Contacts of the strand formed by residues 323 - 329 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LEU 3.5 5.4 - - - +
253B GLU* 3.7 28.9 - - - +
320B GLN* 2.9 28.4 + - - +
321B GLY 4.4 0.2 - - - -
322B SER* 1.3 89.2 - - - +
324B VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 324 (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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250B LEU 3.8 0.7 - - - +
251B HIS* 3.5 2.9 - - - -
252B LEU* 2.9 33.1 + - + +
259B PHE* 3.6 36.3 - - + -
300B VAL* 4.0 7.4 - - + -
317B ILE* 4.3 10.8 - - + +
320B GLN* 3.8 26.7 - - + -
323B CYS* 1.3 74.7 - - - +
325B SER* 1.3 73.0 + - - +
326B LEU* 3.9 27.7 + - + -
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Residues in contact with SER 325 (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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249B CYS* 3.2 22.9 - - - -
250B LEU 3.3 6.7 - - - -
251B HIS* 3.7 21.9 - - - -
300B VAL* 3.6 2.1 - - - -
301B ALA* 3.0 36.2 + - - +
302B GLY* 4.3 10.5 + - - -
320B GLN* 5.4 0.8 + - - +
324B VAL* 1.3 80.0 - - - +
326B LEU* 1.3 58.3 + - - +
327B THR* 4.8 1.6 + - - -
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Residues in contact with LEU 326 (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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248B ARG 3.6 1.6 - - - +
249B CYS* 3.4 1.4 - - - -
250B LEU* 2.8 36.2 + - + +
252B LEU* 3.9 13.7 - - + -
261B PHE* 3.7 20.6 - - + -
291B MET* 3.4 35.0 - - + -
297B LEU* 3.9 17.5 - - + -
299B ALA 3.6 2.0 - - - -
300B VAL* 3.9 24.2 - - + -
317B ILE* 4.1 11.4 - - + -
324B VAL* 3.9 22.2 - - + +
325B SER* 1.3 82.3 + - - +
327B THR* 1.3 62.1 + - - +
328B VAL* 4.1 3.8 + - + +
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Residues in contact with THR 327 (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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247B PRO* 3.7 27.1 - - + -
248B ARG 3.4 12.1 - - - +
249B CYS* 3.8 18.6 - - + +
297B LEU* 3.4 5.7 - - - +
298B VAL* 2.8 39.2 + - + -
299B ALA* 2.9 33.9 + - + +
302B GLY* 5.7 2.3 + - - -
325B SER* 4.8 1.4 + - - -
326B LEU* 1.3 73.9 - - - +
328B VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 328 (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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246B LYS 4.6 0.2 - - - +
247B PRO* 3.2 5.1 - - - +
248B ARG* 2.8 47.2 + - + +
250B LEU* 4.1 15.5 - - + -
277B LEU* 4.3 11.2 - - + -
291B MET* 4.9 5.8 - - + -
295B ASP* 3.6 36.3 - - + +
296B ARG 3.1 12.8 - - - +
297B LEU* 4.1 13.7 - - + -
298B VAL* 4.7 0.9 - - - -
326B LEU* 4.9 7.0 - - + +
327B THR* 1.3 81.3 - - - +
329B VAL* 1.3 63.8 + - - +
330B ASP* 4.0 9.0 + - - +
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Residues in contact with VAL 329 (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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245B MET* 3.7 24.9 - - + +
247B PRO* 4.0 25.4 - - + -
294B GLY 4.4 0.5 - - - +
295B ASP* 3.5 3.1 - - - -
296B ARG* 2.9 44.3 + - + +
298B VAL* 3.9 19.1 - - + -
328B VAL* 1.3 75.1 - - - +
330B ASP* 1.3 73.6 + - - +
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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