Contacts of the strand formed by residues 280 - 283 (chain B) in PDB entry 3RC0
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 GLU 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B GLY 4.0 6.9 - - - +
71B THR* 3.2 18.3 - - + -
72B VAL* 3.0 22.9 + - - +
76B GLY* 3.9 4.7 - - - -
77B MET 3.2 15.5 - - - +
78B VAL* 4.2 6.9 - - + +
251B ASN* 2.6 36.6 + - - +
257B ASN* 3.2 19.1 + - - -
275B ILE* 4.3 1.3 - - - +
278B GLY 4.1 1.2 + - - -
279B HIS* 1.3 77.1 - - - +
281B ILE* 1.3 69.1 + - - +
282B PHE* 3.3 41.0 - - + -
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Residues in contact with ILE 281 (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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64B VAL* 3.7 32.3 - - + -
77B MET* 2.9 28.4 + - + +
78B VAL 3.9 13.7 - - - -
79B ALA* 4.0 13.0 - - + +
83B VAL* 5.2 0.7 - - + -
89B LEU* 3.9 20.4 - - + -
250B LEU* 4.0 24.2 - - + +
251B ASN 4.3 4.0 + - - -
257B ASN* 3.5 3.4 - - - +
258B ALA* 3.7 24.9 - - + -
275B ILE* 3.9 18.8 - - + -
279B HIS 4.2 1.3 - - - +
280B GLU* 1.3 80.4 - - - +
282B PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.8 26.9 - - + -
251B ASN* 3.4 20.9 - - + +
252B HIS 4.0 0.7 - - - -
253B LEU* 3.5 41.3 - - + +
255B ASN 5.3 1.1 - - - -
256B HIS* 3.1 15.0 - - - +
257B ASN* 2.6 24.4 + - - +
258B ALA* 3.0 24.2 + - - -
280B GLU* 3.3 57.7 - - + -
281B ILE* 1.3 71.4 - - - +
283B ASN* 1.3 64.0 + - - +
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Residues in contact with ASN 283 (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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225B PHE* 3.9 29.7 - - - -
247B ALA 4.6 2.8 + - - -
250B LEU* 3.8 24.4 - - + +
251B ASN 2.9 10.0 + - - +
252B HIS* 3.4 19.3 - - - -
253B LEU 3.5 5.4 + - - -
256B HIS* 3.5 4.3 - - - +
258B ALA* 3.6 14.2 - - - +
259B ASN* 3.7 13.2 - - - -
260B LEU* 4.1 4.1 + - - +
269B MET* 4.0 14.2 - - - +
281B ILE 4.0 2.0 + - - -
282B PHE* 1.3 76.7 - - - +
284B THR* 1.3 89.3 + - - +
285B TYR* 4.2 14.1 - - + -
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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