Contacts of the strand formed by residues 2142 - 2147 (chain A) in PDB entry 4ASI
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 MET2142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2108A LEU* 3.7 38.4 - - + +
2115A VAL* 3.3 29.2 - - + +
2117A VAL* 4.6 8.3 - - + -
2133A ILE 3.3 26.2 - - - +
2134A ASP 3.6 12.1 - - - +
2135A SER* 3.7 20.9 - - - -
2137A ILE* 4.3 1.3 - - - -
2138A ASN* 2.7 49.3 + - + +
2139A PRO* 3.9 10.0 - - - +
2141A HIS* 1.3 76.0 - - - +
2143A GLU* 1.3 67.8 + - - +
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Residues in contact with GLU2143 (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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2115A VAL 2.9 6.6 + - - +
2116A LEU* 3.7 14.4 - - + +
2117A VAL* 2.8 35.8 + - - +
2135A SER* 4.5 3.8 - - - -
2141A HIS 5.3 2.7 - - - +
2142A MET* 1.3 79.6 - - - +
2144A MET* 1.3 56.3 + - - +
2145A TYR* 2.7 31.7 + - + -
2240A SER* 4.2 13.2 - - - +
2255A ARG* 3.0 33.0 + - - +
2259A LEU* 3.3 28.1 - - - +
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Residues in contact with MET2144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2117A VAL* 3.5 18.8 - - + -
2119A ILE* 5.4 3.1 - - + -
2125A LEU* 3.7 22.7 - - + -
2130A TRP* 3.4 39.3 - - + +
2133A ILE* 4.0 18.8 - - + +
2134A ASP* 3.8 19.3 - - - +
2135A SER* 3.8 23.4 - - - +
2143A GLU* 1.3 74.2 - - - +
2145A TYR* 1.3 68.6 + - - +
2238A VAL 4.1 13.7 - - - +
2239A ILE* 3.6 9.4 - - + -
2240A SER* 2.9 32.6 + - - -
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Residues in contact with TYR2145 (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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2116A LEU* 4.6 3.4 - - + -
2117A VAL 2.7 17.5 + - - +
2118A TYR* 3.3 4.9 - - + -
2119A ILE* 2.9 28.6 + - - +
2143A GLU* 2.7 43.0 + - + -
2144A MET* 1.3 78.2 - - - +
2146A ALA* 1.3 60.2 + - - +
2239A ILE* 4.6 3.4 - - - -
2240A SER* 3.9 15.1 - - - -
2241A ASP* 3.8 35.0 - - + +
2243A LEU* 3.8 26.5 - - + -
2251A PHE* 3.5 24.5 - + - -
2252A PHE* 3.8 26.0 - + + -
2255A ARG* 3.4 17.1 + - + +
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Residues in contact with ALA2146 (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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2118A TYR* 4.1 2.5 - - - -
2119A ILE* 3.9 13.5 - - + -
2145A TYR* 1.3 76.4 - - - +
2147A ASP* 1.3 62.6 + - - +
2150A SER* 3.4 14.4 - - - +
2230A PRO* 4.5 4.5 - - + -
2233A MET* 4.1 17.0 - - - -
2239A ILE* 3.6 22.6 - - + +
2241A ASP 3.4 5.7 + - - -
2242A ILE* 3.2 9.2 - - - +
2243A LEU 2.9 22.0 + - - -
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Residues in contact with ASP2147 (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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2118A TYR* 2.7 27.6 + - + -
2119A ILE 2.9 22.0 + - - +
2120A PRO 3.8 0.7 - - - -
2121A PRO* 3.4 32.6 - - + +
2146A ALA* 1.3 75.2 - - - +
2148A ARG* 1.3 67.8 + - - +
2149A GLU* 3.0 24.3 + - - +
2150A SER* 2.3 27.8 + - - +
2230A PRO* 3.4 4.0 - - - +
2242A ILE* 4.0 0.2 - - - -
2243A LEU 3.3 7.1 - - - +
2244A ASP* 4.5 1.0 - - - +
2245A TRP* 2.9 24.3 + - - +
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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