Contacts of the helix formed by residues 302 - 310 (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 ARG 302 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303D GLU* 1.3 68.6 + - - +
304D ARG* 3.2 8.3 - - - +
305D ILE* 3.1 29.5 + - - +
306D ILE* 2.9 41.4 + - + +
325D ILE* 3.6 34.2 - - + +
328D LEU* 6.1 1.5 - - - +
442D GLU* 3.4 29.0 + - - +
472D GLU* 4.8 6.1 - - - +
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Residues in contact with GLU 303 (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* 1.3 79.1 - - - +
304D ARG* 1.3 56.5 + - - +
305D ILE 3.2 0.3 + - - -
306D ILE* 3.3 10.1 + - - +
307D LYS* 2.7 39.5 + - + +
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Residues in contact with ARG 304 (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 4.1 2.7 - - - +
303D GLU* 1.3 79.9 - - - +
305D ILE* 1.3 56.1 + - - +
308D ARG* 3.3 5.0 - - - +
472D GLU* 4.5 17.3 - - + +
490D TRP* 5.3 11.2 - - + -
515D MET* 2.9 35.6 - - + +
517D GLN* 3.1 28.2 + - - +
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Residues in contact with ILE 305 (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* 3.1 26.2 + - - +
304D ARG* 1.3 74.7 - - - +
306D ILE* 1.3 53.9 + - - +
308D ARG* 3.3 2.4 + - - +
309D ALA* 2.7 35.7 + - - +
325D ILE* 4.4 13.0 - - + -
440D THR* 3.7 31.6 - - - -
441D MET 3.1 31.4 - - - +
442D GLU* 4.0 6.7 - - + +
470D ILE* 3.7 21.4 - - + +
471D THR 3.6 2.5 - - - -
472D GLU* 3.5 35.4 - - + +
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Residues in contact with ILE 306 (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* 2.9 36.3 + - + +
303D GLU* 3.7 7.4 - - - +
305D ILE* 1.3 72.5 - - - +
307D LYS* 1.3 64.1 + - + +
308D ARG 3.1 1.3 - - - -
309D ALA* 3.6 6.1 - - + +
310D ALA* 2.8 31.4 + - - +
325D ILE* 3.9 22.4 - - + +
328D LEU* 3.3 52.7 - - + +
329D ALA* 3.9 9.0 - - + +
332D PHE* 4.2 15.5 - - + -
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Residues in contact with LYS 307 (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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303D GLU* 2.7 21.8 + - + +
306D ILE* 1.3 77.5 - - + +
308D ARG* 1.3 59.8 + - - +
310D ALA* 4.2 1.4 + - - -
311D LEU* 3.8 1.6 - - - +
332D PHE* 5.2 0.7 - - - -
517D GLN* 3.5 24.0 - - + +
518D ILE* 2.8 52.6 + - + +
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Residues in contact with ARG 308 (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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304D ARG 3.3 18.1 + - - +
305D ILE 3.3 3.7 + - - +
306D ILE 3.1 0.4 - - - -
307D LYS* 1.3 76.5 - - - +
309D ALA* 1.3 67.2 + - - +
310D ALA 3.1 1.3 - - - -
311D LEU* 2.7 30.0 + - - +
312D GLU* 3.1 30.8 + - - +
468D ARG* 3.6 12.3 - - - +
470D ILE* 3.7 22.6 - - + +
475D VAL* 4.0 18.4 - - + +
488D GLU* 2.9 40.4 + - - -
515D MET* 4.2 5.4 - - + -
516D GLN* 3.3 34.5 + - - +
517D GLN* 3.2 9.3 - - - +
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Residues in contact with ALA 309 (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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305D ILE 2.7 20.2 + - - +
306D ILE* 3.6 9.6 - - - +
308D ARG* 1.3 72.1 - - - +
310D ALA* 1.3 56.7 + - - +
312D GLU* 2.9 29.6 + - - +
313D PHE* 4.0 3.1 - - - -
325D ILE* 6.4 0.2 - - + -
329D ALA* 4.2 7.9 - - + -
398D MET* 3.6 27.3 - - - +
440D THR* 3.8 16.2 - - + -
470D ILE* 3.4 14.6 - - + +
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Residues in contact with ALA 310 (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 2.8 19.3 + - - +
307D LYS 4.3 0.4 - - - +
308D ARG 3.0 0.4 + - - -
309D ALA* 1.3 72.2 - - - +
311D LEU* 1.3 57.8 + - - +
312D GLU 3.1 3.6 + - - -
313D PHE* 3.4 30.9 + - - +
329D ALA* 4.3 4.4 - - - +
332D PHE* 3.1 40.2 - - + +
333D ILE* 4.4 2.7 - - - +
334D SER 5.5 0.3 + - - -
337D ILE* 5.6 1.6 - - - +
518D ILE* 3.7 20.6 - - + +
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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