Contacts of the helix formed by residues 280 - 285 (chain A) in PDB entry 5I4A
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 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A PHE* 3.9 3.1 - - + -
275A SER* 2.5 35.0 + - - -
277A TYR* 3.0 25.1 + - - +
279A LYS* 1.3 80.8 - - - +
281A VAL* 1.3 58.1 + - - +
282A PHE 3.0 2.7 - - - -
283A LYS* 2.8 55.2 + - - +
284A TYR* 3.2 27.1 + - + -
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Residues in contact with VAL 281 (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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270A PHE* 3.4 33.2 - - + -
278A ALA 2.9 19.9 + - - +
279A LYS 3.0 0.6 - - - +
280A ASP* 1.3 76.8 - - - +
282A PHE* 1.3 77.0 + - + +
285A SER* 2.8 34.0 + - - +
286A PHE* 3.8 30.7 - - + -
330A LEU* 3.9 10.8 - - + +
417A TYR* 4.0 9.6 - - + -
428A PRO 3.9 4.5 - - - +
610A PRO* 3.9 16.8 - - + -
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS 3.3 16.5 + - - +
280A ASP 3.0 0.8 - - - -
281A VAL* 1.3 86.7 - - + +
283A LYS* 1.3 60.7 + - + +
285A SER 4.6 0.7 - - - -
326A ALA* 4.2 9.4 - - + -
329A GLU* 3.5 50.8 - - + +
330A LEU* 3.6 35.4 - - + -
413A LYS* 3.4 64.4 - - + +
417A TYR* 4.5 6.1 - - + -
610A PRO* 4.1 12.1 - - + -
611A TYR* 4.0 13.5 - + - -
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Residues in contact with LYS 283 (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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272A ASN* 5.4 1.9 + - - +
279A LYS 5.6 0.4 - - - +
280A ASP* 2.8 39.3 + - - +
282A PHE* 1.3 80.6 - - + +
284A TYR* 1.3 92.0 + - + +
285A SER 3.7 0.4 - - - -
329A GLU 5.5 0.2 - - - -
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Residues in contact with TYR 284 (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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270A PHE* 3.6 20.0 - + + -
271A LYS* 3.1 1.4 + - - +
272A ASN* 2.9 53.0 + - + +
273A GLY* 3.4 22.0 - - - +
274A GLU 4.0 15.7 + - - -
280A ASP* 3.2 40.6 + - + +
283A LYS* 1.3 107.4 + - + +
285A SER* 1.3 74.7 + - - +
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Residues in contact with SER 285 (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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270A PHE* 3.2 17.3 - - - +
271A LYS* 4.2 9.6 + - - +
272A ASN* 4.1 12.3 - - - -
281A VAL* 2.8 16.3 + - - -
283A LYS 3.7 0.4 - - - -
284A TYR* 1.3 84.8 - - - +
286A PHE* 1.3 77.1 + - - +
328A ALA 4.7 0.7 + - - -
329A GLU 3.1 20.3 + - - -
330A LEU 3.1 17.9 + - - -
331A GLY* 3.2 11.1 + - - -
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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