Contacts of the strand formed by residues 2042 - 2048 (chain A) in PDB entry 5W0P
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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2027A LEU* 3.4 29.4 - - + -
2032A TYR* 3.5 14.4 - - + +
2041A PRO* 1.3 69.6 - - - +
2043A ASP* 1.3 59.2 + - - +
2062A LEU* 3.8 16.6 - - + -
2119A PHE* 4.0 12.3 - - + +
2120A LEU* 3.5 8.1 - - - +
2121A LEU* 2.9 39.8 + - + +
2123A PHE* 3.5 29.6 - - + -
2150A VAL* 4.0 14.8 - - + -
2175A ILE* 3.8 11.0 - - + -
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Residues in contact with ASP2043 (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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2027A LEU* 3.3 16.4 - - - +
2028A GLY* 3.5 14.4 + - - -
2029A LYS* 5.2 0.9 + - - +
2032A TYR* 3.6 15.9 + - - -
2041A PRO* 3.4 5.2 + - + +
2042A VAL* 1.3 76.0 - - - +
2044A GLY* 1.3 58.5 + - - +
2102A THR* 4.0 20.9 + - + +
2104A LEU* 3.2 29.5 - - - +
2105A GLN* 5.1 1.3 - - - +
2119A PHE* 4.3 4.5 - - - +
2120A LEU* 4.2 12.6 - - + -
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Residues in contact with GLY2044 (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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2026A TYR 3.4 14.6 - - - -
2043A ASP* 1.3 77.0 - - - +
2045A VAL* 1.3 66.1 + - - +
2104A LEU* 4.4 10.9 - - - +
2105A GLN* 3.2 24.3 + - - +
2108A LEU* 5.0 1.8 - - - -
2119A PHE* 3.3 24.8 + - - +
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Residues in contact with VAL2045 (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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2026A TYR* 2.9 45.3 + - + +
2044A GLY* 1.3 79.1 - - - +
2046A VAL* 1.3 68.8 + - - +
2047A LEU 4.3 0.2 - - - -
2105A GLN* 4.0 26.7 - - + +
2108A LEU* 3.7 30.5 - - + -
2109A LEU* 4.9 3.8 - - + -
2112A LEU* 4.3 1.1 - - + -
2116A THR* 3.6 23.3 - - + -
2117A TYR 3.5 9.2 - - - +
2118A PRO* 4.0 14.6 - - + -
2119A PHE* 3.3 3.1 - - - -
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Residues in contact with VAL2046 (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 VAL* 3.7 25.4 - - + -
2024A THR 3.4 11.4 - - - +
2025A ILE* 4.1 13.9 - - + -
2045A VAL* 1.3 80.5 - - - +
2047A LEU* 1.3 67.3 + - - +
2048A VAL* 3.6 16.4 + - + +
2058A VAL* 4.4 7.9 - - + -
2060A VAL* 5.1 1.6 - - + -
2091A VAL* 4.0 20.9 - - + -
2115A ASN 3.9 1.0 - - - +
2116A THR* 3.6 2.9 - - - -
2117A TYR* 2.8 31.4 + - - +
2119A PHE* 3.7 20.9 - - + -
2152A ALA* 4.7 9.2 - - + -
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Residues in contact with LEU2047 (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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2022A SER 3.5 3.7 - - - +
2023A VAL* 3.8 1.4 - - - -
2024A THR* 2.8 45.3 + - - +
2026A TYR* 4.0 32.6 - - + +
2045A VAL 4.3 0.4 - - - -
2046A VAL* 1.3 71.6 - - - +
2048A VAL* 1.3 67.8 + - - +
2112A LEU* 4.5 9.6 - - + -
2113A GLY* 4.9 7.9 - - - +
2115A ASN* 4.0 14.4 - - + +
2116A THR* 3.5 31.4 - - - +
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Residues in contact with VAL2048 (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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2022A SER 3.7 2.9 - - - +
2023A VAL* 4.9 2.5 - - + +
2046A VAL* 4.0 22.7 - - + +
2047A LEU* 1.3 82.4 - - - +
2049A ASP* 1.3 67.1 + - - +
2050A PRO* 3.4 2.5 - - + +
2053A VAL* 3.7 31.4 - - + +
2058A VAL* 3.8 28.9 - - + -
2091A VAL* 4.9 1.1 - - + -
2092A TYR* 4.4 12.6 - - + -
2115A ASN* 3.2 37.7 + - + +
2117A TYR* 4.3 13.9 - - + -
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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