Contacts of the strand formed by residues 323 - 329 (chain E) in PDB entry 2V90
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 323 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251E HIS* 3.6 21.5 - - + +
252E LEU 3.4 4.0 - - - -
253E GLU* 4.3 26.9 - - - -
320E GLN* 3.3 24.1 + - - +
321E GLY 4.5 0.2 - - - -
322E SER* 1.3 90.4 - - - +
324E VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E LEU 3.9 0.5 - - - +
251E HIS* 3.5 7.0 + - - -
252E LEU* 2.8 40.8 + - + +
259E PHE* 3.4 40.2 - - + -
300E VAL* 4.1 6.5 - - + -
317E ILE* 4.5 7.6 - - + +
320E GLN* 3.8 30.1 - - + -
323E CYS* 1.3 74.4 - - - +
325E SER* 1.3 71.6 + - - +
326E LEU* 3.9 28.2 + - + -
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Residues in contact with SER 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E CYS* 3.1 31.4 - - - -
250E LEU 3.5 5.1 + - - -
251E HIS* 3.9 16.7 + - - +
299E ALA 5.4 0.2 - - - -
301E ALA* 2.9 40.6 + - - +
302E GLY* 4.6 5.8 + - - -
320E GLN* 5.7 0.8 + - - -
324E VAL* 1.3 75.9 - - - +
326E LEU* 1.3 65.9 - - - +
327E THR* 5.1 0.3 + - - -
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Residues in contact with LEU 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ARG 3.7 1.2 - - - +
249E CYS* 4.4 0.7 - - - -
250E LEU* 2.9 34.1 + - - +
252E LEU* 3.9 20.6 - - + -
259E PHE* 5.4 0.7 - - + -
261E PHE* 3.8 32.1 - - + -
291E MET* 3.6 20.0 - - + +
297E LEU* 3.9 13.7 - - + -
299E ALA 3.3 3.4 - - - -
300E VAL* 3.7 25.8 - - + -
317E ILE* 4.2 11.4 - - + -
324E VAL* 3.9 25.1 - - + +
325E SER* 1.3 81.7 + - - +
327E THR* 1.3 63.3 + - - +
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Residues in contact with THR 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E PRO* 3.7 20.4 - - + -
248E ARG 3.3 14.8 - - - +
249E CYS* 3.7 20.2 - - + +
297E LEU* 3.4 7.1 - - - +
298E VAL* 2.8 38.6 + - + -
299E ALA* 2.9 32.5 + - + +
302E GLY* 5.6 2.4 - - - -
326E LEU* 1.3 76.3 - - - +
328E VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E LYS 4.2 0.3 - - - +
247E PRO* 3.3 3.5 - - - +
248E ARG* 2.8 63.4 + - + +
250E LEU* 4.2 9.0 - - + -
277E LEU* 4.3 7.4 - - + -
291E MET* 3.7 24.5 - - + -
295E ASP* 3.6 33.9 - - + +
296E ARG 3.1 11.7 - - - +
297E LEU* 4.4 10.1 - - + -
298E VAL* 4.3 2.5 - - - -
327E THR* 1.3 78.1 - - - +
329E VAL* 1.3 62.4 + - - +
330E ASP* 4.2 2.0 + - - +
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Residues in contact with VAL 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E MET* 3.9 22.0 - - + +
246E LYS 4.8 0.9 - - - -
247E PRO* 4.0 26.7 - - + -
294E GLY 4.4 0.5 - - - +
295E ASP* 3.4 3.9 - - - -
296E ARG* 2.9 69.2 + - - +
298E VAL* 4.0 9.0 - - + -
328E VAL* 1.3 78.1 - - - +
330E ASP* 1.3 72.4 + - - +
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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