Contacts of the helix formed by residues 423 - 438 (chain A) in PDB entry 2AG1
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 VAL 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS* 3.3 41.5 - - + +
62A ARG* 5.3 3.6 - - - +
83A THR* 4.3 5.4 - - + -
87A ASN* 3.6 26.5 - - - +
392A ASP* 3.2 0.6 + - - +
415A HIS* 4.7 10.8 - - + +
420A SER* 3.4 35.9 - - - +
421A MSE 3.5 1.0 - - - +
422A GLY* 1.3 76.5 - - - +
424A GLY* 1.3 58.5 + - - +
425A PHE 3.3 0.9 + - - -
426A GLY 3.8 0.9 + - - -
427A THR* 2.7 40.2 + - + +
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Residues in contact with GLY 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A VAL* 3.8 5.3 - - - +
391A ALA 5.1 1.8 - - - -
392A ASP* 2.6 30.1 + - - -
415A HIS* 5.2 0.2 - - - -
423A VAL* 1.3 74.0 - - - +
425A PHE* 1.3 56.3 + - - +
427A THR* 3.2 7.5 + - - -
428A ALA* 2.8 32.7 + - - +
444A LEU* 3.7 17.9 - - - +
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Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ASP* 4.3 0.4 + - - -
422A GLY 3.5 4.8 + - - +
423A VAL 3.3 1.6 + - - -
424A GLY* 1.3 76.1 - - - +
426A GLY* 1.3 63.3 + - - +
428A ALA* 3.2 2.4 + - - +
429A LEU* 3.1 19.6 + - + +
444A LEU* 3.8 14.8 - - + +
450A SER 5.9 0.4 - - - +
451A VAL* 4.2 21.8 - - + +
454A SER* 3.3 43.1 - - - -
455A ILE* 4.2 3.1 - - - -
457A GLU* 3.7 15.3 - - + -
458A PHE* 3.7 51.8 - + - -
461A LEU* 3.6 29.8 - - + -
468A LEU* 4.1 6.7 - - + -
470A VAL* 4.0 10.1 - - + -
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Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.6 31.7 - - - +
55A HIS* 3.9 6.6 - - - +
56A ALA* 3.1 14.4 - - - -
422A GLY 4.8 1.0 + - - -
423A VAL 3.8 2.8 + - - -
424A GLY 3.5 0.2 - - - -
425A PHE* 1.3 77.3 - - - +
427A THR* 1.3 64.8 + - - +
429A LEU* 3.1 8.5 + - - +
430A GLY 3.0 20.1 + - - -
454A SER* 5.0 1.6 + - - -
457A GLU* 5.2 1.5 - - - +
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS* 3.3 19.3 + - - +
58A GLU* 5.1 2.1 + - - +
59A GLY* 3.4 13.8 + - - +
62A ARG* 3.9 19.4 + - - +
390A VAL* 3.9 13.0 - - + -
413A LEU* 3.8 24.5 - - + -
423A VAL* 2.7 32.9 + - - +
424A GLY* 3.2 10.7 + - - -
426A GLY* 1.3 76.5 - - - +
428A ALA* 1.3 57.7 + - - +
431A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL* 3.7 24.7 - - + -
424A GLY 2.8 19.3 + - - +
425A PHE 3.7 2.0 - - - +
427A THR* 1.3 74.1 - - - +
429A LEU* 1.3 53.2 + - - +
431A ALA* 3.3 2.3 + - - +
432A GLN* 2.8 35.2 + - - +
442A THR* 3.6 3.1 - - - +
444A LEU* 3.8 13.0 - - + -
468A LEU* 3.7 32.0 - - + +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.6 1.8 - - + -
45A ILE* 3.9 28.5 - - + -
47A THR* 4.6 7.6 - - + -
52A ALA* 6.2 0.2 - - + -
56A ALA* 4.1 13.7 - - + -
425A PHE* 3.1 12.7 + - + +
426A GLY* 3.1 10.1 + - - +
428A ALA* 1.3 73.7 - - - +
430A GLY* 1.3 66.1 + - - +
432A GLN* 3.4 7.7 + - - +
433A VAL* 3.3 24.6 + - - +
457A GLU* 4.2 19.3 - - + +
460A THR* 3.8 24.9 - - + -
461A LEU* 3.5 29.8 - - + -
466A LEU* 4.0 10.0 - - + +
468A LEU* 4.1 6.8 - - + +
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Residues in contact with GLY 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.1 9.2 - - - -
56A ALA* 3.2 33.2 - - - +
60A TYR* 3.5 12.8 - - - +
426A GLY 3.0 11.3 + - - -
427A THR 3.9 0.4 - - - -
429A LEU* 1.3 71.9 - - - +
431A ALA* 1.3 65.7 + - - +
433A VAL* 3.0 14.4 + - - +
434A ALA 3.1 9.7 + - - -
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY 3.6 13.6 - - - +
60A TYR* 4.5 0.7 - - - +
63A ALA* 3.7 21.8 - - + -
388A THR* 4.3 4.9 - - + -
390A VAL* 4.5 0.2 - - + -
413A LEU* 4.1 10.1 - - + -
427A THR 3.0 18.5 + - - +
428A ALA* 3.5 6.5 - - - +
430A GLY* 1.3 74.6 - - - +
432A GLN* 1.3 58.0 + - - +
434A ALA* 3.2 3.6 + - - +
435A ASP* 2.8 32.4 + - - +
442A THR* 3.7 15.5 - - + -
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ALA 2.8 20.0 + - - +
429A LEU* 3.4 7.4 + - - +
430A GLY 3.2 0.4 - - - -
431A ALA* 1.3 72.9 - - - +
433A VAL* 1.3 61.3 + - - +
435A ASP* 3.7 2.0 - - - +
436A LEU* 3.2 30.0 + - + +
440A ARG 3.3 22.6 + - - -
441A ARG* 3.7 12.2 - - - +
442A THR* 3.0 41.1 + - - +
466A LEU* 4.3 10.5 - - + -
467A PRO* 3.8 36.3 - - + +
468A LEU* 4.0 10.0 + - + +
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS* 3.7 31.8 - - + +
23A PHE* 3.8 24.7 - - + -
45A ILE* 4.2 11.4 - - + -
60A TYR* 4.0 9.9 - - + -
429A LEU 3.3 15.3 + - - +
430A GLY 3.0 8.1 + - - +
432A GLN* 1.3 76.6 - - - +
434A ALA* 1.3 62.5 + - - +
436A LEU* 3.3 20.2 + - + +
437A GLU* 4.1 8.7 - - - +
466A LEU* 3.8 30.7 - - + -
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Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 3.7 43.6 - - + +
63A ALA* 4.7 2.2 - - + -
64A GLY* 4.1 18.9 - - - +
66A LYS* 5.6 2.9 - - - +
430A GLY 3.1 8.6 + - - +
431A ALA* 3.6 7.9 - - - +
433A VAL* 1.3 77.0 - - - +
435A ASP* 1.3 60.9 + - - +
436A LEU 3.4 0.5 + - - -
437A GLU* 3.5 22.0 + - - +
438A ALA* 3.9 7.3 + - - +
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Residues in contact with ASP 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 4.2 5.9 - - - +
388A THR* 3.1 25.0 + - - -
431A ALA 2.8 23.9 + - - +
432A GLN* 3.2 8.7 + - - +
433A VAL 3.2 0.4 - - - -
434A ALA* 1.3 74.4 - - - +
436A LEU* 1.3 58.7 + - - +
437A GLU 3.4 0.2 - - - -
438A ALA* 3.2 5.2 + - - +
439A GLY 2.9 10.9 + - - -
440A ARG* 2.8 78.2 + - + +
442A THR* 2.6 22.3 + - - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A GLN* 3.2 33.3 + - - +
433A VAL* 3.5 13.0 - - + +
434A ALA 3.2 0.8 - - - -
435A ASP* 1.3 78.6 - - - +
437A GLU* 1.3 64.7 + - - +
439A GLY* 3.4 11.3 + - - -
440A ARG 4.8 2.5 - - - +
441A ARG* 6.4 0.2 - - - -
465A GLN 5.4 2.2 - - - +
466A LEU* 3.9 27.8 - - + -
467A PRO* 4.5 15.5 - - + -
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 4.8 5.8 - - - +
21A HIS* 3.5 30.6 + - - -
60A TYR* 3.9 12.8 + - - -
66A LYS* 4.1 16.8 - - - +
433A VAL 4.1 7.2 - - - +
434A ALA 3.5 16.3 - - - +
436A LEU* 1.3 78.9 - - - +
438A ALA* 1.3 59.7 + - + +
439A GLY 3.2 1.5 + - - -
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ALA 4.3 8.1 - - - +
435A ASP* 3.2 8.7 + - - +
437A GLU* 1.3 78.6 - - + +
439A GLY* 1.3 62.0 + - - +
440A ARG* 3.4 33.8 + - - +
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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