Contacts of the helix formed by residues 456 - 465 (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 GLY 456 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A GLY* 4.5 11.9 + - - -
455A ILE* 4.3 9.9 - - - +
48B ARG* 3.6 15.3 - - - +
454B SER 3.0 2.2 + - - -
455B ILE* 1.3 78.5 - - - +
457B GLU* 1.3 55.8 + - - +
458B PHE 3.1 6.1 - - - -
459B ASP* 3.0 30.9 + - - +
511B PHE* 3.8 18.2 - - - -
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Residues in contact with GLU 457 (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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47B THR* 3.3 13.5 - - - +
48B ARG* 3.1 28.0 + - - +
49B HIS* 3.3 7.3 + - - +
52B ALA* 3.3 33.9 - - + +
425B PHE* 3.6 23.6 - - + -
426B GLY 5.2 0.9 - - - +
429B LEU* 4.2 7.9 - - + +
454B SER* 3.0 24.8 + - - +
456B GLY* 1.3 73.9 - - - +
458B PHE* 1.3 64.9 + - - +
459B ASP 3.1 0.4 - - - -
460B THR* 2.6 42.3 + - - +
461B LEU* 2.9 15.2 + - - +
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Residues in contact with PHE 458 (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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425B PHE* 3.7 18.6 - + - -
451B VAL* 4.6 3.1 - - + -
455B ILE* 3.3 41.3 + - + +
456B GLY 3.1 0.8 - - - -
457B GLU* 1.3 76.1 - - - +
459B ASP* 1.3 61.8 + - - +
461B LEU* 3.2 17.2 + - + +
462B VAL* 3.1 24.9 + - - +
470B VAL* 3.7 33.7 - - + -
504B TYR 4.9 0.7 - - - -
508B ALA* 4.1 22.9 - - + -
511B PHE* 3.8 22.0 - + + -
513B ALA* 4.2 11.0 - - + -
538B ALA 3.9 6.7 - - - -
539B CYS* 3.5 39.7 - - + -
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Residues in contact with ASP 459 (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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499A LEU* 6.1 0.2 - - - -
501A ASN* 2.7 48.2 + - - +
502A GLY 4.2 0.2 + - - -
48B ARG* 3.1 30.9 + - + +
456B GLY 3.0 16.1 + - - +
458B PHE* 1.3 78.1 - - - +
460B THR* 1.3 55.3 + - - +
462B VAL* 3.3 2.1 + - - +
463B ARG* 2.6 54.7 + - - +
511B PHE* 3.7 23.2 - - + -
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Residues in contact with THR 460 (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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45B ILE* 4.7 1.6 - - + -
46B ASP 3.5 21.3 - - - +
47B THR* 3.7 7.7 - - + -
48B ARG* 3.5 8.5 - - - +
429B LEU* 3.8 21.8 - - + -
457B GLU* 2.6 32.2 + - - +
459B ASP* 1.3 73.7 - - - +
461B LEU* 1.3 61.5 + - - +
463B ARG* 3.0 20.1 + - - +
464B LYS* 2.8 47.6 + - + +
466B LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 461 (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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425B PHE* 3.6 30.1 - - + -
429B LEU* 3.5 33.0 - - + -
457B GLU 2.9 7.8 + - - +
458B PHE* 3.3 24.7 - - + +
460B THR* 1.3 76.4 - - - +
462B VAL* 1.3 56.4 + - - +
465B GLN* 2.9 23.7 + - - -
466B LEU* 3.0 40.8 + - + +
468B LEU* 4.2 25.8 - - + +
470B VAL* 4.5 1.8 - - + -
537B PRO* 3.9 17.2 - - + +
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Residues in contact with VAL 462 (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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501A ASN* 3.6 24.0 - - - +
458B PHE 3.1 11.1 + - - +
459B ASP 3.8 4.9 - - - +
460B THR 3.2 0.2 - - - -
461B LEU* 1.3 75.7 - - - +
463B ARG* 1.3 67.0 + - - +
464B LYS 3.4 0.3 + - - -
465B GLN* 3.4 15.7 + - - +
511B PHE 3.4 21.5 - - - +
512B GLY* 3.5 26.5 - - - +
513B ALA* 3.6 11.7 - - + +
537B PRO* 4.1 10.3 - - + -
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Residues in contact with ARG 463 (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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498A ARG 4.4 5.4 + - - -
499A LEU* 3.7 31.0 - - - +
500A GLU 4.7 4.0 - - - +
501A ASN* 3.9 20.2 - - + -
46B ASP* 3.0 39.4 + - - -
47B THR 4.1 2.6 + - - -
48B ARG* 3.6 11.1 - - - +
459B ASP* 2.6 42.9 + - - +
460B THR* 3.0 30.1 + - - +
462B VAL* 1.3 73.7 - - - +
464B LYS* 1.3 76.3 + - + +
465B GLN* 4.6 4.2 - - - +
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Residues in contact with LYS 464 (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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496A GLY* 5.7 0.4 - - - -
44B ILE 4.2 7.7 + - - -
45B ILE* 4.4 22.0 - - + +
46B ASP* 2.6 35.3 + - - +
460B THR* 2.8 31.5 + - + +
463B ARG* 1.3 99.7 - - + +
465B GLN* 1.3 71.6 + - - +
466B LEU* 3.3 24.4 + - + +
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Residues in contact with GLN 465 (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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436B LEU* 5.3 2.3 - - - +
461B LEU 2.9 10.9 + - - -
462B VAL* 3.4 12.1 + - - +
463B ARG 3.4 4.2 - - - +
464B LYS* 1.3 81.1 - - - +
466B LEU* 1.3 61.5 + - - +
467B PRO* 3.5 9.8 - - - +
535B ASN* 5.2 2.1 - - - +
537B PRO* 5.5 6.1 - - - -
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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