Contacts of the strand formed by residues 2057 - 2068 (chain B) in PDB entry 4ZWJ
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 LYS2057 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056B LYS* 1.3 79.6 - - - +
2058B VAL* 1.3 64.8 + - - +
2059B TYR* 3.4 46.7 + - + +
2090B GLN* 4.9 11.9 - - - +
2092B TYR 3.7 4.9 - - - +
2093B PRO* 5.0 2.2 - - + -
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Residues in contact with VAL2058 (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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2023B VAL* 4.5 28.5 - - + -
2046B VAL* 5.1 6.5 - - + -
2048B VAL* 4.1 17.5 - - + -
2053B VAL* 3.6 32.1 - - + -
2057B LYS* 1.3 72.1 - - - +
2059B TYR* 1.3 71.3 + - - +
2090B GLN* 3.9 2.3 - - - +
2091B VAL* 3.0 29.9 + - + -
2092B TYR* 3.0 33.1 + - + +
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Residues in contact with TYR2059 (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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2057B LYS* 3.4 53.4 + - + +
2058B VAL* 1.3 80.2 - - - +
2060B VAL* 1.4 60.7 + - - +
2061B THR* 3.8 20.1 + - + +
2088B ARG* 5.5 10.8 - - + -
2089B VAL* 3.5 8.7 - - - +
2090B GLN* 3.5 40.4 + - + -
2091B VAL* 4.5 1.1 - - - -
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Residues in contact with VAL2060 (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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2025B ILE* 4.8 19.1 - - + -
2046B VAL* 5.0 11.4 - - + -
2059B TYR* 1.4 73.1 - - - +
2061B THR* 1.4 59.1 + - - +
2062B LEU 4.2 0.4 + - - -
2089B VAL* 2.4 61.8 + - + +
2090B GLN 4.1 2.7 - - - +
2091B VAL* 3.5 28.1 - - + +
2119B PHE* 3.6 25.1 - - + -
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Residues in contact with THR2061 (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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2059B TYR* 3.8 21.9 + - + +
2060B VAL* 1.4 86.4 - - - +
2062B LEU* 1.3 64.4 + - - +
2063B THR* 3.8 7.8 + - - -
2086B PHE* 4.5 13.1 - - + -
2087B SER 3.8 2.5 - - - -
2088B ARG* 3.7 24.0 - - + +
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Residues in contact with LEU2062 (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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2042B VAL* 4.7 24.5 - - + -
2060B VAL 4.2 0.6 + - - -
2061B THR* 1.3 75.0 - - - +
2063B THR* 1.4 71.3 + - - +
2064B CYS* 5.1 2.0 - - + +
2085B TYR* 5.0 10.3 - - + -
2086B PHE* 3.5 3.1 - - - -
2087B SER* 2.4 70.0 + - - +
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Residues in contact with THR2063 (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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2061B THR* 3.8 9.2 + - - -
2062B LEU* 1.4 84.6 - - - +
2064B CYS* 1.4 68.0 + - - +
2065B ALA* 3.8 8.7 + - + +
2081B ARG* 5.3 5.6 - - - +
2083B ASP* 3.8 22.9 - - - +
2085B TYR 4.1 1.8 - - - +
2086B PHE* 3.3 25.5 - - + -
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Residues in contact with CYS2064 (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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2062B LEU* 4.2 2.9 - - + +
2063B THR* 1.4 75.0 - - - +
2065B ALA* 1.4 63.3 + - - +
2083B ASP* 3.6 7.6 - - - +
2084B LEU* 3.3 32.0 + - - -
2085B TYR* 2.4 62.9 + - + +
2086B PHE* 4.2 0.4 - - - +
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Residues in contact with ALA2065 (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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2063B THR* 3.8 9.4 + - + +
2064B CYS* 1.4 80.0 - - - +
2066B PHE* 1.3 61.2 + - - +
2067B ARG* 3.8 20.8 + - - +
2081B ARG* 4.2 22.0 - - - +
2083B ASP* 4.0 21.3 - - - +
2084B LEU* 4.8 5.2 - - - +
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Residues in contact with PHE2066 (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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142B PRO* 4.3 30.1 - - + -
2065B ALA* 1.3 71.7 - - - +
2067B ARG* 1.3 77.5 + - - +
2068B TYR* 4.0 13.4 - + + -
2081B ARG* 3.5 17.3 - - - +
2082B ARG* 3.0 30.3 + - + +
2084B LEU* 4.0 34.7 - - + +
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Residues in contact with ARG2067 (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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2063B THR* 6.4 0.2 - - - +
2065B ALA* 3.8 18.8 + - + +
2066B PHE* 1.3 86.5 - - - +
2068B TYR* 1.3 61.8 + - - +
2069B GLY 5.4 2.0 - - - +
2071B GLU* 6.4 0.2 - - - +
2081B ARG* 3.0 51.6 - - - +
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Residues in contact with TYR2068 (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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138B VAL* 4.6 15.3 - - + -
139B VAL* 4.4 28.0 + - + +
142B PRO* 4.4 24.7 - - + +
145B ASN* 3.9 20.2 - - + -
2066B PHE* 4.0 28.3 - + + -
2067B ARG* 1.3 75.8 - - - +
2069B GLY* 1.3 64.2 + - - +
2074B ASP* 2.9 29.9 - - + +
2079B THR* 4.9 3.9 + - - +
2080B PHE 3.6 15.8 + - - -
2081B ARG* 3.8 25.8 - - - +
2082B ARG* 3.9 13.5 + - + +
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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