Contacts of the helix formed by residues 311 - 323 (chain D) in PDB entry 3OS8
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 THR 311 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D SER 4.7 4.5 - - - +
310D LEU* 1.3 75.8 - - - +
312D ALA* 1.3 65.3 + - - +
313D ASP* 3.5 8.9 + - - +
314D GLN* 2.8 40.4 + - - +
315D MET* 2.9 23.0 + - - +
481D LYS* 4.8 2.7 - - - +
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Residues in contact with ALA 312 (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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311D THR* 1.3 72.9 - - - +
313D ASP* 1.3 61.2 + - - +
315D MET 3.5 0.2 + - - -
316D VAL* 3.1 30.2 + - + +
481D LYS* 5.2 3.2 - - - +
484D ASP* 4.7 1.8 - - + +
485D THR* 3.5 28.3 - - + +
488D HIS* 3.4 45.1 - - + +
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Residues in contact with ASP 313 (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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311D THR* 3.2 8.7 + - - +
312D ALA* 1.3 74.1 - - - +
314D GLN* 1.3 61.5 + - + +
316D VAL* 3.3 7.4 + - - +
317D SER* 2.9 30.6 + - - -
488D HIS* 3.2 29.7 + - - -
489D LEU* 5.7 2.6 - - - +
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Residues in contact with GLN 314 (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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309D SER 4.1 2.3 - - - +
310D LEU* 3.2 29.2 - - + +
311D THR* 2.8 45.3 + - - +
313D ASP* 1.3 76.9 - - + +
315D MET* 1.3 57.6 + - - +
317D SER* 3.6 6.8 - - - -
318D ALA* 2.9 31.9 + - - +
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Residues in contact with MET 315 (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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307D ALA 4.2 11.2 - - - +
310D LEU* 4.3 15.2 - - + +
311D THR 2.9 15.9 + - - +
312D ALA 3.7 1.8 - - - +
314D GLN* 1.3 76.7 - - - +
316D VAL* 1.3 63.0 + - - +
318D ALA* 3.4 2.5 + - - +
319D LEU* 3.0 42.6 + - + +
364D VAL* 6.3 0.2 - - - -
365D PRO* 3.7 31.6 - - + +
447D CYS* 5.4 0.7 - - - -
478D VAL* 5.1 5.4 - - + +
481D LYS* 3.6 34.5 - - + -
482D ILE* 4.4 20.6 - - + -
485D THR* 3.5 26.2 - - + +
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Residues in contact with VAL 316 (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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312D ALA 3.1 16.4 + - - +
313D ASP* 3.6 8.7 - - - +
315D MET* 1.3 76.7 - - - +
317D SER* 1.3 54.6 + - - +
319D LEU* 3.1 7.4 + - - +
320D LEU* 2.8 47.1 + - + +
443D GLU* 3.6 31.6 - - + +
446D VAL* 5.2 1.6 - - + -
447D CYS* 4.8 3.4 - - - -
485D THR* 3.5 19.5 - - + -
489D LEU* 3.9 25.8 - - + -
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Residues in contact with SER 317 (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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313D ASP 2.9 16.9 + - - -
314D GLN* 3.6 7.9 - - - -
316D VAL* 1.3 79.0 - - - +
318D ALA* 1.3 63.2 + - - +
320D LEU* 3.4 7.1 + - - +
321D ASP* 2.9 41.0 + - - +
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Residues in contact with ALA 318 (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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310D LEU* 5.0 4.0 - - + -
314D GLN 2.9 18.7 + - - +
315D MET 3.6 4.5 - - - +
317D SER* 1.3 76.0 + - - +
319D LEU* 1.3 63.6 + - - +
321D ASP* 3.3 8.7 + - - +
322D ALA* 3.1 23.4 + - - +
363D ARG* 4.9 6.4 + - - +
365D PRO* 4.1 23.1 - - + -
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Residues in contact with LEU 319 (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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315D MET* 3.0 38.7 + - + +
316D VAL* 3.1 4.0 + - - +
318D ALA* 1.3 74.6 - - - +
320D LEU* 1.3 65.3 + - - +
322D ALA* 3.1 13.8 + - + +
323D GLU* 3.3 15.9 + - - +
360D TRP* 4.9 7.0 + - - +
363D ARG 5.1 0.7 - - - +
364D VAL* 4.4 11.4 - - + -
365D PRO* 3.7 27.1 - - + -
446D VAL* 3.7 35.3 - - + +
447D CYS* 4.1 13.0 - - - -
450D SER* 3.3 30.7 - - - +
482D ILE* 5.5 2.0 - - + -
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Residues in contact with LEU 320 (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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316D VAL* 2.8 43.5 + - + +
317D SER* 3.9 7.0 - - - +
319D LEU* 1.3 71.8 - - - +
321D ASP* 1.3 66.4 + - - +
322D ALA 3.3 0.9 + - - -
323D GLU* 3.3 22.7 + - + +
442D GLY* 4.5 13.7 - - - +
443D GLU* 4.3 14.4 - - + +
446D VAL* 4.1 23.3 - - + -
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Residues in contact with ASP 321 (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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317D SER* 2.9 34.0 + - - +
318D ALA* 3.5 7.8 - - - +
320D LEU* 1.3 79.8 - - - +
322D ALA* 1.3 60.3 + - - +
323D GLU 3.3 3.5 + - - +
363D ARG* 3.4 29.2 + - - +
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Residues in contact with ALA 322 (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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318D ALA 3.1 16.3 + - - +
319D LEU* 3.1 9.3 + - + +
321D ASP* 1.3 75.6 - - - +
323D GLU* 1.3 67.1 + - - +
324D PRO* 3.3 3.1 - - - +
360D TRP* 3.3 31.9 - - + +
363D ARG* 3.6 45.8 + - + +
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Residues in contact with GLU 323 (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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319D LEU 3.3 4.5 + - - +
320D LEU* 3.3 22.3 + - + +
321D ASP 3.3 3.3 - - - +
322D ALA* 1.3 79.9 - - - +
324D PRO* 1.3 75.1 - - + +
325D PRO* 3.9 0.9 - - - +
360D TRP* 4.2 5.2 + - - -
393D TRP* 5.4 1.9 + - - -
445D PHE* 3.6 14.6 - - - -
446D VAL* 3.7 28.0 - - + +
449D LYS* 2.6 38.2 + - - -
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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