Contacts of the strand formed by residues 2046 - 2050 (chain B) in PDB entry 3N00
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 HIS2046 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A GLN* 3.3 29.0 + - - -
437A GLU* 2.6 29.8 + - - -
608A SER* 3.3 26.2 - - - +
609A PHE 3.3 4.7 - - - +
610A ARG* 3.8 22.8 - - + +
611A VAL* 3.7 7.9 - - - +
2045B THR* 1.3 101.5 - - - +
2047B ARG* 1.3 61.8 + - - +
2048B LEU* 4.0 11.0 + - + +
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Residues in contact with ARG2047 (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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607A LEU 3.8 0.3 - - - +
608A SER* 3.4 4.0 - - - -
609A PHE* 2.7 60.5 + - + +
611A VAL* 3.4 20.3 - - + +
2046B HIS* 1.3 72.2 - - - +
2048B LEU* 1.3 63.6 + - - +
2049B ILE* 3.8 45.4 + - - +
2054B HIS* 4.9 3.8 + - - -
2057B GLN* 3.8 15.3 + - - +
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Residues in contact with LEU2048 (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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436A TRP* 3.3 36.6 - - + -
606A LEU* 4.5 24.2 - - + +
607A LEU 3.4 5.6 - - - +
608A SER* 3.5 17.5 - - - +
2046B HIS* 4.0 10.0 + - + +
2047B ARG* 1.3 74.4 + - - +
2049B ILE* 1.3 59.7 + - - +
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Residues in contact with ILE2049 (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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606A LEU* 4.1 3.7 - - - +
607A LEU* 2.6 37.8 + - + +
609A PHE* 3.5 38.4 - - + -
2047B ARG* 3.8 21.8 - - - +
2048B LEU* 1.3 74.4 - - - +
2050B THR* 1.3 63.9 + - - +
2053B ASP* 3.7 17.9 - - + +
2054B HIS* 3.9 18.8 - - + +
2057B GLN* 3.4 40.4 - - - +
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Residues in contact with THR2050 (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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603A SER 4.1 3.8 - - - -
604A GLU* 3.4 38.2 + - + +
605A LYS 3.3 6.1 - - - -
606A LEU* 4.0 13.2 - - + +
2049B ILE* 1.3 76.4 - - - +
2051B LEU* 1.3 59.7 + - - +
2052B ALA* 4.0 5.6 + - - +
2053B ASP* 2.9 37.8 + - - +
2054B HIS* 2.9 28.5 + - - +
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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