Contacts of the helix formed by residues 2172 - 2188 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2170B GLN 3.6 0.6 + - - -
2171B MET* 1.3 75.7 - - - +
2173B PRO* 1.3 66.9 - - - +
2174B GLN 3.5 1.8 - - - -
2175B GLU* 3.3 13.4 - - - +
2176B GLU* 2.5 38.3 + - - +
2226B PHE* 4.5 8.5 - - - -
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Residues in contact with PRO2173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172B GLY* 1.3 84.1 - - - +
2174B GLN* 1.3 59.1 + - - +
2176B GLU* 3.6 6.4 - - + +
2177B ASN* 2.9 28.1 + - - +
2226B PHE* 5.2 6.7 - - + -
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Residues in contact with GLN2174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680B ARG* 5.4 13.1 + - - +
1794B GLU 4.1 23.9 + - - +
1795B ALA 3.7 19.6 + - - +
1796B PRO* 4.2 11.1 - - - +
1797B ALA* 4.3 10.2 - - - +
2166B LEU* 5.2 2.6 - - - +
2173B PRO* 1.3 80.2 - - - +
2175B GLU* 1.3 62.5 + - - +
2177B ASN* 3.3 8.7 + - + +
2178B LEU* 2.9 44.4 + - - +
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Residues in contact with GLU2175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2166B LEU* 4.0 29.7 - - + +
2169B VAL* 5.9 1.8 - - + -
2170B GLN 4.4 5.4 - - - +
2171B MET* 4.2 7.4 - - - -
2172B GLY* 3.3 25.4 + - - +
2173B PRO 3.2 0.6 - - - -
2174B GLN* 1.3 85.3 + - - +
2176B GLU* 1.3 57.4 + - - +
2178B LEU* 3.4 2.9 + - - +
2179B MET* 2.9 29.5 + - - +
2229B MET* 6.2 0.2 - - - -
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Residues in contact with GLU2176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171B MET* 5.6 0.6 - - - +
2172B GLY 2.5 23.1 + - - +
2173B PRO* 3.6 5.8 - - + +
2175B GLU* 1.3 72.1 - - - +
2177B ASN* 1.3 59.1 + - - +
2179B MET* 3.3 7.6 + - - +
2180B ILE* 2.9 39.2 + - + +
2226B PHE* 5.0 15.0 - - + -
2229B MET* 4.5 25.1 - - + +
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Residues in contact with ASN2177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794B GLU* 4.3 26.3 + - - +
2173B PRO 2.9 15.8 + - - +
2174B GLN* 3.6 9.9 - - - +
2175B GLU 3.3 0.2 - - - -
2176B GLU* 1.3 76.8 - - - +
2178B LEU* 1.3 58.4 + - - +
2180B ILE* 3.2 9.2 + - - +
2181B GLN* 2.9 50.3 + - - +
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Residues in contact with LEU2178 (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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1796B PRO* 6.2 6.1 - - + -
1797B ALA 6.3 0.2 - - - +
2162B GLN* 3.4 37.5 - - + +
2166B LEU* 3.7 33.2 - - + -
2174B GLN* 2.9 33.3 + - - +
2175B GLU* 3.8 4.9 - - - +
2177B ASN* 1.3 76.5 - - - +
2179B MET* 1.3 58.8 + - - +
2181B GLN* 3.3 10.7 + - + +
2182B SER* 2.9 30.3 + - - +
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Residues in contact with MET2179 (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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2163B ILE* 3.7 40.4 - - + +
2166B LEU* 5.6 9.1 - - + +
2167B LEU* 6.1 1.3 - - - -
2175B GLU 2.9 17.2 + - - +
2176B GLU 3.6 5.6 - - - +
2178B LEU* 1.3 77.7 - - - +
2180B ILE* 1.3 57.8 + - + +
2182B SER* 3.3 3.8 + - - -
2183B ILE* 2.9 57.3 + - + +
2208B VAL* 5.7 7.4 - - + -
2211B VAL* 3.8 32.1 - - + -
2229B MET* 3.6 28.0 - - + -
2232B SER* 5.8 2.0 - - - +
2233B CYS* 5.9 3.1 - - + -
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Residues in contact with ILE2180 (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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2176B GLU* 2.9 27.6 + - + +
2177B ASN* 3.6 8.7 - - - +
2179B MET* 1.3 76.2 - - + +
2181B GLN* 1.3 71.7 + - - +
2183B ILE* 3.3 7.0 + - - +
2184B GLY* 2.9 26.3 + - - -
2228B LYS* 3.6 34.1 - - + +
2229B MET* 4.4 4.7 - - - +
2232B SER* 4.0 23.5 - - - +
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Residues in contact with GLN2181 (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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2177B ASN* 2.9 42.2 + - - +
2178B LEU* 3.7 12.8 - - + +
2180B ILE* 1.3 88.9 - - - +
2182B SER* 1.3 58.1 + - - +
2184B GLY* 3.3 2.2 + - - -
2185B ASN* 2.9 28.6 + - - +
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Residues in contact with SER2182 (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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2159B CYS* 4.9 7.4 - - - -
2162B GLN* 5.7 5.2 - - - -
2163B ILE* 3.6 31.2 - - - -
2178B LEU* 2.9 21.7 + - - +
2179B MET* 3.6 6.5 - - - -
2180B ILE 3.2 0.2 - - - -
2181B GLN* 1.3 77.4 - - - +
2183B ILE* 1.3 58.1 + - - +
2185B ASN* 3.1 6.0 + - - +
2186B ILE* 2.9 36.3 + - - +
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Residues in contact with ILE2183 (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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2163B ILE* 5.0 5.6 - - + -
2179B MET* 2.9 52.1 + - + +
2180B ILE* 3.8 6.1 - - - +
2182B SER* 1.3 75.1 - - - +
2184B GLY* 1.3 61.3 + - - +
2186B ILE* 3.2 33.7 - - + +
2187B MET* 3.3 18.4 - - - +
2208B VAL* 5.3 8.5 - - + -
2232B SER* 3.8 36.3 - - - +
2233B CYS* 5.5 3.4 - - + +
2235B ARG* 5.8 1.8 - - - +
2236B PHE* 3.8 24.9 - - + -
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Residues in contact with GLY2184 (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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2180B ILE 2.9 15.7 + - - -
2181B GLN* 3.7 3.6 - - - -
2183B ILE* 1.3 79.9 - - - +
2185B ASN* 1.3 57.6 + - - +
2187B MET* 3.7 12.5 + - - +
2188B ASN* 2.9 25.0 + - - +
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Residues in contact with ASN2185 (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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2155B SER* 5.3 5.2 + - - +
2156B LEU* 5.9 0.3 - - - +
2159B CYS* 4.3 20.6 - - + +
2181B GLN 2.9 17.0 + - - +
2182B SER* 3.1 8.0 + - - +
2184B GLY* 1.3 73.9 - - - +
2186B ILE* 1.3 65.3 + - + +
2187B MET 3.1 3.1 + - - -
2188B ASN* 3.4 16.2 + - - +
2189B ASN* 4.0 7.1 + - - +
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Residues in contact with ILE2186 (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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2156B LEU* 4.3 15.5 - - + +
2159B CYS* 3.5 30.1 - - + -
2160B LEU* 5.8 0.7 - - + -
2163B ILE* 4.0 16.6 - - + -
2182B SER 2.9 14.8 + - - +
2183B ILE* 3.2 44.4 - - + +
2185B ASN* 1.3 76.8 - - - +
2187B MET* 1.3 60.6 + - - +
2188B ASN 3.4 0.4 - - - -
2189B ASN* 3.8 14.9 - - - +
2192B PHE* 4.4 14.4 - - + +
2208B VAL* 6.0 0.4 - - + -
2236B PHE* 3.5 34.5 - - + -
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Residues in contact with MET2187 (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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2183B ILE* 3.3 28.4 + - - +
2184B GLY* 4.0 9.2 - - - +
2185B ASN 3.1 1.0 - - - -
2186B ILE* 1.3 75.8 - - - +
2188B ASN* 1.3 60.3 + - - +
2189B ASN 3.2 13.6 + - - +
2192B PHE* 5.1 6.7 - - + -
2193B TYR* 4.0 22.2 + - - +
2235B ARG* 4.1 24.2 - - - +
2236B PHE* 4.0 29.2 - - + -
2239B TYR* 3.7 49.1 - - + -
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Residues in contact with ASN2188 (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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2184B GLY 2.9 19.3 - - - +
2185B ASN* 3.4 11.1 + - - +
2187B MET* 1.3 79.9 + - - +
2189B ASN* 1.3 61.9 + - - +
2190B LYS* 3.7 1.4 + - - +
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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
------------------------------------------------------------
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