Contacts of the helix formed by residues 314 - 319 (chain B) in PDB entry 2AR0
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 ASP 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B PRO* 1.3 72.7 - - - +
315B ASN* 1.3 66.2 + - - +
317B LEU* 2.8 22.6 + - - +
318B PHE* 3.2 25.3 + - + -
341B ARG* 2.8 25.4 + - - -
353B LYS* 3.0 37.3 + - + +
355B ASN* 3.0 8.9 - - - +
383B ARG* 2.8 34.5 + - - -
466B ASP* 3.9 8.5 - - - +
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Residues in contact with ASN 315 (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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62B LYS* 5.6 2.2 - - - +
272B GLY* 5.8 1.4 - - - +
289B ASN* 5.1 5.2 - - - +
291B GLN* 4.4 10.7 - - - +
313B PRO* 3.6 22.3 - - - +
314B ASP* 1.3 75.8 + - - +
316B VAL* 1.3 60.8 + - + +
317B LEU 3.0 0.5 + - - -
318B PHE* 3.4 27.1 - - + -
319B GLU* 2.6 47.1 + - - +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASN* 5.2 2.0 - - - +
291B GLN* 3.7 31.4 - - + +
292B LEU* 3.8 31.6 - - + +
295B MSE 4.5 15.0 - - + -
312B VAL* 4.1 20.9 - - + -
313B PRO* 3.3 24.9 + - + +
314B ASP 3.2 0.2 - - - -
315B ASN* 1.3 76.6 - - + +
317B LEU* 1.3 59.8 + - + +
319B GLU* 5.0 0.9 - - - -
327B ARG* 2.9 25.3 + - + +
357B LEU* 4.8 7.0 - - + -
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Residues in contact with LEU 317 (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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312B VAL* 4.8 5.2 - - + -
313B PRO 4.3 4.0 - - - +
314B ASP 2.8 10.8 + - - +
316B VAL* 1.3 82.5 - - + +
318B PHE* 1.3 58.2 + - - +
327B ARG* 3.0 14.8 + - - +
339B ILE* 4.8 4.7 - - + -
341B ARG* 3.5 19.5 - - - +
355B ASN* 3.4 35.7 - - + +
357B LEU* 3.8 30.7 - - + -
464B SER* 3.4 1.2 + - - -
465B LEU* 3.0 66.2 + - + +
466B ASP* 3.8 4.5 - - + +
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Residues in contact with PHE 318 (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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43B LYS* 5.7 8.7 - - - -
59B ASP* 4.7 3.2 - - - +
314B ASP* 3.3 36.1 - - + -
315B ASN* 3.4 30.1 - - + -
317B LEU* 1.3 79.2 - - - +
319B GLU* 1.3 92.5 + - + +
320B GLY* 3.4 2.4 + - - -
327B ARG* 3.5 2.9 + - - -
464B SER* 3.8 10.2 + - - +
466B ASP* 3.5 33.9 - - + +
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Residues in contact with GLU 319 (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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59B ASP* 3.8 12.1 - - - +
62B LYS* 2.9 41.4 + - - +
63B SER* 3.7 19.9 - - - -
289B ASN* 3.6 22.0 - - - +
292B LEU* 4.6 5.2 - - + -
315B ASN* 2.6 32.4 + - - +
318B PHE* 1.3 84.1 - - + +
320B GLY* 1.3 73.1 + - - +
323B GLY* 3.8 10.9 - - - +
324B THR* 3.9 0.3 + - - -
327B ARG* 2.5 34.4 + - - +
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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