Contacts of the helix formed by residues 520 - 534 (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 SER 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B SER* 5.8 2.7 - - - -
370B LEU* 4.1 13.9 - - - +
518B VAL* 4.7 0.2 - - - +
519B ASP* 1.3 87.3 - - - +
521B VAL* 1.3 68.1 + - - +
522B GLU* 3.5 16.5 + - - +
523B SER* 3.1 17.4 + - - -
524B PHE* 3.0 26.0 + - - +
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B SER* 5.9 5.1 - - - -
370B LEU* 3.6 26.8 - - + +
374B HIS* 4.1 21.1 - - + +
378B VAL* 4.3 18.7 - - + +
381B LYS* 6.0 2.0 - - - +
520B SER* 1.3 74.5 + - - +
522B GLU* 1.3 65.1 + - + +
524B PHE* 4.0 2.7 - - - +
525B SER* 3.1 25.5 + - - +
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Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B SER* 3.2 11.9 + - - +
521B VAL* 1.3 80.9 - - + +
523B SER* 1.3 67.7 + - - +
525B SER* 3.5 5.5 + - - -
526B ALA* 3.3 23.0 + - - +
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Residues in contact with SER 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B HIS 5.5 0.4 - - - -
518B VAL* 3.3 21.4 - - - +
519B ASP* 3.4 11.0 + - - -
520B SER* 3.1 32.2 + - - -
522B GLU* 1.3 83.2 - - - +
524B PHE* 1.3 60.7 + - - +
526B ALA* 3.6 4.8 + - - +
527B ALA* 3.1 17.3 + - - +
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Residues in contact with PHE 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 4.9 2.7 - - + -
375B ALA* 3.4 31.9 - - + -
378B VAL* 3.6 20.0 - - + -
379B ILE* 3.7 18.2 - - + -
471B ILE* 3.6 31.2 - - + -
473B MSE 4.3 4.3 - - + -
518B VAL* 3.7 16.7 - - + +
520B SER 3.0 18.5 + - - +
521B VAL* 4.0 2.7 - - - +
523B SER* 1.3 74.2 + - - +
525B SER* 1.3 66.4 + - - +
527B ALA* 3.2 1.0 + - - +
528B LEU* 2.9 34.5 + - + +
540B ILE* 3.8 23.1 - - + -
542B VAL* 3.7 25.8 - - + -
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Residues in contact with SER 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL* 3.8 13.2 - - - +
381B LYS* 2.9 35.7 + - - -
382B HIS* 4.8 3.0 + - - -
521B VAL* 3.1 22.2 + - - +
522B GLU* 3.6 7.9 - - - -
524B PHE* 1.3 77.9 - - - +
526B ALA* 1.3 61.7 + - - +
528B LEU* 3.4 2.3 + - - +
529B ALA* 3.1 25.1 + - - +
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Residues in contact with ALA 526 (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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522B GLU 3.3 13.2 + - - +
523B SER* 3.8 6.5 - - - +
524B PHE 3.3 0.2 - - - -
525B SER* 1.3 77.0 - - - +
527B ALA* 1.3 60.0 + - - +
529B ALA* 3.5 4.8 + - - +
530B GLN* 3.0 31.3 + - - +
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B TYR* 3.9 28.8 - - + -
518B VAL* 3.8 16.8 - - + -
523B SER 3.1 17.5 + - - +
524B PHE 3.2 4.9 + - - +
526B ALA* 1.3 76.1 - - - +
528B LEU* 1.3 63.2 + - - +
530B GLN* 3.3 4.0 + - - +
531B ALA* 3.0 24.4 + - - +
540B ILE* 4.1 16.9 - - + +
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Residues in contact with LEU 528 (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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378B VAL* 3.9 12.6 - - + +
379B ILE* 4.0 16.8 - - + -
382B HIS* 3.4 27.8 - - + +
443B ILE* 5.0 5.8 - - + -
469B ILE* 4.4 10.5 - - + -
471B ILE* 3.9 19.7 - - + -
524B PHE* 2.9 30.8 + - + +
525B SER* 3.9 4.0 - - - +
527B ALA* 1.3 76.4 - - - +
529B ALA* 1.3 57.7 + - - +
531B ALA* 3.4 0.7 + - - -
532B LEU* 3.0 59.9 + - + +
540B ILE* 3.7 15.9 - - + +
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Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B HIS* 4.4 18.1 - - + -
525B SER 3.1 19.0 + - - +
526B ALA* 3.8 5.6 - - - +
528B LEU* 1.3 78.1 - - - +
530B GLN* 1.3 62.5 + - - +
532B LEU* 3.5 5.2 + - - +
533B ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 530 (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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516B TYR* 3.3 31.1 + - - +
526B ALA 3.0 18.3 + - - +
527B ALA* 3.7 5.1 - - - +
529B ALA* 1.3 76.8 - - - +
531B ALA* 1.3 61.5 + - - +
533B ALA* 3.2 14.9 + - + +
534B HIS* 3.3 31.3 + - + +
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Residues in contact with ALA 531 (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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441B ARG* 3.2 6.1 + - - -
469B ILE* 4.0 13.5 - - + -
516B TYR* 3.9 14.3 + - + +
527B ALA 3.0 15.9 + - - +
528B LEU 3.9 2.9 - - - +
530B GLN* 1.3 72.3 - - - +
532B LEU* 1.3 67.4 + - - +
533B ALA 3.1 1.3 - - - -
534B HIS* 3.0 25.8 + - - +
536B ARG 4.6 1.7 - - - +
538B ALA* 3.9 27.6 - - + -
540B ILE* 4.5 8.1 - - + -
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Residues in contact with LEU 532 (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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382B HIS* 3.8 27.8 - - + +
387B VAL* 5.8 3.6 - - + -
441B ARG* 3.2 37.3 + - + +
443B ILE* 3.9 15.7 - - + -
469B ILE* 3.4 18.6 - - + +
528B LEU* 3.0 50.9 + - + +
529B ALA* 3.7 6.3 - - - +
531B ALA* 1.3 76.8 - - - +
533B ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 533 (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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529B ALA 3.1 13.3 + - - +
530B GLN* 3.5 13.0 - - - +
531B ALA 3.1 1.2 - - - -
532B LEU* 1.3 76.3 - - - +
534B HIS* 1.3 70.2 + - + +
535B ASN 4.1 1.0 + - - -
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Residues in contact with HIS 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG* 3.3 15.6 + - - -
514B ASP* 4.7 2.9 - - - +
516B TYR* 4.3 8.5 - - - -
530B GLN* 3.3 37.2 + - + +
531B ALA* 3.0 20.2 + - - +
532B LEU 4.5 0.2 - - - -
533B ALA* 1.3 87.2 + - + +
535B ASN* 1.3 58.0 + - - +
536B ARG* 2.9 54.6 + - + +
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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