Contacts of the strand formed by residues 323 - 329 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D LEU 3.4 6.7 - - - +
253D GLU* 4.1 23.6 - - + -
320D GLN* 3.0 25.6 + - - +
321D GLY 3.3 0.9 - - - -
322D SER* 1.3 92.9 - - - +
324D VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D LEU 3.7 0.9 - - - +
251D HIS* 3.7 2.1 - - - -
252D LEU* 2.9 41.6 + - + +
259D PHE* 3.4 40.2 - - + -
300D VAL* 4.0 12.1 - - + -
301D ALA 4.9 0.2 - - - +
317D ILE* 4.7 8.3 - - + +
320D GLN* 4.0 23.1 - - + -
323D CYS* 1.3 75.6 - - - +
325D SER* 1.3 73.5 + - - +
326D LEU* 3.7 27.8 - - + -
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Residues in contact with SER 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D CYS* 2.9 33.8 - - - -
250D LEU 3.3 5.6 + - - -
251D HIS* 3.7 17.3 + - - +
300D VAL* 3.5 4.0 - - - -
301D ALA* 2.8 42.8 + - - +
302D GLY 4.8 3.5 + - - -
320D GLN* 5.4 0.8 + - - -
324D VAL* 1.3 74.8 - - - +
326D LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D ARG 3.5 2.1 - - - +
249D CYS* 3.5 1.2 - - - -
250D LEU* 2.7 43.6 + - + +
252D LEU* 3.9 24.7 - - + -
261D PHE* 3.7 32.3 - - + -
291D MET* 3.9 11.9 - - + -
297D LEU* 4.0 16.4 - - + -
299D ALA 3.6 1.6 - - - -
300D VAL* 3.9 22.2 - - + -
317D ILE* 4.2 10.1 - - + -
324D VAL* 3.7 22.4 - - + -
325D SER* 1.3 81.5 - - - +
327D THR* 1.3 60.7 + - - +
328D VAL* 4.8 4.7 - - + -
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Residues in contact with THR 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PRO* 3.9 20.9 - - + -
248D ARG 3.3 10.1 - - - +
249D CYS* 3.9 18.4 - - + +
297D LEU* 3.5 5.4 - - - +
298D VAL* 2.8 41.4 + - + -
299D ALA* 3.1 31.2 + - + +
302D GLY* 5.5 4.0 + - - -
326D LEU* 1.3 73.2 - - - +
328D VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PRO* 3.2 6.6 - - - +
248D ARG* 2.8 48.1 + - + +
250D LEU* 3.5 28.5 - - + -
277D LEU* 3.3 30.7 - - + -
291D MET* 5.0 0.2 - - + -
295D ASP* 3.5 25.6 - - + +
296D ARG 3.2 9.6 - - - +
297D LEU* 4.1 10.8 - - + -
298D VAL* 4.4 0.7 - - - -
326D LEU* 4.8 3.8 - - + +
327D THR* 1.3 81.2 - - - +
329D VAL* 1.3 64.6 + - - +
330D ASP* 4.4 2.4 + - - +
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PRO* 4.2 26.9 - - + -
294D GLY 4.4 0.3 - - - +
295D ASP* 3.5 3.3 - - - -
296D ARG* 2.9 48.8 + - + +
298D VAL* 3.7 23.8 - - + -
328D VAL* 1.3 78.3 - - - +
330D ASP* 1.3 70.9 + - - +
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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