Contacts of the strand formed by residues 2064 - 2070 (chain D) in PDB entry 5Z58
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 TRP2064 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2062D GLU* 5.4 0.7 - - + +
2063D GLY* 1.3 75.1 - - - +
2065D TRP* 1.3 63.5 + - - +
2081D ARG* 3.4 6.2 - - - +
2082D LEU* 2.9 43.1 + - + +
2083D THR* 5.8 0.2 - - - -
2084D LEU* 6.1 1.8 - - + +
2109D MET 3.1 10.8 - - - +
2110D SER* 4.6 0.7 - - - +
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Residues in contact with TRP2065 (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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1943D MET* 5.6 6.3 - - + -
2064D TRP* 1.3 76.8 - - - +
2066D VAL* 1.3 60.8 + - - +
2067D VAL* 3.9 7.1 + - + +
2080D LYS 3.5 8.3 - - - +
2081D ARG* 4.6 2.2 - - + +
2107D TYR 4.5 0.2 - - - -
2108D PHE* 3.4 4.7 - - - +
2109D MET* 2.9 42.9 + - + +
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Residues in contact with VAL2066 (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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2039D VAL* 5.7 7.6 - - + -
2064D TRP 4.1 0.6 + - - -
2065D TRP* 1.3 72.7 - - - +
2067D VAL* 1.3 60.6 + - - +
2079D ILE* 3.6 2.4 - - - -
2080D LYS* 2.9 40.8 + - + +
2081D ARG* 5.0 0.2 - - - +
2090D VAL* 5.4 12.6 - - + -
2107D TYR 3.6 6.5 - - - +
2108D PHE* 4.7 2.7 - - + +
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Residues in contact with VAL2067 (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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2065D TRP* 3.9 6.9 - - + +
2066D VAL* 1.3 76.2 - - - +
2068D ILE* 1.3 62.3 + - - +
2078D SER 3.7 9.6 - - - +
2079D ILE* 4.2 7.2 - - + +
2106D LEU* 3.6 4.5 - - - +
2107D TYR* 2.8 46.5 + - + +
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Residues in contact with ILE2068 (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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2037D VAL* 6.1 5.6 - - + -
2067D VAL* 1.3 77.9 - - - +
2069D GLY* 1.3 58.9 + - - +
2076D LEU* 4.0 2.4 - - - +
2077D ILE* 3.1 6.8 + - + -
2078D SER* 2.9 47.8 + - - +
2092D LEU* 6.1 2.9 - - + -
2104D TYR* 6.0 3.6 - - + -
2105D THR 3.4 8.5 - - - +
2106D LEU* 5.0 3.4 - - + -
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Residues in contact with GLY2069 (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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1936D LEU* 5.9 2.5 - - - -
2068D ILE* 1.3 74.8 - - - +
2070D ASP* 1.3 63.5 + - - -
2071D ALA* 3.6 2.6 + - - -
2075D SER 3.4 13.2 - - - -
2076D LEU* 4.5 1.6 - - - -
2077D ILE* 3.6 10.0 - - - +
2104D TYR* 4.5 5.2 - - - +
2105D THR* 2.9 36.9 + - - +
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Residues in contact with ASP2070 (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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2069D GLY* 1.3 71.4 - - - -
2071D ALA* 1.3 63.8 + - - +
2072D LYS* 3.2 5.8 + - + +
2073D SER* 3.6 7.9 + - - +
2074D ASN 3.6 1.6 + - - -
2075D SER* 3.2 35.8 + - - +
2077D ILE* 4.4 6.8 - - + +
2103D ASN 4.9 9.6 - - - +
2104D TYR* 4.7 8.7 - - + +
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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