Contacts of the helix formed by residues 302 - 312 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31X ALA* 3.3 19.8 - - - +
34X GLU* 5.1 0.4 - - - -
271X SER* 4.3 0.2 + - - -
301X TYR* 1.3 74.5 - - - +
303X ARG* 1.3 83.5 + - - +
304X ALA 3.1 0.6 - - - +
305X LEU* 2.8 13.3 + - - -
306X GLN* 3.0 31.4 + - - +
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Residues in contact with ARG 303 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ALA* 4.6 6.9 - - - +
33X ASP* 5.7 1.0 + - - -
34X GLU* 5.2 6.7 - - - +
42X ARG* 3.1 45.1 - - - +
229X LYS* 6.1 1.2 - - - +
270X LEU* 5.3 4.4 - - - +
271X SER* 3.8 12.4 + - - +
272X GLY* 3.7 29.7 - - - +
273X GLY* 4.7 11.6 - - - +
274X MET 5.2 5.4 - - - +
276X GLU* 4.4 0.9 - - - +
300X SER 5.1 4.4 + - - -
301X TYR 5.0 0.2 - - - -
302X GLY* 1.3 89.9 - - - +
304X ALA* 1.3 59.2 + - - +
305X LEU 2.9 6.6 + - - -
306X GLN* 3.1 11.3 + - - +
307X ALA* 3.1 26.6 + - + +
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Residues in contact with ALA 304 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271X SER* 3.5 21.8 + - - +
274X MET 4.5 4.4 + - - +
276X GLU* 3.6 33.2 - - - +
279X ALA* 3.5 29.2 - - + -
301X TYR* 3.6 12.3 - - + -
302X GLY 3.1 1.2 + - - -
303X ARG* 1.3 76.7 - - - +
305X LEU* 1.3 57.6 + - - +
330X ARG* 4.1 2.4 - - - +
334X ASN* 3.8 12.6 + - - -
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Residues in contact with LEU 305 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ILE 4.3 4.0 - - - +
30X LEU* 4.2 17.9 - - + -
73X ILE* 3.7 26.7 - - + -
276X GLU* 4.7 2.5 - - - -
299X PHE* 3.8 14.8 - - + -
301X TYR* 4.1 23.8 - - + +
302X GLY 2.8 9.0 + - - +
304X ALA* 1.3 79.0 - - - +
306X GLN* 1.3 62.9 + - - +
326X ALA 4.5 0.5 - - - +
327X PHE* 3.5 34.1 - - + +
330X ARG* 3.4 47.2 - - + +
331X ALA* 3.6 7.0 - - - +
334X ASN* 3.9 6.7 - - - +
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Residues in contact with GLN 306 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LEU* 4.3 15.7 - - + +
31X ALA 2.9 23.2 + - - -
32X ALA* 4.8 3.4 - - - +
34X GLU* 2.6 34.3 + - - +
39X MET* 5.1 3.1 - - - +
42X ARG* 6.2 2.0 - - - -
58X PHE* 3.5 31.8 - - + -
59X ARG* 5.8 1.9 + - - +
62X LEU* 4.0 11.3 - - + +
302X GLY* 3.0 21.0 + - - +
303X ARG* 3.1 1.1 + - - -
305X LEU* 1.3 83.4 - - - +
307X ALA* 1.3 68.4 + - - +
308X SER 3.2 2.5 - - - -
309X ALA* 2.7 21.8 + - - -
310X LEU* 2.9 17.1 + - + -
327X PHE* 5.4 2.0 - - + -
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Residues in contact with ALA 307 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X ILE* 5.6 0.2 - - - +
276X GLU* 4.1 12.3 - - + +
303X ARG* 3.1 21.0 + - + +
306X GLN* 1.3 73.1 - - - +
308X SER* 1.3 57.7 + - - +
310X LEU* 3.2 9.5 + - - +
311X ALA* 3.0 28.5 + - - +
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Residues in contact with SER 308 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276X GLU* 2.7 33.1 + - - -
306X GLN 2.8 3.9 + - - -
307X ALA* 1.3 72.0 - - - +
309X ALA* 1.3 58.3 + - - -
310X LEU 3.0 4.7 - - - -
311X ALA* 3.1 6.4 + - - +
312X ALA* 3.0 29.5 + - - +
326X ALA* 3.0 29.6 + - - +
330X ARG* 3.9 2.0 - - - +
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Residues in contact with ALA 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X PHE* 3.3 12.0 - - + -
62X LEU* 4.6 1.1 - - + -
305X LEU 4.7 1.8 - - - +
306X GLN* 2.7 12.3 + - - +
308X SER* 1.3 76.6 + - - +
310X LEU* 1.3 57.2 + - - +
311X ALA 3.5 0.2 - - - -
312X ALA* 4.1 1.8 - - - -
313X TRP 3.7 1.0 + - - -
323X THR* 2.9 56.6 + - + +
326X ALA* 3.4 8.7 - - - +
327X PHE* 3.6 29.6 - - + +
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Residues in contact with LEU 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X MET* 4.1 21.5 - - + -
42X ARG* 4.1 26.9 - - + +
43X LEU* 4.5 5.8 - - + -
46X ILE* 3.0 38.5 - - + +
58X PHE* 3.3 44.4 - - + -
306X GLN* 2.9 19.3 + - + +
307X ALA* 3.5 13.0 - - - +
309X ALA* 1.3 79.0 - - - +
311X ALA* 1.3 61.4 + - - +
312X ALA 3.3 0.2 - - - -
313X TRP* 4.0 4.4 - - + +
314X GLY 3.3 12.1 + - - -
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Residues in contact with ALA 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X ILE* 3.5 15.6 - - + +
307X ALA 3.0 14.9 + - - +
308X SER* 3.8 6.7 - - - +
310X LEU* 1.3 75.6 - - - +
312X ALA* 1.3 64.7 + - - +
313X TRP 3.2 1.0 + - - -
314X GLY* 3.7 9.2 + - - -
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Residues in contact with ALA 312 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308X SER 3.0 15.0 + - - +
309X ALA* 4.2 2.7 - - - +
310X LEU 3.3 0.2 - - - -
311X ALA* 1.3 80.0 - - - +
313X TRP* 1.3 59.1 + - - +
316X LYS* 5.6 0.2 + - - -
319X ASN* 3.4 21.7 + - - +
322X ALA* 3.7 26.4 - - + +
323X THR* 3.1 14.6 + - - +
326X ALA* 4.7 3.4 - - + -
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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