Contacts of the helix formed by residues 320 - 339 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F ALA 3.3 20.0 - - - +
314F TRP* 3.3 25.3 - - - +
315F ARG* 4.4 4.9 - - - +
317F GLN* 3.2 18.2 + - - +
319F ASP* 1.3 90.0 + - - +
321F ALA* 1.3 63.9 + - - +
322F GLY 3.4 0.7 - - - -
323F ALA* 3.1 12.9 + - + +
324F ALA* 2.8 23.0 + - - +
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Residues in contact with ALA 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 3.6 13.4 - - + +
314F TRP* 4.2 12.3 - - + +
317F GLN 3.4 5.1 + - - +
318F ARG* 3.2 22.0 - - + +
319F ASP 2.9 2.4 + - - +
320F ASN* 1.3 76.0 - - - +
322F GLY* 1.3 57.3 + - - +
324F ALA* 3.1 5.2 + - - +
325F THR* 2.9 33.8 + - - +
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Residues in contact with GLY 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ASP 3.8 5.2 + - - -
320F ASN 3.4 0.6 - - - -
321F ALA* 1.3 78.7 - - - +
323F ALA* 1.3 56.8 + - - +
325F THR* 3.3 9.0 + - - -
326F GLU* 3.0 33.7 + - - +
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Residues in contact with ALA 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F ALA* 4.4 11.0 - - + -
319F ASP 4.8 1.2 + - - +
320F ASN* 3.1 17.3 + - + +
322F GLY* 1.3 72.1 - - - +
324F ALA* 1.3 67.3 + - - +
326F GLU* 3.0 10.9 + - - +
327F GLU* 2.9 26.1 + - - +
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Residues in contact with ALA 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 3.3 19.1 - - + -
310F ALA* 3.2 32.5 - - - +
313F ALA* 3.8 7.1 - - - +
314F TRP* 3.5 15.9 - - + +
320F ASN 2.8 12.6 + - - +
321F ALA 3.3 9.4 - - - +
323F ALA* 1.3 76.0 - - - +
325F THR* 1.3 63.5 + - - +
327F GLU* 3.0 14.4 + - - +
328F PHE 3.1 9.4 + - - -
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Residues in contact with THR 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 2.8 33.3 + - - +
63F LEU 4.9 0.2 - - - +
65F SER* 3.8 10.1 + - - +
66F ALA* 3.6 30.1 - - + +
67F ASP 5.1 0.4 - - - +
321F ALA* 2.9 15.6 + - - +
322F GLY* 3.5 11.7 - - - -
323F ALA 3.2 0.2 - - - -
324F ALA* 1.3 75.3 - - - +
326F GLU* 1.3 60.1 + - - +
328F PHE* 3.4 5.4 + - + +
329F ILE* 3.0 41.0 + - + +
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Residues in contact with GLU 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ARG* 2.5 44.3 + - - -
322F GLY 3.0 19.4 + - - +
323F ALA* 3.0 12.3 + - - +
325F THR* 1.3 76.2 - - - +
327F GLU* 1.3 70.0 + - - +
329F ILE* 3.2 6.7 + - - +
330F LYS* 2.8 30.0 + - - +
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Residues in contact with GLU 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F SER* 3.1 38.2 - - - +
310F ALA* 3.5 15.7 - - - +
313F ALA* 4.7 6.5 - - + +
323F ALA* 2.9 16.3 + - - +
324F ALA* 3.0 9.8 + - - +
326F GLU* 1.3 78.4 - - - +
328F PHE* 1.3 61.1 + - - +
330F LYS* 3.4 29.9 + - - +
331F ARG* 3.2 28.7 + - - +
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Residues in contact with PHE 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.7 38.6 - - + -
62F VAL 5.0 1.1 - - - -
63F LEU* 3.4 47.3 - - + -
66F ALA* 3.9 17.7 - - + -
70F VAL* 4.0 17.3 - - + -
74F ILE* 4.7 4.5 - - + -
306F LEU* 3.6 30.3 - - + -
307F GLN* 5.4 0.2 - - - -
310F ALA* 3.8 12.5 - - + +
324F ALA 3.1 10.0 + - - +
325F THR* 3.5 8.3 - - - +
326F GLU 3.1 0.4 - - - -
327F GLU* 1.3 72.2 - - - +
329F ILE* 1.3 72.3 + - - +
330F LYS 2.9 2.6 + - - -
331F ARG* 2.9 3.8 + - - +
332F ALA* 2.8 34.6 + - + -
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Residues in contact with ILE 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ALA* 3.7 32.8 - - + -
67F ASP* 3.8 19.1 - - - +
69F ARG* 3.6 60.1 - - + +
70F VAL* 4.8 4.3 - - + +
325F THR* 3.0 24.4 + - + +
326F GLU* 3.7 6.7 - - - +
328F PHE* 1.3 76.1 - - + +
330F LYS* 1.3 62.2 + - - +
332F ALA* 3.6 7.6 - - + +
333F GLU* 2.9 31.6 + - + +
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Residues in contact with LYS 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ARG* 5.6 1.1 - - - +
326F GLU* 2.8 18.9 + - - +
327F GLU* 3.4 33.5 + - - +
328F PHE 2.9 0.2 + - - -
329F ILE* 1.3 76.0 - - - +
331F ARG* 1.3 67.7 + - + +
333F GLU* 3.0 11.9 + - - +
334F VAL* 2.8 30.0 + - + +
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Residues in contact with ARG 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F GLU* 2.8 68.0 + - - +
278F GLU* 2.5 30.4 + - - -
281F SER* 3.0 17.2 + - - -
305F ALA 3.6 3.9 + - - +
306F LEU* 3.7 20.0 - - + +
309F SER* 4.0 3.1 - - - +
327F GLU* 3.2 16.8 - - + +
328F PHE 2.9 4.4 + - - +
330F LYS* 1.3 80.7 - - + +
332F ALA* 1.3 63.1 + - - +
334F VAL* 3.1 31.6 - - - +
335F ASN* 2.9 38.6 + - - +
343F TYR* 4.4 1.0 + - - -
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Residues in contact with ALA 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL* 4.4 2.9 - - + -
73F CYS* 3.1 25.0 - - - +
74F ILE* 4.0 14.6 - - + -
300F PHE* 4.4 3.2 - - - -
306F LEU* 3.6 11.8 - - - +
328F PHE* 2.8 40.1 + - + +
329F ILE* 3.6 9.2 - - - +
331F ARG* 1.3 71.9 - - - +
333F GLU* 1.3 58.0 + - - +
335F ASN* 4.0 1.2 - - - +
336F GLY 3.0 20.4 + - - -
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Residues in contact with GLU 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ARG* 3.2 27.1 + - - +
72F LYS* 2.7 42.4 + - - +
73F CYS* 3.7 13.4 - - - +
329F ILE* 2.9 30.6 + - + +
330F LYS* 3.0 7.7 + - - +
332F ALA* 1.3 75.6 - - - +
334F VAL* 1.3 66.4 + - - +
336F GLY* 3.0 11.4 + - - -
337F LEU* 3.0 18.3 + - + +
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Residues in contact with VAL 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F SER* 3.7 14.1 - - - +
330F LYS* 2.8 24.7 + - + +
331F ARG* 3.1 43.3 - - - +
333F GLU* 1.3 72.9 - - - +
335F ASN* 1.3 57.5 + - - +
337F LEU* 2.9 12.6 + - - +
338F ALA* 2.8 24.1 + - - +
343F TYR* 3.3 42.9 - - + -
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Residues in contact with ASN 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F SER* 2.7 31.9 + - - -
284F LEU* 4.0 1.7 - - + +
300F PHE* 3.5 28.3 - - + -
302F TYR* 3.5 25.4 + - - -
305F ALA 4.0 1.2 + - - -
306F LEU* 3.7 16.0 - - - +
331F ARG* 2.9 41.8 + - - +
332F ALA 4.1 0.2 - - - +
334F VAL* 1.3 72.5 - - - +
336F GLY* 1.3 61.4 + - - +
338F ALA* 3.7 6.5 - - - +
339F ALA* 2.8 30.5 + - - +
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Residues in contact with GLY 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLY* 3.2 30.2 - - - -
73F CYS* 3.7 7.9 - - - -
300F PHE* 3.9 6.9 - - - -
332F ALA 3.0 12.8 + - - -
333F GLU 3.0 10.2 + - - -
335F ASN* 1.3 78.8 - - - +
337F LEU* 1.3 59.7 + - - +
339F ALA* 3.6 2.1 - - - +
340F GLN* 3.1 22.1 + - - +
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Residues in contact with LEU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F GLU* 3.0 15.3 + - + +
334F VAL* 2.9 10.8 + - - +
336F GLY* 1.3 75.3 - - - +
338F ALA* 1.3 53.5 + - - +
339F ALA 2.9 4.9 - - - -
340F GLN* 2.7 32.0 + - - +
342F LYS* 3.1 52.8 + - + +
343F TYR* 3.8 21.8 - - + -
344F GLU 5.5 0.7 - - - +
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Residues in contact with ALA 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F SER* 3.3 29.8 - - - +
284F LEU* 3.6 9.7 - - + +
285F ASN* 3.2 28.8 - - + +
288F ASN* 2.9 16.1 + - - -
334F VAL 2.8 11.9 + - - +
335F ASN* 3.2 12.5 + - - +
337F LEU* 1.3 77.0 - - - +
339F ALA* 1.3 56.6 + - - +
340F GLN 2.9 2.8 + - - -
341F GLY 3.1 6.6 + - - -
343F TYR* 3.7 5.3 - - + +
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Residues in contact with ALA 339 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLY* 4.3 11.5 + - - -
284F LEU* 4.1 3.6 - - - +
288F ASN* 3.2 23.3 + - - +
298F LEU 4.2 3.4 + - - +
299F THR* 3.8 32.6 - - + +
300F PHE* 4.4 4.7 - - + -
335F ASN 2.8 17.0 + - - +
336F GLY* 3.6 12.3 - - - +
337F LEU 2.9 0.8 - - - -
338F ALA* 1.3 75.2 - - - +
340F GLN* 1.3 61.3 + - - +
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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
------------------------------------------------------------
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