Contacts of the strand formed by residues 200 - 206 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.9 27.6 - - + -
23D GLN 3.9 6.1 - - - +
24D CYS* 4.9 7.2 - - + +
168D ASP* 3.3 4.7 - - - -
169D LEU* 2.8 42.3 + - - +
170D ILE* 5.3 1.3 - - - -
171D LEU* 5.8 2.5 - - + +
198D THR 4.8 2.2 - - - +
199D LEU* 1.3 81.7 - - - +
201D ASN* 1.3 60.7 + - - +
202D MET* 3.8 0.5 + - - +
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Residues in contact with ASN 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL 4.3 0.2 - - - +
22D LEU* 3.3 6.7 - - - +
23D GLN* 2.7 50.7 + - + +
24D CYS* 4.8 1.3 - - - +
166D GLY 5.4 5.6 - - - +
167D ASP 4.2 4.5 - - - -
168D ASP* 4.8 2.7 - - - +
199D LEU* 4.9 4.1 - - + +
200D TRP* 1.3 71.2 - - - +
202D MET* 1.3 60.3 + - - +
203D ASN* 4.1 3.0 + - + -
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Residues in contact with MET 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 5.3 13.0 - - + -
20D VAL* 3.6 32.5 - - + -
21D VAL 3.2 34.5 - - - +
22D LEU* 3.6 22.2 - - + +
165D VAL* 4.7 0.7 - - - -
166D GLY* 3.0 28.6 + - - -
167D ASP* 3.3 21.2 + - - +
169D LEU* 4.9 13.9 - - + -
200D TRP 3.8 0.4 + - - -
201D ASN* 1.3 71.0 - - - +
203D ASN* 1.3 73.4 + - - +
204D PRO* 4.4 1.4 - - - +
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Residues in contact with ASN 203 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D VAL* 3.4 27.2 + - - +
23D GLN* 6.1 1.1 - - - +
166D GLY* 4.5 8.7 - - - +
201D ASN* 4.1 3.1 + - + +
202D MET* 1.3 84.2 - - - +
204D PRO* 1.3 71.8 - - + +
205D ILE* 4.2 4.0 - - - +
268D SER* 5.7 8.5 - - - +
269D TRP* 5.3 8.1 - - + +
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Residues in contact with PRO 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.4 23.1 - - + -
18D ASP* 5.5 3.6 - - + -
19D GLU 3.8 10.1 - - - +
20D VAL* 4.3 14.6 - - + -
165D VAL* 4.0 34.1 - - + -
166D GLY 4.7 0.4 - - - +
202D MET* 4.4 2.4 - - + +
203D ASN* 1.3 89.1 - - + +
205D ILE* 1.3 62.1 + - - +
206D CYS 4.9 1.8 - - - +
207D SER* 5.5 8.5 - - - +
268D SER* 5.9 0.2 - - - -
269D TRP* 3.5 41.6 + - + -
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Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D GLU* 3.0 34.8 + - + +
20D VAL 4.3 0.7 - - - +
21D VAL* 3.8 35.4 - - + +
62D LEU 5.9 0.9 - - - +
66D CYS* 5.1 14.8 - - + -
203D ASN 4.2 2.7 - - - +
204D PRO* 1.3 77.4 - - - +
206D CYS* 1.3 63.9 + - + +
207D SER 4.2 1.1 - - - -
267D ILE 5.9 0.2 - - - +
268D SER* 4.9 5.4 - - - -
269D TRP* 3.7 36.3 - - - +
270D SER* 3.2 30.7 - - - +
271D GLY* 3.1 23.2 + - - +
272D SER 4.1 0.2 + - - -
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Residues in contact with CYS 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASP 4.7 0.2 - - - +
18D ASP* 3.3 5.2 - - - +
19D GLU* 3.0 38.5 + - + -
204D PRO* 5.5 0.2 - - - -
205D ILE* 1.3 85.6 - - + +
207D SER* 1.3 63.6 + - - +
208D GLY 4.5 2.2 - - - -
209D CYS* 4.4 29.6 - - - -
215D THR* 5.2 6.3 - - - -
269D TRP* 5.7 0.2 - - - -
271D GLY* 3.7 28.0 - - - -
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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