Contacts of the strand formed by residues 200 - 206 (chain B) in PDB entry 6RUT
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 LEU 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PRO* 6.2 0.7 - - + -
193B GLN* 3.7 1.4 - - - +
194B SER* 2.8 44.0 + - - -
197B SER* 3.3 28.5 + - - +
198B PRO 3.2 1.9 - - - +
199B ASN* 1.3 75.9 - - - +
201B TYR* 1.3 64.3 + - - +
202B PHE* 3.3 38.8 - - + -
342B SER* 4.6 7.0 - - - -
343B PHE 3.7 2.2 - - - +
344B TYR* 3.6 36.6 - - + +
494B ASN 5.1 0.9 - - - +
495B PHE* 3.7 28.7 - - + -
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.6 3.8 - - + -
80B ILE* 3.5 39.0 - - + +
84B ASN* 4.5 2.1 + - - +
88B PHE* 3.9 13.2 - + - -
132B ARG* 3.7 13.3 + - - -
191B VAL* 4.6 1.6 - - + -
192B VAL 3.3 9.4 - - - +
193B GLN* 3.7 30.4 + - + -
199B ASN* 3.6 22.3 + - - -
200B LEU* 1.3 75.7 - - - +
202B PHE* 1.3 73.1 + - - +
342B SER* 3.4 2.4 - - - -
343B PHE* 2.9 52.7 + + + +
345B ASP* 3.5 46.0 + - + -
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Residues in contact with PHE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU 3.8 0.3 - - - +
191B VAL* 3.4 4.3 - - - -
192B VAL* 2.9 58.0 + - + +
194B SER* 4.4 18.8 - - - -
195B PRO* 5.9 0.2 - - + -
200B LEU* 3.3 27.1 - - + -
201B TYR* 1.3 77.2 - - - +
203B VAL* 1.3 62.8 + - - +
340B VAL* 4.4 3.6 - - + -
341B VAL 3.4 7.0 - - - +
342B SER* 3.5 25.6 - - - -
343B PHE* 4.1 1.8 - - - -
457B MET* 4.2 14.9 - - + +
459B ALA* 4.7 4.3 - - + -
464B VAL* 3.6 23.1 - - + -
491B TYR* 3.6 29.8 - + - -
495B PHE* 3.7 15.7 - + - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 3.8 17.0 - - + -
145B LEU* 6.0 4.3 - - + -
188B PRO* 4.6 6.7 - - + -
190B GLU 3.3 10.8 - - - +
191B VAL* 3.8 18.2 - - + -
202B PHE* 1.3 71.5 - - - +
204B LEU* 1.3 62.3 + - - +
205B LEU* 3.9 17.0 + - + +
339B THR 3.7 0.3 - - - +
340B VAL* 3.3 8.5 - - - +
341B VAL* 2.8 58.4 + - + +
343B PHE* 3.6 26.9 - - + -
355B PHE* 6.3 2.2 - - + -
457B MET* 4.3 2.9 - - - -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 4.7 0.4 - - - +
188B PRO* 3.4 2.1 - - - +
189B VAL* 2.8 43.3 + - + +
190B GLU* 2.8 36.2 + - + +
202B PHE 4.3 0.2 + - - -
203B VAL* 1.3 70.0 - - - +
205B LEU* 1.3 65.1 + - - +
206B VAL* 4.9 0.4 - - + -
338B ALA* 4.5 5.2 - - + -
339B THR 3.7 12.8 - - - +
340B VAL* 4.1 9.6 - - + -
361B ILE* 5.2 2.7 - - + -
454B ILE* 3.8 23.3 - - + -
455B GLY* 3.7 35.7 - - - +
457B MET* 4.1 19.1 - - + -
466B ILE* 4.9 5.6 - - + -
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Residues in contact with LEU 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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145B LEU* 3.7 33.2 - - + -
183B ILE* 4.3 19.3 - - + +
186B LYS* 3.7 18.3 - - + +
187B VAL 3.5 2.5 - - - -
188B PRO* 3.6 34.1 - - + -
203B VAL* 4.6 13.7 - - + +
204B LEU* 1.3 74.4 - - - +
206B VAL* 1.3 63.0 + - - +
338B ALA* 3.3 5.9 - - - +
339B THR* 2.9 40.3 + - - +
341B VAL* 3.8 29.2 - - + -
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Residues in contact with VAL 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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70B TRP* 4.3 8.1 - - + -
186B LYS* 3.5 9.6 - - - +
187B VAL* 2.9 46.7 + - + +
189B VAL* 3.6 30.1 - - + -
204B LEU* 4.9 0.4 - - + -
205B LEU* 1.3 77.3 - - - +
207B PRO* 1.4 71.8 - - + +
210B ALA* 4.5 3.4 - - + -
211B LEU* 3.9 12.1 - - + -
337B GLY 4.3 0.9 - - - -
338B ALA* 4.2 1.1 - - + -
451B PHE* 4.1 16.2 - - + -
454B ILE* 3.7 29.4 - - + -
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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