4 + - + +
161C ASN 3.6 2.0 - - - +
162C SER* 2.7 42.6 + - - +
200C THR* 3.4 17.2 + - - -
201C CYS* 1.3 73.0 - - - +
203C VAL* 1.3 62.0 + - - +
212C VAL 3.9 3.6 - - - -
213C ASP* 3.6 22.2 - - - +
238E GLU* 4.4 2.3 - - - +
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PRO* 4.6 5.6 - - + -
127C VAL* 3.8 29.2 - - + -
148C VAL* 3.6 28.3 - - + -
156C VAL* 4.3 24.0 - - + -
157C THR 3.4 4.0 - - - +
158C LEU* 3.9 7.9 - - + -
201C CYS* 3.5 27.1 - - - -
202C ASN* 1.3 75.0 - - - +
204C ALA* 1.3 64.8 + - - +
205C HIS 4.7 0.2 - - - +
210C THR* 3.3 3.7 - - + +
211C LYS* 3.8 2.6 - - - -
212C VAL* 3.0 34.1 + - + +
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Residues in contact with ALA 204 (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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156C VAL* 3.4 2.8 - - - -
157C THR* 2.8 54.4 + - + +
159C THR* 6.2 0.9 - - + -
203C VAL* 1.3 73.5 - - - +
205C HIS* 1.3 62.2 + - - +
206C PRO* 3.4 9.8 - - + +
210C THR 3.3 6.5 - - - +
211C LYS* 5.2 9.2 - - + -
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Residues in contact with HIS 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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123C THR 4.0 4.5 + - - -
125C PRO* 3.5 32.3 - - + -
151C TYR* 3.8 8.1 - + - -
152C PHE 3.2 28.5 + - - -
153C PRO 3.1 21.9 + - - -
155C PRO 4.1 1.8 - - - -
156C VAL* 3.4 25.1 - - + +
203C VAL* 4.1 2.2 - - - +
204C ALA* 1.3 72.7 - - - +
206C PRO* 1.3 61.9 - - - +
207C ALA* 3.8 10.1 - - + -
208C SER* 2.6 44.0 + - - +
209C SER* 3.2 5.7 + - - -
210C THR* 3.0 32.7 + - - +
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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