Contacts of the helix formed by residues 372 - 384 (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 PRO 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359D CYS 4.5 4.9 - - - +
360D LYS* 4.9 4.7 - - + -
363D VAL* 3.6 23.8 - - + +
366D ILE* 3.8 25.5 - - + +
367D PRO 3.3 13.7 - - - +
368D GLY* 3.4 6.5 - - - +
371D PHE* 1.3 86.2 - - - +
373D ALA* 1.3 63.3 + - - +
375D ALA* 3.0 5.7 + - - +
376D VAL* 3.0 26.2 + - - +
411D GLU* 3.0 42.4 - - + +
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Residues in contact with ALA 373 (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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359D CYS* 3.6 16.5 - - - +
371D PHE 3.5 0.2 - - - -
372D PRO* 1.3 81.0 - - - +
374D GLN* 1.3 51.1 + - - +
376D VAL* 3.0 5.0 + - - +
377D ILE* 2.7 39.2 + - + +
390D GLU* 3.7 18.8 - - + +
411D GLU* 4.0 13.9 + - + +
412D PHE 3.2 32.5 - - - +
413D MET 4.6 0.2 - - - +
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Residues in contact with GLN 374 (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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34D TYR 4.7 0.4 - - - -
35D ASN* 5.0 1.0 - - - +
36D PRO* 3.0 24.9 - - - +
371D PHE* 3.3 22.6 + - + +
372D PRO 3.3 0.8 - - - -
373D ALA* 1.3 78.9 - - - +
375D ALA* 1.4 53.7 - - - +
377D ILE* 3.3 17.2 - - - +
378D ASN* 2.5 67.4 + - - +
390D GLU* 3.3 31.1 + - + +
394D PHE* 3.9 15.0 - - + -
447D LEU* 4.2 6.1 - - + -
463D LEU* 4.1 22.9 - - + -
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Residues in contact with ALA 375 (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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366D ILE* 4.0 14.1 - - + -
371D PHE 3.0 17.2 + - - +
372D PRO 3.6 3.6 - - - +
374D GLN* 1.4 74.0 - - - +
376D VAL* 1.3 66.3 + - - +
378D ASN* 4.2 3.4 - - - +
379D ALA* 3.1 25.1 + - - +
444D LEU* 3.5 29.1 - - + +
446D GLY* 4.6 6.1 - - - +
447D LEU* 4.0 17.0 - - + +
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Residues in contact with VAL 376 (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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359D CYS* 3.5 35.9 - - + -
362D LEU* 4.6 7.0 - - + -
363D VAL* 3.9 20.2 - - + -
372D PRO 3.0 15.8 + - - +
373D ALA 3.2 5.8 - - - +
375D ALA* 1.3 75.9 - - - +
377D ILE* 1.3 53.4 + - - +
379D ALA* 3.0 7.3 + - - +
380D LEU* 2.7 34.8 + - - +
413D MET* 4.2 17.9 - - + -
434D LEU* 4.3 8.5 - - + -
437D LEU* 4.4 0.2 - - - +
441D PHE* 4.2 21.3 - - + -
444D LEU* 4.4 4.5 - - + -
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Residues in contact with ILE 377 (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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36D PRO* 3.8 10.3 - - + -
373D ALA 2.7 22.2 + - - +
374D GLN* 3.3 26.4 + - - +
376D VAL* 1.3 72.6 - - - +
378D ASN* 1.3 49.1 + - - +
380D LEU* 3.1 5.2 + - - +
381D TYR* 2.7 33.6 + - + +
386D VAL 4.8 1.2 - - - +
387D ARG* 5.9 0.7 - - - -
388D ALA* 3.6 26.5 + - + +
389D VAL 3.4 7.6 - - - +
390D GLU* 3.1 45.5 - - + +
413D MET* 3.5 33.0 - - + -
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Residues in contact with ASN 378 (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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29D LEU* 4.1 16.6 - - + +
34D TYR* 3.0 42.9 + - + +
36D PRO* 3.6 7.6 - - - +
374D GLN* 2.5 51.3 + - - +
375D ALA* 4.2 4.9 - - - +
377D ILE* 1.3 67.7 - - - +
379D ALA* 1.4 57.5 + - - +
381D TYR* 3.0 9.2 + - - +
382D LEU* 2.6 40.5 + - + +
447D LEU* 3.9 14.7 - - + +
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Residues in contact with ALA 379 (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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375D ALA 3.1 17.0 + - - +
376D VAL 3.0 4.0 + - - +
378D ASN* 1.4 78.9 - - - +
380D LEU* 1.3 63.3 - - - +
382D LEU* 2.9 10.0 + - - +
383D GLU* 2.9 30.2 + - - +
437D LEU* 3.8 21.5 - - + -
440D LYS* 6.5 1.1 - - + -
444D LEU* 4.2 17.7 - - + -
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Residues in contact with LEU 380 (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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376D VAL 2.7 16.5 + - - +
377D ILE* 3.3 8.1 - - - +
379D ALA* 1.3 71.5 - - - +
381D TYR* 1.3 60.3 + - - +
383D GLU* 3.3 2.1 + - + -
384D SER* 2.5 47.4 + - - +
386D VAL* 4.3 24.7 - - + +
388D ALA* 4.6 4.9 - - + +
413D MET* 3.7 32.8 - - + -
415D LEU* 4.3 9.2 - - + -
430D ILE* 4.5 7.0 - - + +
433D ALA* 3.9 22.2 - - + +
434D LEU* 4.1 21.8 - - + +
437D LEU* 3.7 11.3 - - + +
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Residues in contact with TYR 381 (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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20D PRO* 4.3 0.5 - - - +
25D ARG* 3.5 50.5 + - + +
28D ALA* 3.8 3.1 - - - +
29D LEU* 4.0 24.5 - - + -
36D PRO* 5.4 8.1 - - + -
39D LEU* 4.2 24.0 - - + -
43D ALA* 2.4 40.9 + - - +
44D VAL* 4.4 2.2 - - + -
377D ILE* 2.7 17.3 + - + +
378D ASN* 3.0 9.8 + - - +
380D LEU* 1.3 73.2 - - - +
382D LEU* 1.3 65.7 + - + +
385D GLY* 2.8 43.2 + - - +
386D VAL 3.5 23.0 + - - +
387D ARG* 4.8 3.8 - - + -
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Residues in contact with LEU 382 (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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22D ARG* 3.2 32.5 + - - +
25D ARG* 2.5 43.3 + - + +
26D GLU* 3.4 47.6 - - + +
29D LEU* 3.6 29.4 - - + -
34D TYR* 5.8 3.6 - - + -
378D ASN* 2.6 18.2 + - + +
379D ALA* 2.9 6.5 + - - +
381D TYR* 1.3 73.2 - - + +
383D GLU* 1.3 52.0 + - - +
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Residues in contact with GLU 383 (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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22D ARG* 2.5 35.1 + - - -
25D ARG* 3.6 12.0 + - - +
379D ALA* 2.9 20.3 + - - +
380D LEU* 4.0 3.4 - - - +
382D LEU* 1.3 77.4 - - - +
384D SER* 1.4 62.8 + - - +
429D TYR* 4.9 0.3 + - - -
433D ALA* 5.3 7.2 - - + +
436D GLY 5.8 1.6 - - - +
437D LEU* 3.5 28.1 - - + +
440D LYS* 3.0 35.5 + - - +
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Residues in contact with SER 384 (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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19D VAL* 4.3 1.9 - - - +
25D ARG* 4.4 8.5 - - - +
45D TYR* 3.8 4.7 - - - +
380D LEU* 2.5 27.7 + - - +
381D TYR 3.2 0.6 + - - -
383D GLU* 1.4 82.4 - - - +
385D GLY* 1.3 59.8 + - - +
386D VAL* 3.3 16.4 + - - +
429D TYR* 2.7 43.8 + - - -
433D ALA* 3.5 25.8 - - - -
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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