Contacts of the strand formed by residues 2042 - 2047 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1925A HIS* 3.2 15.4 + - - +
1926A ILE 3.1 22.2 + - - +
1927A LEU* 4.0 2.3 - - - +
2011A VAL* 4.3 5.2 - - + -
2021A VAL* 3.1 15.9 - - + +
2023A LEU* 4.1 21.5 - - + -
2031A VAL* 4.1 29.2 - - + +
2035A ALA* 4.0 15.9 - - + -
2038A CYS* 3.7 33.2 - - + -
2040A ARG 3.8 1.3 - - - +
2041A PRO* 1.3 78.7 - - - +
2043A ILE* 1.3 64.8 + - - +
2044A ASN 4.0 0.2 + - - -
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Residues in contact with ILE2043 (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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1924A GLN 5.8 0.2 - - - +
1926A ILE* 3.7 23.6 - - + +
1980A PHE* 3.7 32.5 - - + -
2020A VAL* 3.7 24.2 - - + -
2021A VAL 2.6 14.3 + - - +
2022A VAL* 3.5 8.6 - - + -
2023A LEU* 2.8 31.0 + - - +
2041A PRO* 5.7 1.8 - - + -
2042A VAL* 1.3 78.8 - - - +
2044A ASN* 1.3 63.4 + - - +
2045A ALA 3.1 3.3 + - - -
2054A THR* 3.9 18.4 - - + -
2217A LEU* 4.9 9.0 - - + -
2218A LEU* 4.2 18.8 - - + -
2221A VAL* 5.4 7.9 - - + -
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Residues in contact with ASN2044 (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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1926A ILE 2.9 19.7 + - - +
1927A LEU* 3.1 24.5 + - - +
2023A LEU 3.7 3.6 - - - -
2031A VAL* 3.5 27.4 - - + +
2042A VAL 4.0 1.0 + - - -
2043A ILE* 1.3 74.7 - - - +
2045A ALA* 1.3 58.3 + - - +
2046A GLY 2.9 29.9 + - - -
2047A ASP* 2.8 23.6 + - - +
2051A GLU* 3.5 13.1 + - - +
2052A HIS* 4.4 1.4 + - - -
2053A PRO* 3.8 21.2 - - + +
2054A THR* 4.3 6.8 - - - +
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Residues in contact with ALA2045 (chain A).
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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1969A PHE* 4.1 5.2 - - + -
1976A THR* 3.9 16.8 - - + -
1980A PHE* 4.5 2.5 - - + -
2022A VAL* 3.5 28.0 - - + -
2023A LEU 3.0 16.2 + - - +
2024A ARG* 2.8 47.8 + - + -
2043A ILE* 3.1 3.3 + - - -
2044A ASN* 1.3 71.4 - - - +
2046A GLY* 1.3 51.2 + - - +
2052A HIS* 3.2 13.4 - - - -
2054A THR* 5.2 0.9 - - - -
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Residues in contact with GLY2046 (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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2023A LEU 4.0 0.2 - - - +
2024A ARG* 3.2 7.3 - - - +
2025A HIS 2.9 24.4 + - - +
2044A ASN* 2.9 12.3 + - - +
2045A ALA* 1.3 79.7 - - - +
2047A ASP* 1.3 59.2 + - - +
2051A GLU 3.3 13.5 - - - -
2052A HIS* 4.3 1.8 - - - -
2085A ARG* 3.5 22.2 - - - -
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Residues in contact with ASP2047 (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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2025A HIS* 2.9 9.0 - - + +
2027A GLN 3.6 9.4 - - - +
2028A PRO* 3.3 7.7 - - - +
2029A GLY* 2.5 34.0 + - - -
2031A VAL* 3.7 23.1 - - + +
2032A GLU 5.8 0.2 - - - -
2044A ASN* 2.8 29.6 + - - -
2046A GLY* 1.3 73.8 - - - +
2048A GLY* 1.3 60.4 + - - +
2050A GLY* 2.9 21.8 + - - -
2051A GLU* 3.4 15.1 + - - +
2085A ARG* 3.5 1.6 - - - +
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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