Contacts of the helix formed by residues 303 - 315 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H ALA* 3.5 21.3 - - - +
35H GLU* 4.8 1.3 - - - -
43H ARG* 4.2 6.1 - - - -
272H SER* 3.6 7.0 + - - -
301H SER 4.1 1.2 + - - -
302H TYR* 1.3 74.6 - - - +
304H ARG* 1.3 62.8 + - - +
305H ALA 3.3 0.2 - - - -
306H LEU* 3.4 6.4 + - - +
307H GLN* 2.9 28.8 + - - +
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Residues in contact with ARG 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ARG* 2.8 68.0 - - - +
46H GLN* 2.6 34.6 - - - +
272H SER* 4.0 5.4 + - - +
273H GLY 5.4 5.4 - - - +
275H GLN 5.7 5.2 - - - +
303H GLY* 1.3 69.3 - - - +
305H ALA* 1.3 54.3 + - - +
306H LEU 2.7 16.7 + - - -
307H GLN* 2.8 2.8 + - + -
308H ALA* 2.8 48.1 + - + +
311H LEU* 5.3 5.7 - - + +
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Residues in contact with ALA 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H SER* 3.2 31.5 + - - -
275H GLN 4.8 4.2 + - - +
276H SER 4.6 2.0 - - - +
277H GLU* 3.5 30.7 - - - +
280H ALA* 3.8 13.2 - - + -
302H TYR* 3.4 18.6 - - + -
303H GLY 3.3 0.8 - - - -
304H ARG* 1.3 76.3 - - - +
306H LEU* 1.3 57.3 + - - +
331H ARG* 3.6 15.2 + - - +
335H ASN* 4.0 5.0 + - - -
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Residues in contact with LEU 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ILE 3.7 14.8 - - - +
31H LEU* 3.7 31.9 - - + -
74H ILE* 4.7 2.5 - - + -
277H GLU* 4.0 6.3 - - - +
300H PHE* 3.8 15.3 - - + -
302H TYR* 3.7 23.8 - - + +
303H GLY 3.4 9.1 + - - +
304H ARG 2.7 5.3 + - - -
305H ALA* 1.3 77.1 - - - +
307H GLN* 1.3 58.0 + - - +
308H ALA 3.7 1.3 - - - -
310H ALA* 4.4 0.7 - - - +
328H PHE* 3.6 31.7 - - + -
331H ARG* 3.7 6.6 - - + +
332H ALA* 3.6 39.3 - - + +
335H ASN* 3.7 15.9 - - - +
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Residues in contact with GLN 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.8 16.7 - - + +
32H ALA 3.3 15.4 + - - -
33H ALA* 4.2 0.8 - - - +
35H GLU* 3.3 27.4 + - - +
40H MET* 5.6 0.3 - - - +
43H ARG* 4.2 4.7 + - - +
59H TYR* 2.7 44.7 + - - +
60H ARG* 4.8 0.2 + - - -
63H LEU* 3.6 21.3 - - + +
303H GLY 2.9 21.6 + - - +
304H ARG* 2.8 6.6 + - + -
306H LEU* 1.3 81.1 - - - +
308H ALA* 1.3 57.6 + - - +
309H SER 3.6 1.1 - - - -
310H ALA* 3.8 8.1 - - + -
311H LEU* 2.8 33.9 + - + +
328H PHE* 5.5 0.4 - - + -
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Residues in contact with ALA 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H GLU* 3.3 21.0 + - + +
304H ARG* 2.8 38.8 + - + +
307H GLN* 1.3 73.7 - - - +
309H SER* 1.3 60.3 + - - +
311H LEU* 3.1 5.5 + - - +
312H ASN* 2.9 29.4 + - - +
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Residues in contact with SER 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H GLU* 2.8 28.7 + - - -
308H ALA* 1.3 79.0 - - - +
310H ALA* 1.3 58.3 + - - +
312H ASN* 3.1 9.4 + - - +
313H ALA* 2.8 31.7 + - - +
327H GLU* 3.1 27.3 + - - +
331H ARG* 4.0 8.5 - - - +
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Residues in contact with ALA 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H TYR* 4.8 2.0 - - + +
62H VAL* 5.7 0.2 - - + -
63H LEU* 4.6 6.5 - - + -
277H GLU* 4.4 0.2 + - - -
307H GLN* 3.7 20.1 - - + +
308H ALA 3.1 0.4 - - - -
309H SER* 1.3 82.3 + - - +
311H LEU* 1.3 61.9 + - - +
313H ALA* 3.5 0.3 - - - +
314H TRP* 3.0 20.0 + - - +
324H ALA* 3.2 31.1 - - + +
327H GLU* 3.5 11.4 - - - -
328H PHE* 3.8 22.9 - - + +
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Residues in contact with LEU 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H MET* 4.9 0.7 - - + -
43H ARG* 4.0 39.9 - - + +
44H LEU* 4.4 4.9 - - + -
47H ILE* 3.6 40.0 - - + +
59H TYR* 3.3 48.6 + - + +
304H ARG* 5.3 5.6 - - + +
307H GLN* 2.8 21.6 + - + +
308H ALA* 3.5 4.7 - - - +
310H ALA* 1.3 77.0 - - - +
312H ASN* 1.3 63.7 - - - +
314H TRP* 3.8 4.4 - - + +
315H ARG 3.1 19.6 + - - -
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Residues in contact with ASN 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 4.5 6.5 - - - +
308H ALA 2.9 17.2 + - - +
309H SER* 3.4 10.8 - - - +
311H LEU* 1.3 79.3 - - - +
313H ALA* 1.3 58.8 + - - +
315H ARG* 2.8 51.5 + - - +
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Residues in contact with ALA 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H SER 2.8 16.2 + - - +
310H ALA* 3.5 3.8 - - - +
312H ASN* 1.3 77.0 - - - +
314H TRP* 1.3 69.0 + - - +
315H ARG* 3.2 3.5 + - - +
320H ASN* 3.3 19.2 - - - +
323H ALA* 4.4 11.4 - - + +
324H ALA* 3.8 19.3 - - - +
327H GLU* 4.7 8.1 - - + +
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Residues in contact with TRP 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU* 3.8 20.0 - - + -
47H ILE* 3.7 15.3 - - + -
49H VAL* 4.1 11.9 - - + -
55H ASN* 3.5 22.2 - - - -
58H LEU* 4.0 16.7 + - + +
59H TYR* 3.6 40.8 - + + -
62H VAL* 3.9 23.1 - - + +
310H ALA 3.0 8.8 + - - +
311H LEU* 3.8 3.4 - - + +
313H ALA* 1.3 78.9 - - - +
315H ARG* 1.3 62.0 + - - +
316H GLY* 2.9 38.6 + - - -
317H GLN 2.9 38.3 + - - -
318H ARG* 5.0 2.2 - - - +
320H ASN* 3.3 14.9 - - - +
321H ALA* 4.2 9.5 - - - +
324H ALA* 3.5 20.3 - - + +
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Residues in contact with ARG 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLN 4.5 4.6 + - - -
47H ILE* 3.8 47.6 + - - +
49H VAL* 4.1 7.9 - - - +
311H LEU 3.1 12.9 + - - -
312H ASN* 2.8 41.6 + - - +
313H ALA 3.5 7.6 - - - +
314H TRP* 1.3 80.0 - - - +
316H GLY* 1.3 56.9 + - - +
317H GLN* 3.2 15.7 + - + -
320H ASN* 4.4 6.3 - - - +
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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
------------------------------------------------------------
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