Contacts of the helix formed by residues 2172 - 2188 (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 GLY2172 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2170F GLN 3.6 0.6 + - - -
2171F MET* 1.3 75.1 - - - +
2173F PRO* 1.3 66.8 - - - +
2174F GLN 3.5 1.6 - - - -
2175F GLU* 3.3 14.0 - - - +
2176F GLU* 2.5 38.2 + - - +
2226F PHE* 4.5 9.8 - - - -
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Residues in contact with PRO2173 (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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2172F GLY* 1.3 83.2 - - - +
2174F GLN* 1.3 60.2 + - - +
2176F GLU* 3.2 5.9 + - + +
2177F ASN* 2.9 27.9 + - - +
2226F PHE* 5.2 6.9 - - + -
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Residues in contact with GLN2174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680F ARG* 5.4 12.9 + - - +
1794F GLU* 4.1 24.0 + - - +
1795F ALA 3.7 18.6 + - - +
1796F PRO* 4.2 11.1 - - - +
1797F ALA* 4.3 10.3 - - - +
2166F LEU* 5.2 2.4 - - - +
2172F GLY 3.5 0.2 - - - -
2173F PRO* 1.3 80.6 - - - +
2175F GLU* 1.3 61.8 + - - +
2177F ASN* 3.3 9.3 + - + +
2178F LEU* 2.9 45.3 + - - +
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Residues in contact with GLU2175 (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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2166F LEU* 4.0 29.7 - - + +
2169F VAL* 5.9 1.1 - - + -
2170F GLN 4.4 5.6 - - - +
2171F MET* 4.2 7.6 - - - -
2172F GLY* 3.3 24.9 + - - +
2173F PRO 3.2 0.6 - - - -
2174F GLN* 1.3 83.8 + - - +
2176F GLU* 1.3 56.7 + - - +
2178F LEU* 3.4 2.4 + - - +
2179F MET* 2.9 29.6 + - - +
2229F MET* 6.2 0.4 - - - -
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Residues in contact with GLU2176 (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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2171F MET* 5.6 0.4 - - - +
2172F GLY 2.5 23.3 + - - +
2173F PRO* 3.6 6.3 - - + +
2175F GLU* 1.3 73.5 - - - +
2177F ASN* 1.3 56.9 + - - +
2179F MET* 3.3 7.2 + - - +
2180F ILE* 2.9 39.0 + - + +
2226F PHE* 5.0 14.4 - - + -
2229F MET* 4.5 25.3 - - + +
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Residues in contact with ASN2177 (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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1794F GLU* 4.3 26.3 + - - +
2173F PRO 2.9 16.9 + - - +
2174F GLN* 3.6 9.6 - - - +
2176F GLU* 1.3 78.1 - - - +
2178F LEU* 1.3 56.5 + - - +
2180F ILE* 3.2 9.5 + - - +
2181F GLN* 2.9 49.4 + - - +
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Residues in contact with LEU2178 (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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1796F PRO* 6.2 6.3 - - + -
1797F ALA 6.3 0.2 - - - +
2162F GLN* 3.4 39.0 - - + +
2166F LEU* 3.7 33.0 - - + -
2174F GLN* 2.9 34.5 + - - +
2175F GLU* 3.8 4.7 - - - +
2177F ASN* 1.3 75.8 - - - +
2179F MET* 1.3 57.7 + - - +
2181F GLN* 3.3 9.9 + - + +
2182F SER* 2.9 30.7 + - - +
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Residues in contact with MET2179 (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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2163F ILE* 3.7 40.2 - - + +
2166F LEU* 5.6 9.4 - - + +
2167F LEU* 6.1 1.1 - - - -
2175F GLU 2.9 17.8 + - - +
2176F GLU 3.6 5.6 - - - +
2178F LEU* 1.3 77.2 - - - +
2180F ILE* 1.3 58.4 + - + +
2182F SER* 3.3 3.8 + - - -
2183F ILE* 2.9 56.5 + - + +
2208F VAL* 5.7 7.4 - - + -
2211F VAL* 3.8 32.3 - - + -
2229F MET* 3.6 28.0 - - + -
2232F SER* 5.8 1.6 - - - +
2233F CYS* 5.9 3.6 - - + -
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Residues in contact with ILE2180 (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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2176F GLU* 2.9 25.9 + - + +
2177F ASN* 3.2 9.8 + - - +
2179F MET* 1.3 77.4 - - + +
2181F GLN* 1.3 72.1 + - - +
2183F ILE* 3.3 7.5 + - - +
2184F GLY* 2.9 25.5 + - - -
2228F LYS* 3.6 33.7 - - + +
2229F MET* 4.4 5.6 - - - +
2232F SER* 4.0 23.6 - - - +
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Residues in contact with GLN2181 (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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2177F ASN* 2.9 41.6 + - - +
2178F LEU* 3.7 12.6 - - + +
2179F MET 3.3 0.2 - - - -
2180F ILE* 1.3 88.0 - - - +
2182F SER* 1.3 57.9 + - - +
2184F GLY* 3.3 2.2 + - - -
2185F ASN* 2.9 29.7 + - - +
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Residues in contact with SER2182 (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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2159F CYS* 4.9 6.5 - - - -
2162F GLN* 5.7 5.4 - - - -
2163F ILE* 3.6 31.4 - - - -
2178F LEU* 2.9 22.1 + - - +
2179F MET* 3.6 6.7 - - - -
2180F ILE 3.2 0.2 - - - -
2181F GLN* 1.3 77.3 - - - +
2183F ILE* 1.3 58.1 + - - +
2185F ASN* 3.1 6.7 + - - +
2186F ILE* 2.9 36.2 + - - +
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Residues in contact with ILE2183 (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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2163F ILE* 5.0 5.8 - - + -
2179F MET* 2.9 50.2 + - + +
2180F ILE* 3.8 6.5 - - - +
2182F SER* 1.3 76.2 - - - +
2184F GLY* 1.3 62.3 + - - +
2186F ILE* 3.2 32.8 - - + +
2187F MET* 3.3 18.0 - - - +
2208F VAL* 5.3 8.1 - - + -
2232F SER* 3.8 35.4 - - - +
2233F CYS* 5.5 3.8 - - + +
2235F ARG* 5.8 1.8 - - - +
2236F PHE* 3.8 25.4 - - + -
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Residues in contact with GLY2184 (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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2180F ILE 2.9 14.9 + - - -
2181F GLN* 3.7 3.8 - - - -
2183F ILE* 1.3 78.8 - - - +
2185F ASN* 1.3 58.5 + - - +
2187F MET* 3.7 12.3 + - - +
2188F ASN* 2.9 25.6 - - - +
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Residues in contact with ASN2185 (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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2155F SER* 5.3 5.2 + - - +
2156F LEU* 5.9 0.3 - - - +
2159F CYS* 4.3 20.7 - - + +
2181F GLN 2.9 17.3 + - - +
2182F SER* 3.1 7.2 + - - +
2184F GLY* 1.3 75.0 - - - +
2186F ILE* 1.3 65.4 + - + +
2187F MET 3.1 2.9 + - - -
2188F ASN* 3.4 15.7 + - - +
2189F ASN* 4.0 6.9 + - - +
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Residues in contact with ILE2186 (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* 4.3 17.6 - - + +
2159F CYS* 3.5 30.3 - - - -
2160F LEU* 5.8 0.7 - - + -
2163F ILE* 4.0 16.4 - - + -
2182F SER 2.9 14.8 + - - +
2183F ILE* 3.2 43.3 - - + +
2185F ASN* 1.3 76.5 - - - +
2187F MET* 1.3 60.1 + - - +
2188F ASN 3.4 0.4 + - - -
2189F ASN* 3.8 14.5 - - - +
2192F PHE* 4.4 13.9 - - + +
2204F MET* 6.6 0.2 - - + -
2208F VAL* 6.0 0.4 - - + -
2236F PHE* 3.5 34.9 - - + -
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Residues in contact with MET2187 (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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2183F ILE* 3.3 28.7 + - - +
2184F GLY* 4.0 8.7 - - - +
2185F ASN 3.1 1.0 - - - -
2186F ILE* 1.3 76.4 - - - +
2188F ASN* 1.3 61.1 + - - +
2189F ASN 3.2 14.2 + - - +
2192F PHE* 5.1 5.9 - - + -
2193F TYR* 4.0 22.1 + - - +
2235F ARG* 4.1 24.7 - - - +
2236F PHE* 4.0 29.2 - - + -
2239F TYR* 3.7 49.6 - - + -
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Residues in contact with ASN2188 (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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2184F GLY 2.9 19.9 - - - +
2185F ASN* 3.4 11.7 + - - +
2187F MET* 1.3 79.5 + - - +
2189F ASN* 1.3 60.9 + - - +
2190F LYS* 3.7 1.6 + - - +
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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