Contacts of the helix formed by residues 320 - 339 (chain C) 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 ASN 320 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ALA 3.3 20.0 - - - +
314C TRP* 3.3 24.9 - - - +
315C ARG* 4.4 4.5 - - - +
317C GLN* 3.2 18.9 + - - +
319C ASP* 1.3 88.7 + - - +
321C ALA* 1.3 64.9 + - - +
322C GLY 3.4 0.7 - - - -
323C ALA* 3.1 12.7 + - + +
324C ALA* 2.8 23.4 + - - +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.6 12.5 - - + +
314C TRP* 4.2 13.0 - - + +
317C GLN 3.4 5.1 + - - +
318C ARG* 3.2 22.2 - - + +
319C ASP 2.9 2.6 + - - +
320C ASN* 1.3 75.9 - - - +
322C GLY* 1.3 57.3 + - - +
324C ALA* 3.1 5.1 + - - +
325C THR* 2.9 33.3 + - - -
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Residues in contact with GLY 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASP 3.8 5.0 + - - -
320C ASN 3.4 0.4 - - - -
321C ALA* 1.3 78.8 - - - +
323C ALA* 1.3 56.3 + - - +
325C THR* 3.3 9.7 + - - -
326C GLU* 3.0 33.4 + - - +
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Residues in contact with ALA 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ALA* 4.4 10.5 - - + -
319C ASP 4.8 1.0 + - - +
320C ASN* 3.1 17.5 + - + +
322C GLY* 1.3 72.1 - - - +
324C ALA* 1.3 66.4 + - - +
326C GLU* 3.0 10.9 + - - +
327C GLU* 2.9 26.1 + - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.3 18.6 - - + -
310C ALA* 3.2 31.2 - - - +
313C ALA* 3.8 7.3 - - - +
314C TRP* 3.5 16.8 - - + +
320C ASN 2.8 12.2 + - - +
321C ALA 3.3 9.6 - - - +
323C ALA* 1.3 76.4 - - - +
325C THR* 1.3 63.1 + - - +
327C GLU* 3.0 14.2 + - - +
328C PHE* 3.1 9.7 + - - +
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Residues in contact with THR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 2.8 32.5 + - - +
63C LEU 4.9 0.2 - - - +
65C SER* 3.8 9.6 + - - +
66C ALA* 3.6 30.5 - - + +
67C ASP 5.1 0.2 - - - +
321C ALA 2.9 15.8 + - - -
322C GLY* 3.5 12.1 - - - -
324C ALA* 1.3 74.9 - - - +
326C GLU* 1.3 60.0 + - - +
328C PHE* 3.4 5.7 + - + +
329C ILE* 3.0 41.5 + - + +
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 4.7 0.2 - - - +
69C ARG* 2.5 44.1 + - - -
322C GLY 3.0 19.4 + - - +
323C ALA* 3.0 11.9 + - - +
325C THR* 1.3 77.1 - - - +
327C GLU* 1.3 70.3 + - - +
328C PHE 3.1 0.2 + - - -
329C ILE* 3.2 7.1 + - - +
330C LYS* 2.8 29.5 + - - +
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Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C SER* 3.1 38.0 - - - +
310C ALA* 3.5 15.3 - - - +
313C ALA* 4.7 6.4 - - + +
323C ALA* 2.9 16.1 + - - +
324C ALA* 3.0 9.4 + - - +
326C GLU* 1.3 79.8 - - - +
328C PHE* 1.3 62.5 + - - +
330C LYS* 3.4 29.6 + - + +
331C ARG* 3.2 28.4 + - - +
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Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 3.7 39.5 - - + -
62C VAL 5.0 0.9 - - - -
63C LEU* 3.4 47.6 - - + -
66C ALA* 3.9 17.5 - - + -
70C VAL* 4.0 19.1 - - + -
74C ILE* 4.7 3.8 - - + -
306C LEU* 3.6 30.3 - - + -
310C ALA* 3.8 12.7 - - + +
324C ALA 3.1 10.4 + - - +
325C THR* 3.5 8.5 - - - +
326C GLU 3.1 0.2 - - - -
327C GLU* 1.3 72.2 - - - +
329C ILE* 1.3 72.5 + - - +
330C LYS 2.9 1.8 + - - -
331C ARG* 2.9 4.0 + - - +
332C ALA* 2.8 35.3 + - + -
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Residues in contact with ILE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA* 3.7 32.8 - - + -
67C ASP* 3.8 18.6 - - - +
69C ARG* 3.6 62.8 - - + +
70C VAL* 4.8 4.9 - - + +
325C THR* 3.0 24.0 + - + +
326C GLU* 3.7 6.1 - - - +
328C PHE* 1.3 76.7 - - + +
330C LYS* 1.3 62.6 + - - +
332C ALA* 3.6 7.6 - - - +
333C GLU* 2.9 30.6 + - + +
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 5.6 0.6 - - - +
326C GLU* 2.8 17.9 + - - +
327C GLU* 3.4 33.9 + - + +
328C PHE 2.9 0.2 + - - -
329C ILE* 1.3 76.6 - - - +
331C ARG* 1.3 67.0 + - + +
333C GLU* 3.0 12.6 + - - +
334C VAL* 2.8 30.1 + - + +
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Residues in contact with ARG 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLU* 2.8 68.6 + - - +
278C GLU* 2.5 29.5 + - - -
281C SER* 3.0 17.6 + - - -
305C ALA 3.6 3.5 + - - +
306C LEU* 3.7 20.6 - - + +
309C SER* 4.0 3.1 - - - +
327C GLU 3.2 16.2 - - - +
328C PHE 2.9 4.6 + - - +
330C LYS* 1.3 80.1 - - + +
332C ALA* 1.3 63.3 + - - +
334C VAL* 3.1 30.9 - - - +
335C ASN* 2.9 38.1 + - - +
343C TYR* 4.4 1.4 + - - -
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C VAL* 4.4 2.9 - - + -
73C CYS* 3.1 25.3 - - - +
74C ILE* 4.0 14.8 - - + -
300C PHE* 4.4 2.8 - - - -
306C LEU* 3.6 10.9 - - - +
328C PHE* 2.8 40.9 + - + +
329C ILE* 3.6 9.4 - - - +
331C ARG* 1.3 72.1 - - - +
333C GLU* 1.3 58.2 + - - +
335C ASN* 4.0 2.0 - - - +
336C GLY* 3.0 20.6 + - - -
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ARG* 3.2 28.3 + - - +
72C LYS* 2.7 42.1 + - - +
73C CYS* 3.7 13.1 - - - +
329C ILE* 2.9 30.2 + - + +
330C LYS* 3.5 7.3 - - - +
332C ALA* 1.3 75.6 - - - +
334C VAL* 1.3 66.6 + - - +
336C GLY* 3.0 11.4 + - - -
337C LEU* 3.0 17.8 + - + +
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Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C SER* 3.7 14.8 - - - +
330C LYS* 2.8 24.8 + - + +
331C ARG* 3.1 43.7 - - - +
333C GLU* 1.3 73.0 - - - +
335C ASN* 1.3 57.0 + - - +
337C LEU* 2.9 12.4 + - - +
338C ALA* 2.8 24.4 + - - +
343C TYR* 3.3 42.7 - - + +
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Residues in contact with ASN 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C SER* 2.7 31.9 + - - -
284C LEU* 4.0 2.2 - - + +
300C PHE* 3.5 29.1 - - + -
302C TYR* 3.5 24.5 + - - -
305C ALA 4.0 1.6 + - - -
306C LEU* 3.7 15.4 - - - +
331C ARG* 2.9 42.8 + - - +
334C VAL* 1.3 73.2 - - - +
336C GLY* 1.3 60.5 + - - +
338C ALA* 3.7 6.7 - - - +
339C ALA* 2.8 30.0 + - - +
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Residues in contact with GLY 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLY* 3.2 30.6 - - - -
73C CYS* 3.7 7.4 - - - -
300C PHE* 4.1 6.5 - - - -
332C ALA 3.0 13.4 + - - -
333C GLU 3.0 10.0 + - - -
335C ASN* 1.3 77.2 - - - +
337C LEU* 1.3 60.0 + - - +
339C ALA* 3.6 1.9 - - - +
340C GLN* 3.1 22.4 + - - +
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Residues in contact with LEU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C GLU 3.0 14.6 + - - +
334C VAL* 2.9 12.2 + - - +
336C GLY* 1.3 76.0 - - - +
338C ALA* 1.3 54.0 + - - +
339C ALA 2.9 4.5 - - - -
340C GLN* 2.7 31.4 + - - +
342C LYS* 3.2 52.5 + - + +
343C TYR* 3.8 21.8 - - + -
344C GLU 5.5 0.2 - - - +
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Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C SER* 3.3 28.9 - - - +
284C LEU* 3.6 10.1 - - + +
285C ASN* 3.2 30.8 - - + +
288C ASN* 2.9 16.5 + - - -
334C VAL 2.8 12.9 + - - +
335C ASN* 3.2 12.8 + - - +
337C LEU* 1.3 76.2 - - - +
339C ALA* 1.3 57.3 + - - +
340C GLN 2.9 3.0 + - - -
341C GLY 3.1 6.1 + - - -
343C TYR* 3.7 5.5 - - + +
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Residues in contact with ALA 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY* 4.3 11.2 + - - -
284C LEU* 4.1 4.5 - - - +
288C ASN* 3.2 22.9 + - - +
298C LEU 4.2 3.2 + - - +
299C THR* 3.8 32.2 - - + +
300C PHE* 4.4 4.5 - - + -
335C ASN 2.8 17.6 + - - +
336C GLY* 3.6 12.8 - - - +
337C LEU 2.9 0.8 - - - -
338C ALA* 1.3 75.4 - - - +
340C GLN* 1.3 59.4 + - - +
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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
------------------------------------------------------------
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