Contacts of the helix formed by residues 302 - 312 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30W LEU* 4.7 1.6 - - - -
31W ALA 3.3 21.1 - - - -
301W TYR* 1.3 76.8 - - - +
303W ARG* 1.3 78.9 + - - +
304W ALA 3.2 0.6 - - - +
305W LEU* 3.1 2.0 + - - +
306W GLN* 2.8 42.3 + - - +
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Residues in contact with ARG 303 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31W ALA* 4.8 6.9 + - - +
34W GLU* 5.5 8.3 - - - +
42W ARG* 4.3 32.9 - - - +
146W LYS* 6.0 1.4 - - - +
148W ARG* 5.6 7.3 - - - +
229W LYS* 5.7 4.6 - - - +
270W LEU* 5.3 8.7 - - - +
271W SER* 2.7 29.3 + - - +
272W GLY* 4.0 15.8 - - - +
273W GLY* 4.4 8.3 - - - +
274W MET 5.5 4.9 - - - +
276W GLU* 3.7 1.0 - - - +
301W TYR 5.5 0.2 - - - -
302W GLY* 1.3 90.4 - - - +
304W ALA* 1.3 55.5 + - - +
306W GLN* 4.6 2.2 - - - +
307W ALA* 3.0 38.3 + - + +
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Residues in contact with ALA 304 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271W SER* 3.6 19.0 + - - -
274W MET 4.7 1.5 + - - +
276W GLU* 2.9 39.6 - - - +
279W ALA* 3.9 12.1 - - + -
301W TYR* 3.6 29.8 - - + -
302W GLY 3.2 2.0 - - - +
303W ARG* 1.3 76.2 - - - +
305W LEU* 1.3 58.9 + - - +
330W ARG* 3.4 16.1 + - - +
334W ASN* 4.4 1.0 + - - +
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Residues in contact with LEU 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 3.4 42.8 - - + -
73W ILE* 4.2 6.1 - - + -
276W GLU* 3.7 4.1 - - - +
299W PHE* 4.0 17.5 - - + -
301W TYR* 3.7 21.3 - - + +
302W GLY 3.1 3.4 + - - +
303W ARG 3.1 0.2 - - - -
304W ALA* 1.3 78.1 - - - +
306W GLN* 1.3 63.2 + - - +
307W ALA 3.5 0.9 - - - -
309W ALA* 4.1 3.1 + - - +
327W PHE* 3.7 28.8 - - + -
330W ARG* 3.6 8.0 - - + +
331W ALA* 3.1 39.9 - - + +
334W ASN* 3.5 20.9 - - + +
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Residues in contact with GLN 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 4.1 9.5 - - + +
31W ALA 3.1 25.7 + - - -
32W ALA* 3.5 13.0 - - - +
34W GLU* 2.9 28.5 + - - +
39W MET* 4.5 3.3 - - - +
58W PHE* 3.7 23.6 - - + -
59W ARG* 5.3 1.6 + - - +
62W LEU* 3.8 24.1 - - + +
302W GLY* 2.8 20.3 + - - +
303W ARG* 4.9 1.8 - - - -
305W LEU* 1.3 80.7 - - - +
307W ALA* 1.3 55.2 + - - +
308W SER 3.7 0.4 - - - -
309W ALA* 4.0 5.4 - - - -
310W LEU* 2.7 43.2 + - + +
327W PHE* 5.3 0.4 - - + -
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Residues in contact with ALA 307 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276W GLU* 2.9 25.6 + - + +
303W ARG* 3.0 18.9 + - + +
306W GLN* 1.3 80.9 - - - +
308W SER* 1.3 63.7 + - - +
310W LEU* 3.4 8.8 - - - +
311W ALA* 3.0 20.8 + - - +
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Residues in contact with SER 308 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276W GLU* 2.7 24.5 + - - -
305W LEU 4.9 0.2 + - - -
307W ALA* 1.3 73.2 - - - +
309W ALA* 1.3 55.5 + - - +
311W ALA* 3.3 6.6 + - - +
312W ALA* 2.7 37.4 + - - +
326W ALA* 3.5 13.4 - - - +
329W LYS* 6.0 1.7 - - - +
330W ARG* 3.8 13.3 - - - +
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Residues in contact with ALA 309 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62W LEU* 4.5 4.9 - - + -
305W LEU 4.1 6.2 + - - +
306W GLN* 3.4 9.1 + - - +
307W ALA 3.3 0.4 - - - -
308W SER* 1.3 77.7 + - - +
310W LEU* 1.3 64.3 + - - +
312W ALA 3.1 9.4 + - - -
323W THR* 3.1 48.6 + - + +
326W ALA* 3.2 12.9 - - - +
327W PHE* 3.4 26.0 - - + +
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Residues in contact with LEU 310 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W MET* 4.7 10.8 - - + -
42W ARG* 4.0 24.9 - - + +
43W LEU* 4.9 6.7 - - + -
45W ARG* 5.8 0.7 - - + -
46W ILE* 3.3 47.5 - - + +
58W PHE* 3.4 41.9 - - + -
306W GLN* 2.7 26.3 + - + +
307W ALA* 3.4 7.2 - - - +
309W ALA* 1.3 73.0 - - - +
311W ALA* 1.3 52.5 + - + +
313W TRP* 2.8 24.5 + - + +
314W GLY* 2.8 13.5 + - - -
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Residues in contact with ALA 311 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46W ILE* 3.7 21.5 - - + +
307W ALA 3.0 15.4 + - - +
308W SER* 3.7 7.4 - - - +
310W LEU* 1.3 71.9 - - + +
312W ALA* 1.3 58.4 + - - +
313W TRP 2.8 12.3 + - - -
314W GLY* 3.4 9.4 + - - -
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Residues in contact with ALA 312 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308W SER 2.7 22.1 + - - +
309W ALA* 3.1 7.4 + - - +
311W ALA* 1.3 71.2 - - - +
313W TRP* 1.3 54.4 + - - +
319W ASN* 3.0 24.0 + - - +
322W ALA* 3.2 42.2 - - + +
323W THR* 3.4 2.9 + - - -
326W ALA* 4.6 2.5 - - + -
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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