Contacts of the helix formed by residues 302 - 312 (chain D) in PDB entry 1XDM
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 302 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.7 1.6 - - - -
31D ALA 3.3 20.9 - - - -
34D GLU* 5.8 0.7 - - - -
301D TYR* 1.3 75.1 - - - +
303D ARG* 1.3 79.6 - - - +
304D ALA 3.1 0.7 - - - -
305D LEU* 3.1 1.8 + - - -
306D GLN* 2.8 41.4 + - - +
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Residues in contact with ARG 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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31D ALA* 4.9 6.5 + - - +
34D GLU* 5.5 8.3 - - - +
42D ARG* 4.3 32.7 - - - +
146D LYS* 6.1 0.8 - - - +
148D ARG* 5.5 6.7 - - - +
270D LEU* 5.3 8.2 - - - +
271D SER* 2.7 29.3 + - - +
272D GLY* 4.0 16.2 - - - +
273D GLY* 4.4 8.5 - - - +
274D MET 5.5 4.7 - - - +
276D GLU* 3.7 0.8 - - - +
301D TYR* 4.7 0.9 - - - -
302D GLY* 1.3 87.7 - - - +
304D ALA* 1.3 57.3 + - - +
305D LEU 3.1 0.2 - - - -
306D GLN* 4.6 2.0 - - - +
307D ALA* 3.0 37.7 + - + +
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Residues in contact with ALA 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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271D SER* 3.7 16.4 + - - -
274D MET 4.7 2.0 + - - +
276D GLU* 2.9 48.2 - - - +
279D ALA* 3.9 4.0 - - + -
301D TYR* 3.6 29.8 - - + -
302D GLY 3.1 1.6 - - - +
303D ARG* 1.3 76.7 - - - +
305D LEU* 1.3 59.5 + - - +
330D ARG* 3.4 16.1 + - - +
334D ASN* 4.4 1.1 + - - +
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Residues in contact with LEU 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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30D LEU* 3.4 43.3 - - + -
73D ILE* 4.2 4.9 - - + -
276D GLU* 3.7 3.8 - - - +
299D PHE* 4.0 17.9 - - + -
301D TYR* 3.6 21.8 - - + +
302D GLY 3.1 3.2 + - - +
303D ARG 3.1 0.2 - - - -
304D ALA* 1.3 79.0 - - - +
306D GLN* 1.3 66.1 + - - +
307D ALA 3.5 0.9 - - - -
309D ALA* 4.1 3.3 + - - +
327D PHE* 3.8 29.2 - - + -
330D ARG* 3.5 8.3 - - + +
331D ALA* 3.2 40.6 - - + +
334D ASN* 3.5 20.6 - - - +
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Residues in contact with GLN 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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30D LEU* 4.1 10.1 - - + +
31D ALA 3.1 24.7 + - - -
32D ALA* 3.6 12.0 - - - +
34D GLU* 3.0 29.8 + - - +
39D MET* 4.6 2.9 - - - +
58D PHE* 3.7 23.3 - - + -
59D ARG* 5.3 1.2 + - - -
62D LEU* 3.9 23.7 - - + +
302D GLY* 2.8 21.1 + - - +
303D ARG* 4.8 1.6 - - - +
305D LEU* 1.3 81.2 - - - +
307D ALA* 1.3 55.1 + - - +
308D SER 3.7 0.4 - - - -
309D ALA* 4.0 5.2 - - - -
310D LEU* 2.7 43.2 + - + +
327D PHE* 5.4 0.7 - - + -
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Residues in contact with ALA 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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276D GLU* 2.9 25.7 + - + +
303D ARG* 3.0 18.6 + - + +
306D GLN* 1.3 80.7 - - - +
308D SER* 1.3 64.0 + - - +
310D LEU* 3.4 8.6 - - - +
311D ALA* 3.0 20.4 + - - +
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Residues in contact with SER 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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276D GLU* 2.6 24.5 + - - -
307D ALA* 1.3 74.4 - - - +
309D ALA* 1.3 56.2 + - - +
311D ALA* 3.4 7.0 + - - +
312D ALA* 2.7 36.9 + - - +
326D ALA* 3.6 12.1 - - - +
329D LYS* 6.0 1.2 - - - +
330D ARG* 3.8 13.5 - - - +
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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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62D LEU* 4.5 5.4 - - + -
305D LEU 4.1 6.0 + - - +
306D GLN* 3.7 8.2 - - - +
307D ALA 3.2 0.4 - - - -
308D SER* 1.3 77.9 + - - +
310D LEU* 1.3 64.7 + - - +
312D ALA* 3.1 11.8 + - - +
313D TRP 3.3 0.2 + - - -
323D THR* 3.1 48.1 + - + +
326D ALA* 3.2 12.9 - - - +
327D PHE* 3.5 25.4 - - + +
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Residues in contact with LEU 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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39D MET* 4.8 10.5 - - + -
42D ARG* 4.0 24.2 - - + +
43D LEU* 5.0 5.8 - - + -
45D ARG* 5.8 0.7 - - + -
46D ILE* 3.3 48.1 - - + +
58D PHE* 3.4 42.9 - - + -
306D GLN* 2.7 27.0 + - + +
307D ALA* 3.4 6.7 - - - +
309D ALA* 1.3 72.4 - - - +
311D ALA* 1.3 53.6 + - + +
313D TRP* 2.8 23.9 + - - +
314D GLY* 2.8 13.3 + - - -
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Residues in contact with ALA 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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46D ILE* 3.7 20.2 - - + -
307D ALA 3.0 15.6 + - - +
308D SER* 3.8 7.0 - - - +
310D LEU* 1.3 70.9 - - + +
312D ALA* 1.3 58.7 + - - +
313D TRP 2.8 12.4 + - - -
314D GLY* 3.4 9.7 + - - -
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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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308D SER 2.7 23.2 + - - +
309D ALA 3.1 6.9 + - - +
311D ALA* 1.3 71.4 - - - +
313D TRP* 1.3 55.0 + - - +
319D ASN* 2.9 28.4 + - - +
322D ALA* 3.2 36.3 - - + +
323D THR* 3.5 2.7 - - - -
326D ALA* 4.7 2.2 - - + -
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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