Contacts of the helix formed by residues 284 - 289 (chain A) in PDB entry 3RBL
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 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ALA* 3.5 38.8 - - + +
279A PHE* 3.6 11.8 - - + -
281A CYS* 3.1 16.9 + - + -
283A GLU* 1.3 106.3 - - + +
285A ARG* 1.3 65.6 + - - +
286A HIS* 3.0 10.7 + + - -
287A LEU* 3.2 32.8 + - + +
378A ILE* 4.6 1.8 - - + -
379A ARG* 5.2 2.9 - - + -
382A VAL* 4.0 32.8 - - + -
405A ILE* 4.1 23.6 - - + -
406A LEU* 4.6 6.5 - - + -
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Residues in contact with ARG 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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126A LEU 2.7 26.8 + - - -
127A GLU* 2.5 44.3 + - + +
128A LEU* 4.1 1.0 - - - +
129A PRO* 3.9 17.6 - - - +
279A PHE* 3.9 17.3 - - - +
281A CYS 3.2 13.6 + - - +
282A PRO* 3.7 10.3 + - + +
283A GLU 3.6 1.2 - - - -
284A PHE* 1.3 77.4 - - - +
286A HIS* 1.3 61.6 + - - +
288A LEU* 3.0 44.5 + - - +
289A ASN* 3.3 20.5 + - - +
291A VAL* 5.5 1.4 - - - +
292A GLU* 6.3 0.6 - - - +
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Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO 4.8 2.6 + - - +
283A GLU 3.0 28.7 + - - -
284A PHE* 3.0 5.5 + + - -
285A ARG* 1.3 77.4 - - - +
287A LEU* 1.3 95.2 + - + +
288A LEU 3.0 0.2 - - - -
289A ASN* 2.8 48.5 + - - +
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Residues in contact with LEU 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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243A LEU* 3.6 25.2 - - - +
251A PHE* 3.8 48.4 - - + +
254A LEU* 5.2 2.3 - - - +
279A PHE* 4.1 11.4 - - + -
284A PHE* 3.2 22.6 + - + +
286A HIS* 1.3 104.9 - - + +
288A LEU* 1.3 57.3 + - - +
289A ASN 3.4 3.3 + - - +
405A ILE* 4.0 19.1 - - + -
406A LEU* 5.3 1.1 - - + -
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Residues in contact with LEU 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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126A LEU* 4.1 4.0 - - + +
128A LEU* 3.8 27.8 - - + -
243A LEU* 3.5 14.4 - - + -
254A LEU* 3.9 1.5 - - - +
270A VAL* 5.0 0.2 - - + -
279A PHE* 3.5 41.5 - - + -
284A PHE 4.3 0.6 + - - -
285A ARG* 3.0 39.6 + - - +
287A LEU* 1.3 75.7 - - - +
289A ASN* 1.3 64.3 + - - +
290A GLY 3.2 0.5 + - - -
291A VAL* 2.8 51.8 + - + +
297A PHE* 3.9 18.6 - - + -
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Residues in contact with ASN 289 (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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254A LEU* 3.5 18.0 + - - +
255A LEU* 3.7 27.0 + - + +
285A ARG* 3.3 18.4 + - - +
286A HIS* 2.8 37.9 + - - +
287A LEU 4.6 1.6 - - - +
288A LEU* 1.3 76.6 - - - +
290A GLY* 1.3 58.9 + - - +
291A VAL 3.5 0.2 - - - -
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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