Contacts of the helix formed by residues 372 - 384 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B CYS 4.5 2.9 - - - +
360B LYS* 5.1 2.9 - - + -
363B VAL* 3.6 28.2 - - + +
366B ILE* 3.5 28.9 - - + +
367B PRO 3.8 3.6 - - - +
368B GLY* 3.4 20.6 - - - +
371B PHE* 1.3 83.6 - - - +
373B ALA* 1.3 62.2 + - - +
375B ALA* 3.0 20.0 + - + +
376B VAL* 3.1 15.9 + - - +
411B GLU* 3.4 33.2 - - + +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B CYS* 3.7 14.3 - - - +
371B PHE 3.5 0.2 - - - -
372B PRO* 1.3 80.7 - - - +
374B GLN* 1.3 57.7 + - - +
376B VAL* 3.2 4.7 + - - +
377B ILE* 3.1 33.0 + - - +
390B GLU* 3.6 14.4 - - + +
411B GLU* 3.6 22.0 + - + +
412B PHE 3.2 29.2 - - - +
413B MET* 4.3 1.1 - - - +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR 4.4 0.9 + - - -
35B ASN* 5.4 0.8 - - - +
36B PRO* 3.4 20.0 - - - +
371B PHE* 3.4 15.9 + - + +
372B PRO 3.2 0.8 - - - -
373B ALA* 1.3 74.2 - - - +
375B ALA* 1.3 65.4 + - - +
377B ILE* 3.5 15.3 + - - +
378B ASN* 2.9 48.1 + - - +
390B GLU* 3.0 34.6 + - + +
394B PHE* 3.7 18.6 - - + -
447B LEU* 3.5 25.1 - - + -
463B LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B ILE* 4.0 23.1 - - + -
371B PHE 2.9 14.2 + - - +
372B PRO 3.0 10.3 + - - +
374B GLN* 1.3 80.2 - - - +
376B VAL* 1.3 60.1 + - - +
378B ASN* 3.7 4.1 + - - +
379B ALA* 3.3 22.0 + - - +
444B LEU* 4.0 13.0 - - + +
446B GLY* 4.6 12.8 - - - +
447B LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B CYS* 3.9 17.9 - - + -
362B LEU* 4.5 7.2 - - + -
363B VAL* 3.9 21.1 - - + -
372B PRO 3.1 13.8 + - - +
373B ALA 3.2 7.4 + - - +
375B ALA* 1.3 74.7 - - - +
377B ILE* 1.3 65.5 + - - +
379B ALA* 3.0 5.4 + - - +
380B LEU* 2.8 22.2 + - - +
413B MET* 4.0 25.4 - - + -
434B LEU* 4.4 6.5 - - + -
437B LEU* 4.7 1.0 - - + +
441B PHE* 4.2 22.0 - - + -
444B LEU* 4.1 15.9 - - + -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO* 3.9 12.3 - - + -
373B ALA 3.1 20.1 + - - +
374B GLN* 3.6 21.1 - - - +
376B VAL* 1.3 76.2 - - - +
378B ASN* 1.3 57.0 + - - +
380B LEU* 3.2 4.8 + - - +
381B TYR* 2.9 28.2 + - + +
386B VAL 5.0 0.5 - - - +
388B ALA* 3.5 31.1 + - + +
389B VAL 3.4 7.0 - - - +
390B GLU* 3.3 44.2 - - + +
413B MET* 3.6 30.3 - - + -
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Residues in contact with ASN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.9 15.2 - - + +
34B TYR* 2.9 45.3 + - + +
36B PRO* 3.4 10.9 - - - +
374B GLN* 2.9 40.5 + - - +
375B ALA* 4.2 4.7 - - - +
377B ILE* 1.3 74.0 - - - +
379B ALA* 1.3 58.5 + - - +
381B TYR* 3.3 7.0 + - - +
382B LEU* 3.0 35.1 + - + +
447B LEU* 4.3 13.8 - - + +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ALA 3.3 11.1 + - - +
376B VAL 3.0 8.7 + - - +
378B ASN* 1.3 75.0 - - - +
380B LEU* 1.3 67.6 + - - +
382B LEU* 3.3 9.0 + - - +
383B GLU* 2.9 29.2 + - + +
437B LEU* 4.1 20.0 - - + -
440B LYS* 6.3 0.7 - - + -
444B LEU* 4.1 23.6 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B VAL 2.8 12.6 + - - +
377B ILE* 3.5 9.0 - - - +
379B ALA* 1.3 78.8 - - - +
381B TYR* 1.3 58.1 + - - +
383B GLU* 3.3 1.9 + - + +
384B SER* 2.7 45.4 + - - +
386B VAL* 4.2 26.0 - - + +
388B ALA* 4.5 6.7 - - + -
413B MET* 4.0 24.7 - - + -
415B LEU* 4.2 12.3 - - + -
430B ILE* 4.8 4.7 - - + +
433B ALA* 3.9 22.7 - - + +
434B LEU* 4.2 22.2 - - + +
437B LEU* 3.8 12.9 - - + +
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Residues in contact with TYR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 3.4 48.9 - - + +
28B ALA* 4.0 1.9 - - - +
29B LEU* 4.1 22.9 - - + -
36B PRO* 5.2 7.4 - - + -
39B LEU* 3.9 27.8 - - + -
43B ALA* 2.6 42.5 + - - +
44B VAL* 4.6 2.5 - - + -
377B ILE* 2.9 14.7 + - + +
378B ASN* 3.7 9.2 - - - +
379B ALA 3.2 0.2 - - - -
380B LEU* 1.3 74.5 - - - +
382B LEU* 1.3 64.5 + - - +
385B GLY* 2.7 44.4 + - - -
386B VAL 3.2 24.2 + - - +
387B ARG* 4.7 5.4 - - - -
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 3.2 30.5 + - - +
25B ARG* 2.8 39.2 + - + +
26B GLU* 3.7 48.7 - - + +
29B LEU* 3.9 21.8 - - + -
34B TYR* 5.3 5.4 - - + -
378B ASN* 3.0 22.7 + - + +
379B ALA* 3.8 6.7 - - - +
381B TYR* 1.3 79.2 - - + +
383B GLU* 1.3 56.4 + - - +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 3.0 25.5 + - - +
25B ARG* 3.3 11.2 + - - -
379B ALA* 2.9 21.7 + - + +
380B LEU* 3.7 4.9 - - - +
382B LEU* 1.3 78.4 - - - +
384B SER* 1.3 62.6 + - - +
433B ALA* 5.2 7.0 - - + +
436B GLY 5.7 0.7 - - - +
437B LEU* 3.4 25.1 - - + +
440B LYS* 3.8 29.6 + - - +
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.4 2.6 - - - +
25B ARG* 4.2 9.0 - - - +
45B TYR* 4.1 5.5 - - - +
380B LEU* 2.7 23.9 + - - +
383B GLU* 1.3 80.6 - - - +
385B GLY* 1.3 59.2 + - - +
386B VAL* 3.2 19.8 + - - +
429B TYR* 2.7 41.3 + - - -
433B ALA* 3.6 26.2 - - - -
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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