Contacts of the helix formed by residues 324 - 333 (chain D) in PDB entry 3DLX
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 GLY 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D ILE* 1.3 74.3 - - - +
325D ILE* 1.3 65.8 + - - +
326D PRO* 3.3 4.1 - - - -
327D LEU* 3.5 23.1 + - - +
328D LEU* 4.3 1.4 + - - +
400D GLY* 5.8 1.8 - - - -
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Residues in contact with ILE 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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302D ARG* 3.6 38.4 - - + +
305D ILE* 4.4 14.1 - - + -
306D ILE* 3.9 23.8 - - + -
324D GLY* 1.3 71.1 - - - -
326D PRO* 1.4 60.9 - - + +
328D LEU* 2.7 33.7 + - - +
329D ALA* 3.6 3.0 + - + -
400D GLY* 5.5 1.6 - - - -
440D THR* 3.8 33.2 - - - +
441D MET* 4.5 11.9 - - - -
442D GLU* 4.5 13.9 - - + +
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Residues in contact with PRO 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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321D LEU* 3.7 14.6 - - + +
322D GLY 3.2 18.2 - - - +
323D ILE 4.0 0.7 - - - +
324D GLY 3.3 5.8 - - - -
325D ILE* 1.4 92.3 - - + +
327D LEU* 1.3 57.0 + - - +
329D ALA* 2.9 30.3 + - + +
398D MET* 3.3 44.6 - - + +
399D LEU* 3.6 9.0 - - - -
400D GLY* 3.7 10.5 - - - +
440D THR* 3.6 18.2 - - - +
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Residues in contact with LEU 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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321D LEU* 4.3 23.8 - - + +
322D GLY 3.4 17.5 + - - +
323D ILE* 3.8 18.6 - - + -
324D GLY 3.6 13.5 - - - +
326D PRO* 1.3 78.5 - - - +
328D LEU* 1.3 57.4 + - - +
329D ALA 3.2 4.2 + - - -
330D SER* 3.5 18.9 + - - -
331D ASN* 4.8 2.4 + - - -
350D LEU* 6.4 0.9 - - + -
353D TYR* 4.0 12.0 + - - +
365D ASN* 3.9 23.8 - - + +
366D ALA* 5.0 2.0 - - + +
367D GLY* 4.0 20.9 - - - +
369D GLU* 3.9 26.0 - - - +
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Residues in contact with LEU 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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302D ARG* 6.1 2.0 - - - +
306D ILE* 3.3 33.8 - - + +
324D GLY 4.3 0.8 + - - +
325D ILE* 2.7 21.4 + - - +
327D LEU* 1.3 72.5 - - - +
329D ALA* 1.3 58.3 + - - -
331D ASN* 4.6 15.1 + - - +
332D PHE* 4.9 2.1 + - - +
353D TYR* 5.2 2.2 - - - -
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Residues in contact with ALA 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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306D ILE* 4.0 15.9 - - + +
309D ALA* 4.2 24.9 - - + -
310D ALA* 4.3 3.9 - - - +
313D PHE* 4.6 15.0 - - + -
325D ILE* 3.6 1.4 + - + -
326D PRO* 2.9 20.3 + - + +
328D LEU* 1.3 79.0 - - - +
330D SER* 1.3 57.9 + - - +
331D ASN 3.4 0.2 - - - -
332D PHE* 2.9 29.8 + - - +
333D ILE* 3.6 2.1 + - - +
398D MET* 4.6 3.8 - - - -
440D THR* 6.2 0.2 - - + -
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Residues in contact with SER 330 (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 PHE* 5.1 0.9 - - - -
321D LEU* 3.6 25.3 - - - +
326D PRO 3.9 2.0 + - - -
327D LEU 3.5 11.6 + - - -
329D ALA* 1.3 72.5 - - - +
331D ASN* 1.3 67.3 + - - +
332D PHE 3.0 5.6 - - - -
333D ILE* 2.9 36.3 + - - +
341D LEU* 3.9 18.6 - - - -
351D GLY 5.5 2.3 + - - -
352D PRO* 5.8 1.7 - - - +
353D TYR* 5.8 1.6 - - - -
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Residues in contact with ASN 331 (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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327D LEU 4.9 4.4 + - - -
328D LEU* 4.6 10.5 + - - +
329D ALA 3.4 1.0 - - - -
330D SER* 1.3 86.6 + - - +
332D PHE* 1.3 56.3 + - - +
333D ILE 3.5 3.4 + - - +
352D PRO* 4.3 19.8 - - - +
353D TYR* 3.5 37.4 + - - -
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Residues in contact with PHE 332 (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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306D ILE* 4.2 20.9 - - + -
307D LYS* 5.2 0.7 - - - -
310D ALA* 3.1 14.4 - - + +
328D LEU 4.9 1.1 + - - +
329D ALA 2.9 14.9 + - - +
331D ASN* 1.3 78.8 - - - +
333D ILE* 1.3 58.3 + - - +
518D ILE* 3.0 37.5 - - + +
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Residues in contact with ILE 333 (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 ALA* 4.7 2.5 - - - -
313D PHE* 3.6 34.3 - - + -
329D ALA 3.6 0.6 + - - +
330D SER* 2.9 22.7 + - - +
331D ASN 3.5 3.1 - - - +
332D PHE* 1.3 77.7 - - - +
334D SER* 1.3 77.1 + - - +
335D PRO* 3.6 4.3 - - - +
337D ILE* 4.1 9.2 - - + +
339D VAL* 3.8 45.1 - - + -
341D LEU* 4.1 20.0 - - + -
518D ILE* 4.5 1.3 - - - -
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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