Contacts of the strand formed by residues 265 - 270 (chain A) in PDB entry 6BM0
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 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 3.1 25.3 - - + +
220A LEU* 4.6 8.7 - - + -
222A GLU* 5.1 1.0 + - - +
238A CYS* 4.0 19.7 - - + -
261A LEU* 4.3 5.6 - - - -
262A PRO* 3.5 37.0 - - - -
263A PHE 3.7 3.8 + - - -
264A ASP* 1.3 75.9 - - - +
266A THR* 1.3 64.9 + - - +
280A VAL* 4.1 20.4 - - + -
281A PHE 3.7 6.1 - - - +
282A ALA* 4.3 7.2 - - - -
283A VAL* 5.6 0.4 - - - -
287A LEU* 5.7 0.7 - - - -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ILE* 4.1 9.2 - - - -
220A LEU* 3.4 13.7 - - - +
264A ASP 4.1 1.8 + - - -
265A CYS* 1.3 76.1 - - - +
267A GLN* 1.3 81.8 + - + +
280A VAL* 4.4 0.3 - - - +
281A PHE* 2.9 33.8 + - + +
282A ALA 4.5 1.1 - - - -
283A VAL* 4.9 4.2 - - + +
322A LEU 3.4 26.2 - - - +
323A ASP* 3.9 19.5 + - - +
325A ALA* 5.8 3.2 + - + +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 4.6 1.9 - - - +
205A ASP* 3.3 22.6 - - - +
266A THR* 1.3 90.0 + - + +
268A ALA* 1.3 60.7 + - - +
269A LEU* 4.9 12.5 - - + +
281A PHE* 3.2 42.4 + - + +
325A ALA 2.5 33.6 + - - +
326A GLN* 3.8 21.2 + - - +
327A ALA* 4.1 5.9 - - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASP* 2.9 23.4 + - + +
207A GLN* 3.4 18.0 - - + +
218A LEU* 4.5 10.8 - - + -
220A LEU* 3.8 24.0 - - + -
266A THR 3.8 0.2 + - - -
267A GLN* 1.3 73.4 - - - +
269A LEU* 1.3 69.2 + - - +
278A VAL* 4.1 13.2 - - + -
279A VAL 3.6 8.7 - - - +
280A VAL* 4.2 7.2 - - + +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLN* 4.7 7.2 - - - +
267A GLN* 4.9 14.1 - - + +
268A ALA* 1.3 81.7 - - - +
270A ALA* 1.3 63.2 + - - +
271A VAL 3.3 0.3 + - - -
278A VAL* 3.3 5.8 - - - +
279A VAL* 2.8 47.7 + - + +
281A PHE* 3.7 38.8 - - + -
327A ALA* 3.7 26.5 - - + +
328A THR* 5.6 1.1 - - - -
329A PHE* 4.0 11.4 - - + -
335A MET* 3.7 16.8 - - - -
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLN* 4.4 18.0 - - + +
208A PHE 3.3 26.2 - - - +
209A LEU* 4.3 13.7 - - + -
210A HIS* 4.1 19.6 - - + +
268A ALA 4.3 0.6 + - - -
269A LEU* 1.3 70.2 - - - +
271A VAL* 1.3 65.2 + - - +
272A PRO* 3.6 2.8 - - - +
277A GLY 4.1 5.2 - - - -
278A VAL* 4.6 0.9 - - - -
329A PHE* 3.2 15.8 - - - -
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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