Contacts of the strand formed by residues 2085 - 2092 (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 TYR2085 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLU* 3.9 23.6 - - - -
2062B LEU* 5.0 10.3 - - + -
2064B CYS* 2.4 56.2 + - + +
2083B ASP* 4.6 2.5 - - - -
2084B LEU* 1.3 83.0 - - + +
2086B PHE* 1.3 65.9 + - - +
2087B SER* 3.4 32.1 - - - -
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Residues in contact with PHE2086 (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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239B GLU* 5.1 3.5 + - - +
240B SER* 5.6 9.6 - - - +
2061B THR* 4.5 9.9 - - + -
2062B LEU 3.5 9.2 - - - -
2063B THR* 3.3 36.1 - - + -
2064B CYS 4.2 0.2 - - - +
2083B ASP* 5.0 11.2 - - + +
2085B TYR* 1.3 89.2 - - - +
2087B SER* 1.3 63.2 + - - +
2088B ARG* 3.4 63.0 - - + -
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Residues in contact with SER2087 (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* 2.4 63.4 + - - +
2085B TYR* 3.4 28.4 - - - -
2086B PHE* 1.3 77.5 - - - +
2088B ARG* 1.3 56.8 + - - +
2089B VAL* 5.0 6.0 - - - +
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Residues in contact with ARG2088 (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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239B GLU 6.0 0.2 + - - -
241B ALA* 6.3 1.2 - - - +
2059B TYR* 5.5 12.1 - - + -
2061B THR* 3.7 21.8 - - + +
2086B PHE* 3.4 37.8 - - + -
2087B SER* 1.3 72.3 - - - +
2089B VAL* 1.3 69.5 + - - +
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Residues in contact with VAL2089 (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* 3.4 8.0 - - - -
2060B VAL* 2.4 59.1 + - + +
2087B SER* 4.3 6.7 + - - +
2088B ARG* 1.3 78.2 - - - +
2090B GLN* 1.3 68.7 + - + +
2095B VAL* 6.5 0.4 - - + -
2119B PHE* 6.2 0.9 - - + -
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Residues in contact with GLN2090 (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* 4.9 10.9 - - + +
2058B VAL 4.1 5.4 - - - +
2059B TYR* 3.5 34.6 + - + -
2089B VAL* 1.3 90.6 - - + +
2091B VAL* 1.3 77.4 + - - +
2092B TYR 4.5 1.9 + - - +
2093B PRO* 3.6 34.8 + - - +
2095B VAL* 3.7 27.5 - - + +
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Residues in contact with VAL2091 (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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2046B VAL* 3.5 22.4 - - + -
2048B VAL* 5.8 0.2 - - + -
2058B VAL* 3.0 15.1 + - + +
2059B TYR 4.5 0.4 - - - -
2060B VAL* 3.5 35.7 - - + +
2090B GLN* 1.3 85.3 - - - +
2092B TYR* 1.3 64.2 + - + +
2093B PRO 3.2 16.6 - - - +
2094B PRO* 3.4 12.8 - - - +
2117B TYR* 3.3 39.8 - - + +
2118B PRO 4.5 4.7 - - - +
2119B PHE* 4.5 7.9 - - + -
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Residues in contact with TYR2092 (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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2048B VAL* 4.2 11.2 - - + -
2049B ASP 5.7 0.2 - - - -
2050B PRO* 4.9 10.4 + - + +
2053B VAL* 3.7 34.8 + - + -
2054B LYS* 5.5 1.1 - - - -
2055B GLY 6.1 0.4 - - - -
2056B LYS 4.6 6.3 - - - -
2057B LYS* 3.7 3.3 - - - -
2058B VAL* 3.0 54.7 + - + +
2090B GLN* 4.5 2.9 + - - -
2091B VAL* 1.3 80.0 - - + +
2093B PRO* 1.3 81.1 - - + +
2094B PRO* 4.3 1.3 - - + -
2117B TYR* 3.4 47.6 - + + -
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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