Contacts of the strand formed by residues 200 - 206 (chain N) in PDB entry 5C7X
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 SER 200 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112N ALA* 5.9 8.1 - - - -
113N PRO* 5.7 1.4 - - - +
195N VAL 3.9 0.5 - - - +
196N THR* 3.5 0.2 - - - -
197N HIS* 2.6 46.6 + - - +
198N GLU* 3.2 5.9 + - - +
199N GLY* 1.3 76.0 - - - +
201N THR* 1.3 55.8 + - - +
202N VAL* 5.8 2.9 - - - -
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Residues in contact with THR 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194N GLN* 4.3 13.2 - - + -
195N VAL 3.5 19.7 - - - +
196N THR* 3.3 27.1 + - - +
199N GLY 3.4 10.4 + - - -
200N SER* 1.3 77.0 - - - +
202N VAL* 1.3 66.4 + - - +
203N GLU* 4.1 13.1 + - + +
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Residues in contact with VAL 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N ALA* 4.9 8.5 - - + -
113N PRO* 3.9 32.3 - - + +
115N VAL* 3.8 27.5 - - + +
193N CYS 4.2 0.2 - - - +
195N VAL* 3.2 30.7 + - - +
200N SER* 5.8 2.0 - - - -
201N THR* 1.3 74.8 - - - +
203N GLU* 1.3 64.8 + - - +
204N LYS* 4.4 8.7 - - + +
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Residues in contact with GLU 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N SER* 4.9 7.1 - - - -
193N CYS 3.4 12.8 - - - +
194N GLN* 2.7 42.2 + - + +
201N THR* 4.1 13.6 + - + +
202N VAL* 1.3 77.4 - - - +
204N LYS* 1.3 65.9 + - - +
205N THR* 4.8 4.5 + - - +
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Residues in contact with LYS 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M SER* 6.6 0.2 - - - -
115N VAL* 3.2 46.7 + - + +
116N THR* 5.1 2.7 - - - +
117N LEU* 3.2 27.9 - - + +
192N SER* 3.4 4.3 - - - -
193N CYS 3.1 31.0 + - - +
202N VAL* 4.4 7.6 + - + +
203N GLU* 1.3 76.6 - - - +
205N THR* 1.3 63.1 + - - +
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Residues in contact with THR 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N LEU* 4.2 0.7 - - - -
190N SER* 3.3 30.7 - - - +
191N TYR 3.6 4.0 - - - +
192N SER* 2.7 18.8 + - - +
203N GLU* 4.3 5.4 + - - +
204N LYS* 1.3 77.6 - - - +
206N VAL* 1.3 75.6 + - - +
207N ALA* 5.7 0.4 - - + -
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Residues in contact with VAL 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N LEU* 3.3 39.9 - - + +
119N PRO* 4.5 16.8 - - + -
132N LEU* 3.9 19.1 - - + -
185N TRP* 3.8 20.3 - - + -
190N SER* 3.3 3.6 - - - -
191N TYR* 2.8 46.3 + - + +
205N THR* 1.3 80.2 - - - +
207N ALA* 1.3 59.2 + - - +
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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