Contacts of the helix formed by residues 320 - 339 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D ALA 3.3 19.7 - - - +
314D TRP* 3.3 24.9 - - - +
315D ARG* 4.4 4.5 - - - +
317D GLN* 3.2 19.5 + - - +
319D ASP* 1.3 89.8 + - - +
321D ALA* 1.3 64.3 + - - +
322D GLY 3.4 0.7 - - - -
323D ALA* 3.1 12.7 + - + +
324D ALA* 2.8 23.4 + - - +
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Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.6 12.8 - - + +
314D TRP* 4.2 13.7 - - + +
317D GLN 3.4 5.1 + - - +
318D ARG* 3.2 21.1 - - + +
319D ASP 2.9 2.4 + - - +
320D ASN* 1.3 75.5 - - - +
322D GLY* 1.3 58.0 + - - +
324D ALA* 3.1 5.3 + - - +
325D THR* 2.9 32.2 + - - +
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Residues in contact with GLY 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D ASP 3.8 5.0 + - - -
320D ASN 3.4 0.6 - - - -
321D ALA* 1.3 79.0 - - - +
323D ALA* 1.3 57.3 + - - +
325D THR* 3.3 9.4 + - - -
326D GLU* 3.0 32.9 + - - +
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Residues in contact with ALA 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D ALA* 4.4 11.2 - - + -
319D ASP 4.8 1.0 + - - +
320D ASN* 3.1 17.2 + - + +
322D GLY* 1.3 72.5 - - - +
324D ALA* 1.3 67.3 + - - +
326D GLU* 3.0 11.1 + - - +
327D GLU* 2.9 26.5 + - - +
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.3 18.4 - - + -
310D ALA* 3.2 31.6 - - - +
313D ALA* 3.8 7.1 - - - +
314D TRP* 3.5 16.6 - - + +
320D ASN 2.8 12.1 + - - +
321D ALA 3.3 9.9 - - - +
323D ALA* 1.3 76.4 - - - +
325D THR* 1.3 62.4 + - - +
327D GLU* 3.0 14.2 + - - +
328D PHE 3.1 9.7 + - - -
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Residues in contact with THR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D VAL* 2.8 32.9 + - - +
65D SER* 3.8 9.6 + - - +
66D ALA* 3.6 31.2 - - + +
321D ALA 2.9 16.2 + - - -
322D GLY* 3.5 11.5 - - - -
323D ALA 3.2 0.2 - - - -
324D ALA* 1.3 76.2 - - - +
326D GLU* 1.3 60.6 + - - +
328D PHE* 3.4 5.4 + - + +
329D ILE* 3.0 40.2 + - + +
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 2.5 42.7 + - - -
322D GLY 3.0 19.1 + - - +
323D ALA* 3.2 11.9 - - - +
325D THR* 1.3 77.5 - - - +
327D GLU* 1.3 70.8 + - - +
329D ILE* 3.2 7.5 + - - +
330D LYS* 2.8 30.1 + - - +
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Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D SER* 3.1 38.1 - - - +
310D ALA* 3.5 14.1 - - - -
313D ALA* 4.7 6.6 - - + +
323D ALA* 2.9 16.6 + - - +
324D ALA* 3.4 9.4 - - - +
326D GLU* 1.3 78.7 - - - +
328D PHE* 1.3 61.6 + - - +
330D LYS* 3.4 29.3 + - + +
331D ARG* 3.2 28.2 + - - +
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Residues in contact with PHE 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.7 40.2 - - + -
62D VAL 5.0 1.1 - - - -
63D LEU* 3.4 47.8 - - + -
66D ALA* 3.9 18.6 - - + -
70D VAL* 4.0 18.2 - - + -
74D ILE* 4.7 4.0 - - + -
306D LEU* 3.6 29.8 - - + -
310D ALA* 3.8 12.3 - - + +
324D ALA 3.1 11.0 + - - +
325D THR* 3.5 8.3 - - - +
327D GLU* 1.3 72.8 - - - +
329D ILE* 1.3 71.7 + - - +
330D LYS 2.9 1.6 + - - -
331D ARG* 2.9 4.2 + - - +
332D ALA* 2.8 35.4 + - + -
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Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ALA* 3.7 33.0 - - + -
67D ASP* 3.8 18.4 - - - +
69D ARG* 3.6 62.1 - - + +
70D VAL* 4.8 5.2 - - + +
325D THR* 3.0 23.8 + - + +
326D GLU* 3.7 7.2 - - - +
328D PHE* 1.3 76.2 - - + +
330D LYS* 1.3 63.6 + - - +
332D ALA* 3.6 8.4 - - - +
333D GLU* 2.9 30.6 + - + +
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 5.6 0.8 - - - +
326D GLU* 2.8 18.3 + - - +
327D GLU* 3.4 33.7 + - - +
329D ILE* 1.3 75.5 - - - +
331D ARG* 1.3 66.8 + - + +
333D GLU* 3.0 12.4 + - - +
334D VAL* 2.8 28.9 + - + +
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Residues in contact with ARG 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D GLU* 2.8 68.3 + - - +
278D GLU* 2.5 30.6 + - - -
281D SER* 3.0 17.2 + - - -
305D ALA 3.6 4.0 + - - +
306D LEU* 3.7 19.1 - - + +
309D SER* 4.0 3.1 - - - +
327D GLU 3.2 15.9 - - - +
328D PHE 2.9 4.4 + - - +
330D LYS* 1.3 80.3 - - + +
332D ALA* 1.3 63.7 + - - +
334D VAL* 3.2 30.9 - - - +
335D ASN* 2.9 37.2 + - - +
343D TYR* 4.4 1.0 + - - -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D VAL* 4.4 2.5 - - + -
73D CYS* 3.1 24.7 - - - +
74D ILE* 4.0 15.3 - - + -
300D PHE* 4.4 2.8 - - - -
306D LEU* 3.6 11.8 - - - +
328D PHE* 2.8 39.8 + - + +
329D ILE* 3.6 9.4 - - - +
331D ARG* 1.3 73.1 - - - +
333D GLU* 1.3 59.1 + - - +
335D ASN* 4.0 2.0 - - - +
336D GLY 3.0 20.8 + - - -
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Residues in contact with GLU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ARG* 3.2 28.6 + - - +
72D LYS* 2.7 41.9 + - - +
73D CYS* 3.7 13.6 - - - +
329D ILE* 2.9 30.1 + - + +
330D LYS* 3.0 7.5 + - - +
332D ALA* 1.3 76.2 - - - +
334D VAL* 1.3 66.7 + - - +
336D GLY* 3.0 10.9 + - - -
337D LEU* 3.0 17.4 + - - +
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Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D SER* 3.7 14.1 - - - +
330D LYS* 2.8 24.4 + - + +
331D ARG* 3.1 45.1 - - - +
333D GLU* 1.3 72.4 - - - +
335D ASN* 1.3 57.1 + - - +
337D LEU* 2.9 13.0 + - - +
338D ALA* 2.8 23.7 + - - +
343D TYR* 3.3 43.1 - - + +
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Residues in contact with ASN 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D SER* 2.7 31.7 + - - -
284D LEU* 4.0 2.0 - - + +
300D PHE* 3.5 28.5 - - + -
302D TYR* 3.5 24.3 + - - -
305D ALA 4.0 1.6 + - - -
306D LEU* 3.7 15.4 - - - +
331D ARG* 2.9 41.6 + - - +
332D ALA 4.1 0.2 - - - +
334D VAL* 1.3 72.9 - - - +
336D GLY* 1.3 59.9 - - - +
338D ALA* 3.7 6.6 - - - +
339D ALA* 2.8 30.7 + - - +
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Residues in contact with GLY 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLY* 3.2 29.7 - - - -
73D CYS* 3.7 7.9 - - - -
300D PHE* 3.9 6.7 - - - -
332D ALA 3.0 13.2 + - - -
333D GLU 3.0 9.5 + - - -
335D ASN* 1.3 77.6 - - - +
337D LEU* 1.3 60.0 + - - +
339D ALA* 3.6 2.0 - - - +
340D GLN* 3.1 22.2 + - - +
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Residues in contact with LEU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D GLU 3.0 14.6 + - - +
334D VAL* 2.9 10.6 + - - +
336D GLY* 1.3 76.0 - - - +
338D ALA* 1.3 54.3 + - - +
339D ALA 2.9 4.9 - - - -
340D GLN* 2.7 32.1 + - - +
342D LYS* 3.2 51.5 + - + +
343D TYR* 3.8 23.1 - - + -
344D GLU 5.5 0.4 - - - +
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D SER* 3.3 30.3 - - - +
284D LEU* 3.6 9.5 - - + +
285D ASN* 3.2 28.8 - - + +
288D ASN* 2.9 16.7 + - - -
334D VAL 2.8 12.8 + - - +
335D ASN* 3.2 13.4 + - - +
337D LEU* 1.3 75.4 - - - +
339D ALA* 1.3 56.4 + - - +
340D GLN 2.9 3.6 + - - -
341D GLY 3.1 6.4 + - - -
343D TYR* 3.7 5.7 - - + +
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLY* 4.3 10.6 + - - -
284D LEU* 4.1 4.2 - - - +
288D ASN* 3.2 23.0 + - - +
298D LEU 4.2 3.0 + - - +
299D THR* 3.8 33.5 - - + +
300D PHE* 4.4 4.9 - - + -
335D ASN 2.8 16.7 + - - +
336D GLY* 3.6 12.3 - - - +
337D LEU 2.9 0.4 - - - -
338D ALA* 1.3 76.3 - - - +
340D GLN* 1.3 61.0 + - - +
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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