Contacts of the helix formed by residues 306 - 320 (chain D) in PDB entry 1AX4
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 306 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500C K 4.4 1.2 - - - -
68D GLY* 4.4 1.8 - - - -
69D ASP 3.4 23.8 - - - -
70D GLU* 2.8 14.7 + - - +
77D ASN* 3.6 14.4 - - - +
301D TYR* 5.6 0.4 - - - +
304D LEU 3.7 1.4 + - - -
305D ALA* 1.4 71.1 - - - +
307D ARG* 1.3 61.7 + - - +
309D MET* 3.2 19.6 + - - +
310D ALA* 3.0 18.4 + - - +
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Residues in contact with ARG 307 (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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57C MET* 3.6 14.6 - - - +
62C TRP* 4.7 11.0 - - - -
65C MET* 3.8 28.8 - - - +
270C LEU* 6.1 0.4 - - - +
271C ASN* 2.9 36.8 + - - +
272C ILE* 4.2 10.9 - - - +
307C ARG* 4.7 4.0 - - - +
308C ASP* 2.7 28.9 + - - -
311C ALA* 5.6 0.4 - - - +
65D MET* 3.3 56.8 - - + +
68D GLY* 4.2 3.7 - - - -
70D GLU* 2.9 19.2 + - - +
305D ALA* 3.7 12.3 - - + +
306D GLY* 1.3 76.4 - - - +
308D ASP* 1.3 65.6 + - - +
310D ALA* 3.3 6.4 + - - +
311D ALA 3.0 21.7 + - - -
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Residues in contact with ASP 308 (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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272C ILE* 5.0 1.2 - - - +
307C ARG* 2.7 29.4 + - - -
308C ASP* 4.2 11.4 - - - +
65D MET* 4.1 4.9 - - - +
270D LEU* 4.5 3.5 - - + +
272D ILE* 3.7 25.2 - - + +
304D LEU* 4.1 21.2 - - + +
305D ALA* 3.0 28.2 + - - +
307D ARG* 1.3 77.5 + - - +
309D MET* 1.4 60.9 + - - +
311D ALA* 3.3 5.9 + - - +
312D MET* 2.9 30.9 + - - +
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Residues in contact with MET 309 (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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75D SER* 4.0 18.6 - - - +
77D ASN* 3.9 13.2 - - + +
78D TYR* 4.0 16.2 - - - +
81D LEU* 4.3 13.0 - - + +
96D PRO* 4.2 11.4 - - + -
300D THR 3.4 26.9 - - - +
301D TYR* 3.7 23.3 - - + -
304D LEU* 4.0 21.5 - - + -
305D ALA 3.2 6.2 + - - +
306D GLY* 3.2 23.8 + - - +
308D ASP* 1.4 77.0 - - - +
310D ALA* 1.3 61.4 + - - +
312D MET* 3.3 7.2 + - - +
313D VAL* 3.1 27.4 + - - +
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Residues in contact with ALA 310 (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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64D ALA* 3.3 39.6 - - + +
68D GLY* 4.2 1.1 - - - -
77D ASN* 3.5 27.1 - - - +
306D GLY 3.0 11.3 + - - +
307D ARG* 3.4 10.1 - - - +
308D ASP 3.2 0.2 - - - -
309D MET* 1.3 72.9 - - - +
311D ALA* 1.3 64.4 + - - +
313D VAL* 3.3 15.9 + - - +
314D GLN* 3.4 8.8 + - - +
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Residues in contact with ALA 311 (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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307C ARG* 5.7 0.4 - - - +
57D MET* 4.2 12.1 - - - -
61D GLN* 3.7 14.2 + - + +
64D ALA* 4.3 2.2 - - - +
65D MET* 3.8 20.6 - - + -
270D LEU* 3.6 18.8 - - + +
307D ARG 3.0 16.3 + - - +
308D ASP* 3.3 8.0 + - - +
310D ALA* 1.3 75.4 - - - +
312D MET* 1.3 51.7 + - - +
314D GLN* 3.2 5.4 + - - +
315D GLY* 2.7 34.3 + - - -
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Residues in contact with MET 312 (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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81D LEU* 3.8 31.9 - - + -
262D MET* 5.8 0.9 - - - +
264D ALA* 3.9 17.5 - - + -
268D PRO* 5.0 1.1 - - + +
270D LEU* 3.5 19.7 - - + +
273D GLY* 3.9 4.3 - - - -
274D GLY 3.5 34.3 - - - +
275D LEU* 4.6 9.9 - - - -
304D LEU* 3.6 24.7 - - + -
308D ASP 2.9 15.4 + - - +
309D MET* 3.6 6.1 - - - +
310D ALA 3.2 0.2 - - - -
311D ALA* 1.3 73.6 - - - +
313D VAL* 1.3 65.4 + - - +
315D GLY* 4.8 0.2 - - - -
316D LEU* 2.9 35.7 + - + +
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Residues in contact with VAL 313 (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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77D ASN* 4.2 2.7 - - + +
80D ASP* 3.9 24.0 - - + +
81D LEU* 3.6 38.1 - - + +
84D LYS* 4.0 20.6 - - + +
309D MET 3.1 15.4 + - - +
310D ALA* 3.3 9.4 + - - +
312D MET* 1.3 77.8 - - - +
314D GLN* 1.3 61.5 + - - +
316D LEU* 3.6 9.6 + - - +
317D GLU* 3.6 13.7 + - - +
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Residues in contact with GLN 314 (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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60D HIS* 3.8 20.6 + - + +
61D GLN* 3.5 34.1 - - + +
64D ALA* 4.7 5.6 - - + -
310D ALA 3.4 8.3 + - - +
311D ALA* 3.2 7.7 + - - +
313D VAL* 1.3 78.3 - - - +
315D GLY* 1.3 61.1 + - - +
317D GLU* 3.2 16.7 + - - +
318D GLU* 2.9 52.5 + - - +
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Residues in contact with GLY 315 (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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61D GLN* 3.3 16.7 - - - +
268D PRO* 3.1 30.4 - - - +
269D LEU* 4.8 0.4 - - - -
311D ALA 2.7 17.4 + - - -
312D MET 3.8 0.7 - - - -
314D GLN* 1.3 70.6 - - - +
316D LEU* 1.3 58.5 + - - +
318D GLU* 3.9 3.9 - - - +
319D GLY* 2.8 29.6 + - - -
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 3.9 25.6 - - + -
84D LYS* 4.0 18.6 - - + -
85D ALA 5.5 2.0 - - - +
88D LEU* 3.8 19.9 - - + +
89D PHE* 4.6 3.6 - - + -
227D PHE* 3.9 27.1 - - + -
228D CYS* 5.2 1.2 - - - -
262D MET* 4.1 13.7 - - + -
268D PRO* 3.9 22.2 + - + -
275D LEU* 5.1 7.9 - - + -
312D MET* 2.9 28.3 + - + +
313D VAL* 3.9 4.7 - - - +
314D GLN 3.3 0.2 - - - -
315D GLY* 1.3 75.6 - - - +
317D GLU* 1.3 61.7 + - - +
319D GLY* 4.3 0.9 - - - -
320D THR* 3.3 24.9 + - - +
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Residues in contact with GLU 317 (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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84D LYS* 2.7 32.7 + - - +
88D LEU* 6.0 0.2 - - - -
247D LYS* 2.7 39.3 + - - -
313D VAL 3.6 4.9 + - - +
314D GLN* 3.2 19.6 + - - +
315D GLY 3.1 0.4 - - - -
316D LEU* 1.3 77.8 - - - +
318D GLU* 1.3 65.5 + - - +
320D THR* 2.8 24.3 + - - -
321D GLU* 4.0 16.2 + - - +
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Residues in contact with GLU 318 (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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16B LYS* 6.2 1.1 - - - -
58D SER* 2.6 32.2 + - - -
60D HIS* 4.1 2.6 - - - +
61D GLN* 3.5 5.9 - - - +
269D LEU* 3.7 13.5 - - + -
314D GLN* 2.9 45.5 + - - +
315D GLY* 3.2 2.2 + - - +
317D GLU* 1.3 76.2 - - + +
319D GLY* 1.3 62.7 + - - +
321D GLU* 3.1 39.8 + - - +
324D TYR* 3.9 9.7 - - - +
420D ARG* 2.9 33.1 + - - +
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Residues in contact with GLY 319 (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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228D CYS* 3.3 28.0 - - - +
267D ASP 3.6 23.3 - - - -
268D PRO* 5.1 0.4 - - - -
269D LEU* 3.5 6.7 - - - +
315D GLY 2.8 13.5 + - - -
316D LEU 4.3 2.0 - - - -
317D GLU 3.3 0.4 - - - -
318D GLU* 1.3 76.4 - - - +
320D THR* 1.3 55.6 + - - +
321D GLU 3.4 0.4 - - - -
324D TYR* 4.1 5.9 - - - -
325D LEU* 3.7 14.7 - - - +
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Residues in contact with THR 320 (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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88D LEU* 4.3 16.2 - - + -
227D PHE* 5.0 2.0 - - + -
228D CYS* 3.9 7.9 - - - -
246D ILE* 3.3 33.9 - - - +
247D LYS* 3.7 23.3 - - + +
250D ILE* 3.6 25.4 - - + -
316D LEU 3.3 17.5 - - - +
317D GLU* 2.8 17.7 + - - -
318D GLU 3.2 0.4 - - - -
319D GLY* 1.3 75.2 - - - +
321D GLU* 1.3 63.8 + - - +
322D GLU 3.4 0.9 + - - -
325D LEU* 4.0 2.5 - - - -
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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