Contacts of the helix formed by residues 283 - 288 (chain A) in PDB entry 2FBW
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 PHE 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 3.8 24.8 + - + -
276A ILE 3.6 22.2 - - - -
277A ASN* 3.6 16.4 - - + +
281A GLU* 3.0 41.0 + - - +
282A ARG* 1.3 67.3 - - - +
284A MET* 1.3 89.7 + - + +
285A GLU 3.1 2.7 - - - -
286A ARG* 3.0 24.9 + - - +
287A TYR* 3.1 19.9 + + - -
304A MET* 3.9 28.9 - - + -
307A GLU* 3.6 24.9 - - + +
321A VAL* 4.3 11.4 - - + -
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Residues in contact with MET 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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275A LEU* 4.2 7.2 + - + -
282A ARG* 3.2 2.2 + - + -
283A PHE* 1.3 92.4 - - + +
285A GLU* 1.3 60.0 + - - +
286A ARG 3.0 0.2 - - - -
287A TYR* 3.8 11.2 - - + +
288A ALA* 2.9 44.2 + - + +
292A LYS* 3.4 34.7 - - - +
293A ASP* 3.7 27.1 + - - +
295A ALA* 4.2 3.6 - - + -
299A VAL* 4.4 2.7 - - + -
300A VAL* 3.9 25.8 - - + -
303A SER* 3.5 36.6 - - - +
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Residues in contact with GLU 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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282A ARG* 3.1 49.1 + - - +
283A PHE 3.1 1.0 - - - -
284A MET* 1.3 78.8 - - - +
286A ARG* 1.3 56.2 + - - +
288A ALA 4.5 0.2 - - - -
289A PRO* 3.4 25.8 - - - +
292A LYS* 3.7 35.2 - - + +
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Residues in contact with ARG 286 (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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281A GLU* 2.9 44.4 + - - +
282A ARG 4.6 0.2 + - - -
283A PHE* 3.0 11.1 + - - +
284A MET 3.0 0.4 - - - -
285A GLU* 1.3 80.3 - - + +
287A TYR* 1.3 90.3 + - + +
288A ALA 3.5 0.4 + - - -
289A PRO* 4.2 9.1 - - - +
307A GLU* 3.0 27.1 + - - -
310A GLU* 5.3 0.6 + - - -
312A ARG* 4.0 11.8 - - - +
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Residues in contact with TYR 287 (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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283A PHE* 3.1 28.4 + + - -
284A MET* 4.0 8.3 - - + -
286A ARG* 1.3 99.1 + - + +
288A ALA* 1.3 60.2 + - - +
289A PRO* 4.0 4.0 - - - +
299A VAL* 5.0 6.8 - - + +
303A SER* 3.4 40.4 - - - +
306A ILE* 3.2 42.4 - - + +
307A GLU* 2.5 41.1 + - + -
310A GLU* 4.4 0.5 + - - -
312A ARG* 4.1 1.2 + - - -
621A TYR* 4.8 1.2 - - - +
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Residues in contact with ALA 288 (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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284A MET* 2.9 17.9 + - + +
287A TYR* 1.3 79.3 - - - +
289A PRO* 1.3 69.9 - - - +
290A VAL 3.2 2.5 - - - -
292A LYS* 2.8 31.3 + - - +
295A ALA* 4.1 18.6 - - + -
299A VAL* 5.0 3.4 - - + -
621A TYR* 3.5 24.2 - - + +
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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