Contacts of the helix formed by residues 423 - 439 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B HIS* 3.4 42.0 - - + +
62B ARG* 5.5 3.4 - - - +
83B THR* 4.3 4.3 - - + -
87B ASN* 3.7 26.5 - - - +
415B HIS* 4.6 10.5 - - + +
420B SER* 3.2 38.6 - - - +
421B MSE 3.4 0.8 - - - +
422B GLY* 1.3 76.0 - - - +
424B GLY* 1.3 57.2 + - - +
425B PHE 3.4 0.2 - - - -
426B GLY 4.0 0.6 + - - -
427B THR* 2.6 41.1 + - - +
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Residues in contact with GLY 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B VAL* 3.8 5.1 - - - +
391B ALA 5.2 1.6 - - - -
392B ASP* 2.6 30.3 + - - -
415B HIS* 5.4 0.4 - - - -
422B GLY 3.0 0.2 - - - -
423B VAL* 1.3 72.6 - - - +
425B PHE* 1.3 59.4 + - - +
427B THR* 3.3 6.6 + - - -
428B ALA* 2.8 32.4 + - - +
444B LEU* 3.7 17.3 - - - +
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Residues in contact with PHE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ASP* 4.3 1.2 + - - -
422B GLY 3.7 4.2 + - - +
423B VAL 3.4 1.0 - - - -
424B GLY* 1.3 78.7 - - - +
426B GLY* 1.3 64.5 + - - +
428B ALA* 3.1 2.3 + - - +
429B LEU* 3.1 17.6 + - + +
444B LEU* 3.7 14.3 - - + +
450B SER 5.9 2.2 - - - +
451B VAL* 4.2 19.3 - - + +
454B SER* 3.3 41.3 - - - -
455B ILE* 4.2 3.8 - - - -
457B GLU* 3.6 16.6 - - + -
458B PHE* 3.7 55.4 - + - -
461B LEU* 3.6 25.1 - - + -
468B LEU* 4.2 7.0 - - + -
470B VAL* 4.0 9.2 - - + -
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Residues in contact with GLY 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 3.6 31.4 - - - +
55B HIS* 4.0 7.2 - - - +
56B ALA* 3.0 27.0 - - - +
422B GLY 4.9 1.0 + - - -
423B VAL 4.0 2.8 + - - -
425B PHE* 1.3 77.8 - - - +
427B THR* 1.3 61.6 + - - +
429B LEU* 3.3 6.9 + - - +
430B GLY 3.1 9.9 + - - -
454B SER* 4.9 1.8 + - - -
457B GLU* 5.3 1.1 - - - -
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B HIS* 3.3 18.2 + - - +
58B GLU* 5.0 2.3 + - + +
59B GLY* 3.3 14.5 - - - +
62B ARG* 4.0 18.2 + - - +
390B VAL* 3.9 12.6 - - + -
413B LEU* 3.8 25.8 - - + +
423B VAL* 2.6 36.2 + - - +
424B GLY* 3.3 6.2 + - - -
425B PHE 3.2 0.4 - - - -
426B GLY* 1.3 75.2 - - - +
428B ALA* 1.3 58.0 + - - +
431B ALA* 2.9 24.8 + - - +
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B VAL* 3.7 25.8 - - + +
424B GLY 2.8 19.9 + - - +
425B PHE 3.1 2.0 + - - +
427B THR* 1.3 71.3 - - - +
429B LEU* 1.3 60.0 + - - +
431B ALA* 4.1 0.4 - - - -
432B GLN* 2.9 30.0 + - - +
442B THR* 3.5 4.7 - - - +
444B LEU* 3.7 13.0 - - + -
468B LEU* 3.6 31.2 - - + +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.6 2.2 - - + -
45B ILE* 3.9 28.3 - - + -
47B THR* 4.6 6.5 - - + -
56B ALA* 4.2 12.6 - - + -
425B PHE* 3.1 11.8 + - + +
426B GLY* 3.5 10.8 - - - +
427B THR 3.2 0.2 - - - -
428B ALA* 1.3 74.7 - - - +
430B GLY* 1.3 65.2 + - - +
432B GLN* 3.4 7.0 + - - +
433B VAL* 3.3 24.9 + - - +
457B GLU* 4.2 20.0 - - + +
460B THR* 3.8 26.2 - - + -
461B LEU* 3.5 29.8 - - + -
466B LEU* 3.9 9.3 - - + +
468B LEU* 4.1 6.4 - - + +
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Residues in contact with GLY 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.1 10.1 - - - -
56B ALA* 3.2 32.8 - - - +
60B TYR* 3.5 14.3 - - - +
426B GLY 3.1 10.7 + - - -
427B THR 3.8 0.7 - - - -
429B LEU* 1.3 72.3 - - - +
431B ALA* 1.3 66.2 + - - +
433B VAL* 3.1 13.2 + - - +
434B ALA 3.1 9.7 + - - -
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY 3.6 12.7 - - - +
60B TYR* 4.5 0.2 - - - +
63B ALA* 3.8 19.5 - - + +
388B THR* 4.3 4.9 - - + -
390B VAL* 4.5 0.2 - - + -
413B LEU* 4.1 10.1 - - + -
427B THR 2.9 17.4 + - - +
428B ALA* 3.6 6.5 - - - +
429B LEU 3.3 0.2 - - - -
430B GLY* 1.3 75.6 - - - +
432B GLN* 1.3 58.2 + - - +
434B ALA* 3.1 3.7 + - - +
435B ASP* 2.8 31.7 + - - -
442B THR* 3.7 15.9 - - + -
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Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ALA 2.9 16.1 + - - +
429B LEU* 3.7 7.4 - - - +
430B GLY 3.2 0.2 - - - -
431B ALA* 1.3 76.5 - - - +
433B VAL* 1.3 64.2 + - - +
435B ASP* 3.7 1.8 - - - +
436B LEU* 3.1 28.8 + - + +
440B ARG 3.4 22.2 + - - -
441B ARG* 3.8 11.0 - - - +
442B THR* 2.9 41.1 + - - +
466B LEU* 4.3 11.4 - - + -
467B PRO* 3.9 36.5 - - + +
468B LEU* 4.4 8.3 - - + +
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Residues in contact with VAL 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 3.7 33.4 - - + +
23B PHE* 3.8 24.5 - - + -
45B ILE* 4.2 11.0 - - + -
60B TYR* 4.0 9.9 - - + -
429B LEU 3.3 15.1 + - - +
430B GLY 3.1 7.2 + - - +
432B GLN* 1.3 78.3 - - - +
434B ALA* 1.3 62.6 + - - +
436B LEU* 3.3 19.1 + - + +
437B GLU* 4.2 8.3 - - - +
466B LEU* 3.8 30.5 - - + -
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.7 43.2 - - + +
63B ALA* 4.6 2.9 - - + -
64B GLY* 4.1 17.8 - - - +
66B LYS* 5.5 2.8 - - - -
430B GLY 3.1 8.0 + - - +
431B ALA* 3.1 7.4 + - - +
433B VAL* 1.3 78.6 - - - +
435B ASP* 1.3 60.7 + - - +
436B LEU 3.4 0.7 + - - -
437B GLU* 3.4 22.4 - - - +
438B ALA* 3.8 7.1 + - - +
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.4 4.4 - - - +
388B THR* 3.1 25.0 + - - +
431B ALA 2.8 21.5 + - - +
432B GLN* 3.7 8.7 - - - +
433B VAL 3.3 0.2 - - - -
434B ALA* 1.3 71.5 - - - +
436B LEU* 1.3 59.6 + - - +
437B GLU 3.4 0.2 - - - -
438B ALA* 3.2 4.5 + - - +
439B GLY 2.8 24.9 + - - -
440B ARG* 2.8 67.0 + - + +
442B THR* 2.7 21.5 + - - -
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Residues in contact with LEU 436 (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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432B GLN* 3.1 34.8 + - - +
433B VAL* 3.5 13.0 - - + +
434B ALA 3.2 0.6 - - - -
435B ASP* 1.3 77.1 - - - +
437B GLU* 1.3 64.1 + - - +
439B GLY* 3.4 11.4 + - - -
440B ARG 4.7 2.9 - - - +
441B ARG* 6.3 0.2 - - - -
465B GLN 5.3 2.7 - - - +
466B LEU* 3.9 27.8 - - + -
467B PRO* 4.6 14.8 - - + -
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Residues in contact with GLU 437 (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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20B GLU* 4.9 6.4 - - - +
21B HIS* 3.6 30.8 + - - -
60B TYR* 3.9 10.9 + - - -
66B LYS* 3.9 19.4 - - - +
433B VAL 4.2 7.8 - - - +
434B ALA 3.4 16.2 - - - +
436B LEU* 1.3 80.9 - - - +
438B ALA* 1.3 59.2 + - + +
439B GLY 3.2 1.3 + - - -
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ALA 4.3 7.6 - - - +
435B ASP* 3.2 8.2 + - - +
437B GLU* 1.3 79.4 - - + +
439B GLY* 1.3 61.2 + - - +
440B ARG* 3.3 34.5 + - + +
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY* 4.5 3.8 - - - +
435B ASP 2.8 6.7 + - - -
436B LEU* 3.4 7.5 + - - -
437B GLU 3.2 6.1 + - - -
438B ALA* 1.3 77.0 - - - +
440B ARG* 1.3 60.0 + - - -
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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
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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