Contacts of the helix formed by residues 2189 - 2194 (chain F) in PDB entry 6X34
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 ASN2189 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152F ASP* 3.4 32.3 + - - +
2155F SER* 4.3 5.7 + - - -
2156F LEU* 3.7 26.3 - - + +
2185F ASN 4.0 4.7 + - - +
2186F ILE 3.8 15.7 + - - +
2187F MET 3.2 6.7 - - - +
2188F ASN* 1.3 79.7 - - - +
2190F LYS* 1.3 61.4 + - - +
2191F VAL* 2.5 38.8 + - - +
2192F PHE* 3.2 23.4 + - + +
2193F TYR* 4.4 10.6 + - - -
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Residues in contact with LYS2190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152F ASP* 5.5 4.1 - - + +
2188F ASN 3.7 2.4 + - - +
2189F ASN* 1.3 75.2 + - - +
2191F VAL* 1.3 66.7 + - + +
2192F PHE 3.2 2.7 + - - -
2193F TYR* 3.3 13.9 + - - +
2194F GLN* 3.3 27.8 - - - +
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Residues in contact with VAL2191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2145F ILE* 5.5 2.5 - - + -
2149F SER* 3.7 25.1 - - - +
2152F ASP* 3.9 20.6 - - + -
2153F THR* 4.3 19.7 - - + +
2156F LEU* 5.6 6.5 - - + -
2189F ASN* 2.5 19.3 + - - +
2190F LYS* 1.3 72.0 - - + +
2192F PHE* 1.3 62.5 + - - -
2193F TYR 3.2 0.2 - - - -
2194F GLN* 3.0 21.3 + - - +
2195F HIS* 3.1 42.5 + - + +
2198F LEU* 4.8 11.7 - - + -
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Residues in contact with PHE2192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156F LEU* 5.4 10.7 - - + +
2186F ILE* 4.4 13.2 - - + +
2187F MET* 5.1 6.1 - - + +
2189F ASN* 3.2 27.0 + - + +
2190F LYS 3.2 0.6 - - - -
2191F VAL* 1.3 79.3 - - - +
2193F TYR* 1.3 77.8 + + - +
2194F GLN 3.6 0.3 + - - -
2195F HIS 4.4 10.7 + - - +
2196F PRO* 4.6 3.1 - - - +
2199F MET* 4.4 9.2 - - + +
2204F MET* 3.6 33.0 - - + -
2236F PHE* 4.3 18.2 - + - -
2239F TYR* 4.8 7.9 - - + -
2240F PHE* 3.5 30.5 - + - -
2243F ILE* 3.8 32.9 - - + +
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Residues in contact with TYR2193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2187F MET* 4.0 20.6 + - - +
2189F ASN 4.5 8.3 - - - -
2190F LYS* 3.3 9.6 + - - +
2191F VAL 3.2 0.4 - - - -
2192F PHE* 1.3 100.1 - + - +
2194F GLN* 1.3 62.3 + - + +
2196F PRO* 4.9 6.6 - - - +
2239F TYR* 3.9 26.0 - + - -
2243F ILE* 3.6 28.1 - - + +
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Residues in contact with GLN2194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2146F SER* 6.1 2.2 - - - -
2149F SER* 4.6 7.7 + - - -
2190F LYS* 3.3 26.5 - - - +
2191F VAL* 3.0 19.9 + - - +
2193F TYR* 1.3 81.5 - - + +
2195F HIS* 1.3 85.2 + - + +
2196F PRO* 3.3 10.2 - - - +
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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