Contacts of the helix formed by residues 304 - 317 (chain D) in PDB entry 3UDB
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 SER 304 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D ARG* 3.8 1.9 - - - +
297D GLU* 3.2 14.6 - - - -
302D GLY 4.2 0.4 - - - -
303D GLN* 1.3 87.3 - - - +
305D ILE* 1.3 53.9 + - - +
306D GLU* 3.2 20.8 + - - +
307D GLU* 2.8 45.8 + - - +
308D ILE 3.0 3.5 + - - -
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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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67D ILE* 3.7 36.6 - - + -
70D ARG* 3.7 21.9 - - - +
297D GLU* 2.8 29.0 + - - +
303D GLN 3.3 1.3 + - - -
304D SER* 1.3 70.8 - - - +
306D GLU* 1.3 78.7 + - + +
308D ILE* 3.9 5.8 - - + +
309D MET* 2.9 39.7 + - + +
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Residues in contact with GLU 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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297D GLU* 4.8 2.9 - - - +
304D SER* 3.0 22.5 + - - +
305D ILE* 1.3 96.6 + - + +
307D GLU* 1.3 56.0 + - - +
309D MET* 4.0 4.6 - - - +
310D GLN* 3.1 27.9 + - - +
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Residues in contact with GLU 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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302D GLY 4.8 1.0 - - - +
303D GLN* 3.6 30.7 - - + +
304D SER* 2.8 25.2 + - - +
306D GLU* 1.3 76.1 - - - +
308D ILE* 1.3 63.2 + - - +
310D GLN* 3.4 5.9 + - - +
311D ILE* 3.2 34.3 + - + +
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Residues in contact with ILE 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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66D ILE* 4.4 12.1 - - + -
67D ILE* 4.5 9.4 - - + -
70D ARG* 3.4 35.2 - - + +
80D PHE* 4.6 4.9 - - + -
83D VAL* 3.8 30.0 - - + +
303D GLN* 2.6 46.2 - - + +
304D SER 3.0 6.1 + - - +
305D ILE* 4.0 7.6 - - + +
307D GLU* 1.3 75.0 - - - +
309D MET* 1.3 65.3 + - - +
311D ILE* 3.2 5.2 + - - +
312D ILE* 3.0 37.5 + - + +
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Residues in contact with MET 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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63D LYS* 2.6 56.1 - - + +
67D ILE* 3.8 22.0 - - + -
305D ILE* 2.9 31.1 + - + +
306D GLU* 4.0 5.4 - - - +
308D ILE* 1.3 76.8 - - - +
310D GLN* 1.3 61.7 + - - +
312D ILE* 3.3 16.0 + - + +
313D ALA* 3.0 24.6 + - - +
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Residues in contact with GLN 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 GLU 3.1 20.3 + - - +
307D GLU* 3.6 8.1 - - - +
308D ILE 3.2 0.2 - - - -
309D MET* 1.3 78.3 - - - +
311D ILE* 1.3 63.5 + - + +
313D ALA* 3.6 5.3 + - + +
314D GLU* 3.2 36.1 + - - +
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Residues in contact with ILE 311 (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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83D VAL* 3.6 27.1 - - + +
84D ILE* 4.4 3.8 - - - -
85D LEU* 3.6 32.7 - - + +
90D LEU* 3.9 15.3 - - + -
303D GLN* 4.3 10.1 - - - +
307D GLU* 3.2 20.9 - - + +
308D ILE 3.2 8.1 + - - +
310D GLN* 1.3 78.7 - - + +
312D ILE* 1.3 65.6 + - - +
314D GLU* 3.8 5.2 + - - +
315D ALA* 3.3 20.8 + - - +
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Residues in contact with ILE 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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58D ILE* 2.8 46.1 - - + +
59D ASP 5.2 1.3 - - - +
62D VAL* 5.8 0.9 - - + -
63D LYS* 4.0 28.0 - - + +
66D ILE* 4.0 26.7 - - + -
67D ILE* 4.3 5.8 - - + -
83D VAL* 5.1 2.0 - - + -
90D LEU* 4.9 10.8 - - + -
308D ILE* 3.0 33.2 + - + +
309D MET* 3.3 29.6 + - + +
311D ILE* 1.3 76.0 - - - +
313D ALA* 1.3 64.0 + - - +
315D ALA* 3.1 6.8 + - - -
316D THR* 5.1 2.7 - - + -
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Residues in contact with ALA 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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309D MET 3.0 16.6 + - - +
310D GLN* 3.9 6.3 - - - +
312D ILE* 1.3 72.7 - - - +
314D GLU* 1.3 57.7 + - - +
315D ALA 2.9 9.4 + - - -
316D THR* 2.3 36.5 + - - -
317D VAL* 3.9 2.6 + - - +
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Residues in contact with GLU 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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54D ARG* 3.1 28.2 + - - -
85D LEU* 4.7 17.3 - - + +
310D GLN* 3.2 28.1 + - - +
311D ILE* 4.0 6.1 - - - +
312D ILE 3.4 0.2 - - - -
313D ALA* 1.3 77.4 - - - +
315D ALA* 1.3 56.0 + - - +
317D VAL* 4.0 14.9 - - + +
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Residues in contact with ALA 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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54D ARG* 2.4 51.4 - - - +
58D ILE* 3.1 10.4 - - + +
85D LEU* 4.7 5.8 - - + -
90D LEU* 4.4 24.0 - - + -
311D ILE 3.3 13.7 + - - +
312D ILE* 3.2 14.4 - - - +
313D ALA 2.9 1.0 - - - -
314D GLU* 1.3 78.2 - - - +
316D THR* 1.3 53.0 + - - +
317D VAL 3.1 3.0 + - - -
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Residues in contact with THR 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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54D ARG 3.1 6.8 - - - +
55D GLY 3.2 10.4 - - - +
56D GLU* 4.3 4.1 + - - +
58D ILE* 2.6 46.4 - - + +
59D ASP 5.7 0.7 - - - +
312D ILE* 3.6 8.5 - - + +
313D ALA* 2.3 30.6 + - - +
315D ALA* 1.3 76.8 - - - +
317D VAL* 1.3 64.4 + - - +
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Residues in contact with VAL 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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54D ARG* 3.7 32.7 - - - +
55D GLY* 4.8 4.3 - - - -
313D ALA 4.9 1.1 - - - +
314D GLU* 4.0 21.5 - - + +
315D ALA 3.1 0.6 - - - -
316D THR* 1.3 91.9 + - - +
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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