Contacts of the strand formed by residues 2042 - 2047 (chain D) in PDB entry 5G1N
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 VAL2042 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1925D HIS* 3.1 27.0 - - + +
1926D ILE 2.9 23.7 + - - -
1927D LEU* 4.4 1.5 - - + +
2011D VAL* 4.7 4.9 - - + -
2021D VAL* 3.1 17.0 - - + +
2023D LEU* 4.4 12.3 - - + -
2031D VAL* 3.8 29.2 - - + +
2035D ALA* 3.7 25.6 - - + +
2038D CYS* 4.0 14.6 - - + -
2040D ARG 3.7 6.3 - - - +
2041D PRO* 1.3 76.3 - - - +
2043D ILE* 1.3 66.1 + - - +
2044D ASN 3.9 0.9 + - - -
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Residues in contact with ILE2043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926D ILE* 3.8 24.2 - - + -
1980D PHE* 3.8 25.8 - - + -
2020D VAL* 4.0 23.8 - - + -
2021D VAL 2.6 12.4 + - - +
2022D VAL* 3.6 8.0 - - + -
2023D LEU* 3.1 23.7 + - - -
2041D PRO* 5.2 0.9 - - + -
2042D VAL* 1.3 79.8 - - - +
2044D ASN* 1.3 65.3 + - - +
2045D ALA* 3.2 1.2 + - - +
2054D THR* 3.6 31.2 - - + -
2217D LEU* 4.1 16.8 - - + +
2218D LEU* 4.1 10.8 - - + -
2221D VAL* 4.8 9.4 - - + -
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Residues in contact with ASN2044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926D ILE 2.9 19.3 + - - +
1927D LEU* 3.4 25.7 + - + +
2031D VAL* 3.7 30.0 - - + +
2042D VAL 3.9 1.4 + - - -
2043D ILE* 1.3 78.4 - - - +
2045D ALA* 1.3 56.9 + - - +
2046D GLY* 2.7 38.3 + - - -
2047D ASP* 3.0 27.2 + - - -
2051D GLU* 4.0 2.6 + - - +
2052D HIS* 4.5 0.5 + - - -
2053D PRO* 3.5 27.7 - - + +
2054D THR* 4.1 6.8 - - - +
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Residues in contact with ALA2045 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1969D PHE* 4.2 5.4 - - + -
1976D THR* 3.7 19.5 - - + -
1980D PHE* 4.4 5.2 - - + -
2022D VAL* 3.8 24.9 - - + -
2023D LEU 2.9 19.1 + - - +
2024D ARG* 2.9 31.7 + - - +
2043D ILE 3.2 0.8 + - - +
2044D ASN* 1.3 72.3 - - - +
2046D GLY* 1.3 56.3 - - - +
2052D HIS* 3.2 16.5 - - - -
2054D THR* 5.5 0.7 - - - -
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Residues in contact with GLY2046 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2023D LEU 4.7 0.2 - - - -
2024D ARG* 3.4 5.1 - - - +
2025D HIS 2.9 27.2 + - - +
2044D ASN* 2.7 9.3 + - - -
2045D ALA* 1.3 80.1 - - - +
2047D ASP* 1.3 59.0 + - - -
2051D GLU 3.4 12.1 - - - -
2052D HIS* 4.1 2.8 + - - -
2085D ARG* 3.3 26.2 + - - -
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Residues in contact with ASP2047 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025D HIS 3.2 6.3 - - - -
2027D GLN 3.8 8.7 - - - +
2028D PRO* 3.1 13.1 - - - +
2029D GLY* 2.8 27.5 + - - +
2031D VAL* 3.8 24.7 - - + +
2032D GLU 5.8 0.4 + - - -
2044D ASN* 3.0 19.5 + - - +
2046D GLY* 1.3 69.2 - - - -
2048D GLY* 1.3 58.9 + - - +
2050D GLY* 2.9 19.8 + - - -
2051D GLU* 2.8 27.5 + - - +
2085D ARG* 3.6 0.6 - - - +
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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