Contacts of the strand formed by residues 200 - 206 (chain B) in PDB entry 6X34
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 TRP 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.9 26.9 - - + -
23B GLN 3.9 4.9 - - - +
24B CYS* 4.9 8.3 - - + +
168B ASP* 3.3 5.2 - - - -
169B LEU* 2.8 42.5 + - - +
170B ILE* 5.3 1.6 - - - -
171B LEU* 5.8 2.9 - - + +
198B THR 4.8 2.2 - - - +
199B LEU* 1.3 81.9 - - - +
201B ASN* 1.3 60.5 + - - +
202B MET* 3.8 0.6 + - - -
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Residues in contact with ASN 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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21B VAL 4.3 0.2 - - - +
22B LEU* 3.3 7.4 - - - +
23B GLN* 2.7 51.5 + - + +
24B CYS* 4.8 0.9 - - - +
166B GLY* 5.4 5.6 - - - +
167B ASP 4.2 4.3 - - - -
168B ASP* 4.8 2.0 - - - +
199B LEU* 4.9 3.7 - - + +
200B TRP* 1.3 71.0 - - - +
202B MET* 1.3 60.8 + - - +
203B ASN* 4.1 3.1 + - + -
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Residues in contact with MET 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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14B LEU* 5.3 13.2 - - + -
20B VAL* 3.6 31.2 - - + -
21B VAL 3.2 35.7 - - - +
22B LEU* 3.6 22.7 - - + +
165B VAL* 4.7 0.7 - - - -
166B GLY* 3.0 28.9 + - - -
167B ASP* 3.3 20.6 + - - +
169B LEU* 4.9 13.9 - - + -
200B TRP 3.8 0.2 + - - -
201B ASN* 1.3 71.9 - - - +
203B ASN* 1.3 72.0 + - - +
204B PRO* 4.4 1.8 - - + +
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Residues in contact with ASN 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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21B VAL* 3.4 27.6 + - - +
23B GLN* 6.1 1.3 - - - +
166B GLY* 4.5 8.5 - - - +
201B ASN* 4.1 2.8 + - + +
202B MET* 1.3 84.1 - - - +
204B PRO* 1.3 71.3 - - + +
205B ILE* 4.2 4.3 - - + +
268B SER* 5.7 8.1 - - - +
269B TRP* 5.3 8.1 - - + +
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Residues in contact with PRO 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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14B LEU* 4.4 23.8 - - + -
18B ASP* 5.5 3.1 - - + -
19B GLU 3.8 10.5 - - - +
20B VAL* 4.3 14.1 - - + -
165B VAL* 4.0 34.5 - - + -
166B GLY 4.7 0.2 - - - +
202B MET* 4.4 2.7 - - + +
203B ASN* 1.3 89.8 - - + +
205B ILE* 1.3 61.3 + - - +
206B CYS 4.9 2.0 - - - +
207B SER* 5.5 8.5 - - - +
268B SER* 5.9 0.2 - - - -
269B TRP* 3.5 41.4 + - + -
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Residues in contact with ILE 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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19B GLU* 3.0 34.7 + - + +
20B VAL 4.3 0.7 - - - +
21B VAL* 3.8 36.3 - - + -
62B LEU 5.9 0.7 - - - +
66B CYS* 5.1 14.8 - - + -
203B ASN 4.2 2.7 - - - +
204B PRO* 1.3 77.5 - - - +
206B CYS* 1.3 64.8 + - + +
207B SER 4.2 0.7 - - - -
267B ILE 5.9 0.4 - - - +
268B SER* 4.9 5.2 - - - -
269B TRP* 3.7 36.3 - - - +
270B SER* 3.2 31.0 - - - +
271B GLY* 3.1 23.2 + - - +
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Residues in contact with CYS 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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17B ASP 4.7 0.2 - - - +
18B ASP* 3.3 5.8 - - - +
19B GLU* 3.0 38.2 + - + -
204B PRO* 5.5 0.9 - - - -
205B ILE* 1.3 83.9 - - + +
207B SER* 1.3 64.7 + - - +
208B GLY 4.5 2.5 - - - -
209B CYS* 4.4 30.1 - - - -
215B THR* 5.2 5.8 - - - -
271B GLY* 3.7 28.7 - - - -
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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