Contacts of the strand formed by residues 305 - 310 (chain B) in PDB entry 1R6U
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 CYS 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL* 5.5 0.2 - - - -
156B PHE* 5.5 0.7 - - - -
157B TYR* 3.5 24.2 - - + -
159B TYR* 3.4 32.8 - - - -
288B SER* 3.4 30.9 + - - +
303B ILE 3.9 0.4 + - - -
304B GLN* 1.3 82.7 - - - +
306B LEU* 1.3 65.1 + - - +
307B ILE* 3.8 13.0 - - - -
330B PRO* 5.6 0.6 + - - +
331B LYS 4.8 0.4 + - - -
332B PRO* 3.8 10.4 - - + +
333B ALA* 2.7 32.9 + - - +
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Residues in contact with LEU 306 (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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143B MSE 3.8 33.9 - - + -
146B VAL* 4.4 2.0 - - + -
156B PHE* 3.8 24.0 - - + -
157B TYR 2.8 15.8 + - - +
158B LEU* 3.3 24.2 - - + -
159B TYR 3.0 22.5 + - - -
183B LEU* 4.4 7.6 - - + -
187B PHE* 5.8 0.7 - - + -
305B CYS* 1.3 75.2 - - - +
307B ILE* 1.3 65.7 + - - +
308B PRO* 3.5 7.0 - - + +
333B ALA* 3.6 27.6 - - + +
334B LEU 4.2 2.0 - - - +
335B LEU* 4.2 22.9 - - + -
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 3.6 31.9 - - + +
160B THR* 5.3 2.0 - - - -
288B SER* 3.5 24.2 - - - +
305B CYS* 3.8 7.0 - - - -
306B LEU* 1.3 78.9 - - - +
308B PRO* 1.3 72.9 - - - +
309B CYS* 3.3 5.9 + - + -
317B PHE* 3.8 43.1 - - + -
332B PRO* 3.7 20.4 - - + -
333B ALA 2.9 13.8 + - - +
334B LEU* 3.6 8.8 - - + -
335B LEU 3.4 17.0 + - - -
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Residues in contact with PRO 308 (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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137B PHE* 4.3 16.2 - - + -
158B LEU* 4.4 6.1 - - + -
159B TYR 3.7 10.8 - - - +
160B THR* 4.3 12.5 + - - +
176B PRO* 4.9 8.9 - - + +
179B PHE* 4.3 7.4 - - + -
180B THR* 3.7 25.4 - - + +
183B LEU* 3.7 26.5 - - + -
306B LEU 3.5 11.2 - - - +
307B ILE* 1.3 87.6 - - - +
309B CYS* 1.3 61.1 + - - +
335B LEU* 3.6 13.9 - - + +
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Residues in contact with CYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PHE* 3.7 4.8 - - - -
176B PRO* 6.1 5.2 - - - -
307B ILE* 3.9 11.7 - - + +
308B PRO* 1.3 75.6 - - - +
310B ALA* 1.3 64.5 + - - +
313B GLN* 4.8 2.2 - - + -
314B ASP 5.3 0.2 - - - -
317B PHE* 3.8 35.7 - - + -
334B LEU* 4.7 4.9 - - - -
335B LEU 2.9 15.1 + - - +
336B HIS* 3.2 30.0 - - - -
337B SER* 3.0 24.9 + - - -
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Residues in contact with ALA 310 (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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309B CYS* 1.3 81.6 - - - +
311B ILE* 1.3 66.3 + - + +
312B ASP* 3.3 19.1 - - - +
313B GLN* 2.9 30.9 + - + +
336B HIS* 3.9 1.6 + - - -
337B SER* 3.9 13.2 - - - +
338B THR 5.1 4.5 - - - +
339B PHE* 6.0 2.0 - - + -
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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