Contacts of the strand formed by residues 323 - 329 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LEU 3.3 6.5 - - - +
253C GLU* 4.3 19.3 - - - -
320C GLN* 3.0 27.3 + - - +
321C GLY 3.4 0.6 - - - -
322C SER* 1.3 87.2 - - - +
324C VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C LEU 3.8 0.7 - - - +
251C HIS* 3.5 3.7 - - - -
252C LEU* 2.8 47.5 + - + +
259C PHE* 3.7 34.5 - - + -
300C VAL* 4.4 5.6 - - + -
317C ILE* 4.5 11.4 - - + +
320C GLN* 3.8 28.0 - - + -
323C CYS* 1.3 73.7 - - - +
325C SER* 1.3 70.8 + - - +
326C LEU* 4.0 28.7 - - + -
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Residues in contact with SER 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C CYS* 2.9 30.5 - - - -
250C LEU 3.5 5.4 - - - -
251C HIS* 3.9 12.9 + - - -
300C VAL* 3.5 3.1 - - - -
301C ALA* 2.8 45.3 + - - +
302C GLY* 4.5 5.9 + - - -
320C GLN* 5.7 0.6 + - - -
324C VAL* 1.3 74.8 - - - +
326C LEU* 1.3 62.2 + - - +
327C THR* 5.2 0.5 + - - -
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ARG 3.5 2.1 - - - +
249C CYS* 4.3 0.7 - - - -
250C LEU* 2.8 39.8 + - - +
252C LEU* 3.6 33.2 - - + -
261C PHE* 3.9 20.0 - - + -
277C LEU* 6.0 0.2 - - + -
291C MET* 4.1 9.9 - - + -
297C LEU* 3.8 17.9 - - + -
299C ALA 3.4 2.7 - - - -
300C VAL* 3.8 24.7 - - + -
317C ILE* 4.2 12.1 - - + -
324C VAL* 4.0 20.2 - - + -
325C SER* 1.3 81.3 + - - +
327C THR* 1.3 63.8 + - - +
328C VAL* 4.8 5.4 - - + -
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Residues in contact with THR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C PRO* 4.0 16.4 - - + -
248C ARG 3.3 17.9 - - - +
249C CYS* 4.0 15.7 - - + +
297C LEU* 3.6 4.3 - - - +
298C VAL* 2.7 52.3 + - + +
299C ALA* 2.9 26.5 + - - +
302C GLY* 5.4 4.5 + - - -
325C SER* 5.2 0.3 + - - -
326C LEU* 1.3 73.3 + - - +
328C VAL* 1.3 58.3 + - - +
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C PRO* 3.1 4.7 - - - +
248C ARG* 2.8 54.4 + - + +
250C LEU* 3.8 22.9 - - + -
277C LEU* 3.6 28.9 - - + -
291C MET* 4.7 1.6 - - + -
295C ASP* 3.4 26.0 - - - +
296C ARG 3.1 9.9 - - - +
297C LEU* 4.2 9.6 - - + -
298C VAL* 4.3 0.7 - - - -
326C LEU* 4.6 4.7 - - + +
327C THR* 1.3 80.1 - - - +
329C VAL* 1.3 63.6 + - - +
330C ASP* 4.2 2.3 + - - +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C PRO* 4.1 25.6 - - + -
294C GLY 4.4 0.3 - - - +
295C ASP* 3.5 3.3 - - - -
296C ARG* 2.9 54.5 + - + +
298C VAL* 3.7 22.9 - - + -
328C VAL* 1.3 75.9 - - - +
330C ASP* 1.3 73.4 + - - +
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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