Contacts of the helix formed by residues 303 - 315 (chain G) in PDB entry 1XFB
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 303 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ALA* 3.5 21.1 - - - +
35G GLU* 4.8 1.3 - - - -
43G ARG* 4.2 6.1 - - - -
272G SER* 3.6 7.2 + - - -
301G SER 4.1 1.0 + - - -
302G TYR* 1.3 75.1 - - - +
304G ARG* 1.3 62.9 + - - +
305G ALA 3.3 0.2 - - - -
306G LEU* 3.4 6.4 + - - +
307G GLN* 2.9 29.3 + - - +
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Residues in contact with ARG 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ARG* 2.8 67.2 - - - +
46G GLN* 2.6 35.6 + - - +
272G SER* 4.0 5.6 + - - +
273G GLY 5.4 5.8 - - - +
275G GLN 5.7 4.9 - - - +
303G GLY* 1.3 69.3 - - - +
305G ALA* 1.3 54.5 + - - +
306G LEU 2.7 16.7 + - - -
307G GLN* 2.8 3.0 + - + -
308G ALA* 2.8 47.7 + - + +
311G LEU* 5.3 5.6 - - + +
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Residues in contact with ALA 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G SER* 3.2 32.0 + - - -
275G GLN 4.8 5.2 + - - +
276G SER 4.6 1.6 - - - +
277G GLU* 3.5 29.8 - - - +
280G ALA* 3.8 13.9 - - + -
302G TYR* 3.4 17.7 - - + -
303G GLY 3.3 0.6 - - - -
304G ARG* 1.3 76.1 - - - +
306G LEU* 1.3 57.2 + - - +
331G ARG* 3.6 15.8 + - - +
335G ASN* 4.0 4.2 + - - -
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Residues in contact with LEU 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ILE 3.7 15.5 - - - +
31G LEU* 3.7 32.5 - - + -
74G ILE* 4.7 2.2 - - + -
277G GLU* 4.0 6.8 - - - +
300G PHE* 3.8 14.6 - - + -
302G TYR* 3.7 23.1 - - + +
303G GLY 3.4 8.6 + - - +
304G ARG 2.7 5.7 + - - -
305G ALA* 1.3 76.7 - - - +
307G GLN* 1.3 58.6 + - - +
308G ALA 3.7 0.7 - - - -
310G ALA* 4.4 0.7 - - - +
328G PHE* 3.6 32.1 - - + -
331G ARG* 3.7 6.1 - - + +
332G ALA* 3.6 38.4 - - + +
335G ASN* 3.7 17.3 - - - +
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Residues in contact with GLN 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.8 16.5 - - + +
32G ALA 3.3 15.6 + - - -
33G ALA* 4.2 1.0 - - - +
35G GLU* 3.3 27.3 + - - +
40G MET* 5.6 0.2 - - - +
43G ARG* 4.2 5.1 + - - +
59G TYR* 2.7 45.5 + - - +
60G ARG* 4.8 0.3 + - - -
63G LEU* 3.6 21.5 - - + +
303G GLY 2.9 21.8 + - - +
304G ARG* 2.8 6.6 + - + -
306G LEU* 1.3 81.1 - - + +
308G ALA* 1.3 59.7 + - - +
309G SER 3.6 1.1 - - - -
310G ALA* 3.8 9.0 - - + -
311G LEU* 2.8 33.4 + - + +
328G PHE* 5.5 0.2 - - + -
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Residues in contact with ALA 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G GLU* 3.3 20.4 + - + +
304G ARG* 2.8 39.6 + - + +
307G GLN* 1.3 73.7 - - - +
309G SER* 1.3 59.3 + - - +
311G LEU* 3.5 6.0 - - - +
312G ASN* 2.9 30.2 + - - +
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Residues in contact with SER 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G GLU* 2.8 28.1 + - - -
308G ALA* 1.3 79.0 - - - +
310G ALA* 1.3 57.9 + - - +
312G ASN* 3.1 9.9 + - - +
313G ALA* 2.8 32.1 + - - +
327G GLU* 3.1 28.5 + - - +
331G ARG* 4.0 8.5 - - - +
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Residues in contact with ALA 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G TYR* 4.8 2.9 - - + +
63G LEU* 4.6 7.0 - - + -
277G GLU* 4.4 0.2 + - - -
306G LEU 4.4 0.2 - - - +
307G GLN* 3.5 19.0 + - + +
308G ALA 3.1 0.6 - - - -
309G SER* 1.3 82.7 + - - +
311G LEU* 1.3 61.7 + - - +
313G ALA* 3.2 0.5 + - - +
314G TRP* 3.0 19.9 + - - +
324G ALA* 3.2 29.7 - - + +
327G GLU* 3.5 11.4 - - - -
328G PHE* 3.8 24.0 - - + +
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Residues in contact with LEU 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G MET* 4.9 0.9 - - + -
43G ARG* 4.0 39.5 - - + +
44G LEU* 4.4 4.9 - - + -
46G GLN* 6.2 0.2 - - - +
47G ILE* 3.6 39.0 - - + +
59G TYR* 3.3 49.1 + - + +
304G ARG* 5.3 4.9 - - + +
307G GLN* 2.8 22.4 + - + +
308G ALA* 3.5 4.7 - - - +
310G ALA* 1.3 75.2 - - - +
312G ASN* 1.3 61.9 + - - +
314G TRP* 3.8 5.0 - - + +
315G ARG 3.1 19.4 + - - -
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Residues in contact with ASN 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ILE* 4.5 7.1 - - - +
308G ALA 2.9 17.2 + - - +
309G SER* 3.1 10.7 + - - +
311G LEU* 1.3 79.0 - - - +
313G ALA* 1.3 59.4 + - - +
315G ARG* 2.8 51.7 + - - +
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Residues in contact with ALA 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G SER 2.8 16.2 + - - +
310G ALA* 3.5 4.7 - - - +
312G ASN* 1.3 76.9 - - - +
314G TRP* 1.3 69.3 + - - +
315G ARG* 3.2 3.6 + - - +
320G ASN* 3.3 19.2 - - - +
323G ALA* 4.4 10.5 - - + +
324G ALA* 3.8 18.2 - - - +
327G GLU* 4.7 9.0 - - + -
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Residues in contact with TRP 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 3.8 19.5 - - + -
47G ILE* 3.7 15.3 - - + -
49G VAL* 4.1 12.3 - - + -
55G ASN* 3.5 21.8 - - + -
58G LEU* 4.0 16.9 + - + +
59G TYR* 3.6 40.4 - + + -
62G VAL* 3.9 23.5 - - + +
310G ALA 3.0 8.8 + - - +
311G LEU* 3.5 4.2 + - + +
313G ALA* 1.3 78.5 - - - +
315G ARG* 1.3 62.9 + - - +
316G GLY* 2.9 38.4 + - - -
317G GLN 2.9 37.4 + - - -
318G ARG* 4.8 2.2 - - - +
320G ASN* 3.3 14.9 - - - +
321G ALA* 4.2 9.7 - - - +
324G ALA* 3.5 18.9 - - + +
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Residues in contact with ARG 315 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLN 4.5 5.7 + - - -
47G ILE* 3.8 48.2 + - - +
49G VAL* 4.1 7.5 - - - +
311G LEU 3.1 13.3 + - - -
312G ASN* 2.8 42.6 + - - +
313G ALA 3.5 7.6 - - - +
314G TRP* 1.3 79.4 - - - +
316G GLY* 1.3 55.6 + - - +
317G GLN* 3.2 15.8 + - + +
320G ASN* 4.4 5.4 - - - +
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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