Contacts of the helix formed by residues 2172 - 2188 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2170H GLN 3.6 0.6 + - - -
2171H MET* 1.3 74.5 - - - +
2173H PRO* 1.3 66.9 - - - +
2174H GLN 3.5 2.0 - - - -
2175H GLU* 3.3 14.5 - - - +
2176H GLU* 2.5 39.4 + - - +
2226H PHE* 4.5 9.8 - - - -
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Residues in contact with PRO2173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172H GLY* 1.3 83.4 - - - +
2174H GLN* 1.3 59.5 + - - +
2176H GLU* 3.2 5.2 + - + +
2177H ASN* 2.9 28.6 + - - +
2226H PHE* 5.2 7.2 - - + -
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Residues in contact with GLN2174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680H ARG* 5.4 13.4 + - - +
1794H GLU 4.1 25.0 + - - +
1795H ALA 3.7 19.4 + - - +
1796H PRO* 4.2 10.7 - - - +
1797H ALA* 4.3 10.2 - - - +
2166H LEU* 5.2 2.6 - - - +
2173H PRO* 1.3 79.8 - - - +
2175H GLU* 1.3 62.6 + - - +
2177H ASN* 3.3 8.8 + - + +
2178H LEU* 2.9 45.3 + - - +
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Residues in contact with GLU2175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2166H LEU* 4.0 30.3 - - + +
2169H VAL* 5.9 1.3 - - + -
2170H GLN 4.4 6.1 - - - +
2171H MET* 4.2 8.1 - - + -
2172H GLY* 3.3 24.9 + - - +
2173H PRO 3.2 0.4 - - - -
2174H GLN* 1.3 84.3 + - - +
2176H GLU* 1.3 57.7 + - - +
2178H LEU* 3.4 2.6 + - - +
2179H MET* 2.9 29.3 + - - +
2229H MET* 6.2 0.2 - - - -
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Residues in contact with GLU2176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171H MET* 5.6 1.5 - - + +
2172H GLY 2.5 22.7 + - - +
2173H PRO* 3.6 6.1 - - + +
2175H GLU* 1.3 72.7 - - - +
2177H ASN* 1.3 58.6 + - - +
2179H MET* 3.3 6.7 + - - +
2180H ILE* 2.9 40.5 + - + +
2226H PHE* 5.0 14.8 - - + -
2229H MET* 4.5 24.4 - - + +
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Residues in contact with ASN2177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794H GLU* 4.3 26.3 + - - +
2173H PRO 2.9 16.9 + - - +
2174H GLN* 3.6 9.6 - - + +
2175H GLU 3.3 0.2 - - - -
2176H GLU* 1.3 76.8 - - - +
2178H LEU* 1.3 57.2 + - - +
2180H ILE* 3.2 9.5 + - - +
2181H GLN* 2.9 49.6 + - - +
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Residues in contact with LEU2178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1796H PRO* 6.2 5.8 - - + -
1797H ALA 6.3 0.2 - - - +
2162H GLN* 3.4 37.0 - - + +
2166H LEU* 3.7 33.0 - - + -
2174H GLN* 2.9 34.2 + - - +
2175H GLU* 3.8 4.9 - - - +
2177H ASN* 1.3 76.0 - - - +
2179H MET* 1.3 58.2 + - - +
2181H GLN* 3.3 11.5 + - + -
2182H SER* 2.9 30.3 + - - +
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Residues in contact with MET2179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2163H ILE* 3.7 40.4 - - + +
2166H LEU* 5.6 8.9 - - + +
2167H LEU* 6.1 0.9 - - - -
2175H GLU 2.9 18.3 + - - +
2176H GLU 3.6 5.4 - - - +
2177H ASN 3.3 0.2 - - - -
2178H LEU* 1.3 78.3 - - - +
2180H ILE* 1.3 58.8 + - + +
2182H SER* 3.3 3.6 + - - -
2183H ILE* 2.9 56.9 + - + +
2208H VAL* 5.7 7.4 - - + -
2211H VAL* 3.8 33.0 - - + -
2229H MET* 3.6 27.6 - - + -
2232H SER* 5.8 1.3 - - - +
2233H CYS* 5.9 3.1 - - + -
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Residues in contact with ILE2180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2176H GLU* 2.9 27.0 + - + +
2177H ASN* 3.2 8.5 + - - +
2179H MET* 1.3 76.6 - - + +
2181H GLN* 1.3 72.1 + - - +
2183H ILE* 3.3 6.4 + - - +
2184H GLY* 2.9 26.7 + - - -
2228H LYS* 3.6 34.1 - - + +
2229H MET* 4.4 4.9 - - + +
2232H SER* 4.0 24.4 - - - +
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Residues in contact with GLN2181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177H ASN* 2.9 41.8 + - - +
2178H LEU* 3.7 12.1 - - + +
2179H MET 3.3 0.2 - - - -
2180H ILE* 1.3 89.5 - - - +
2182H SER* 1.3 58.0 + - - +
2184H GLY* 3.3 2.5 + - - -
2185H ASN* 2.9 29.6 + - - +
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Residues in contact with SER2182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2159H CYS* 4.9 7.0 - - - -
2162H GLN* 5.7 5.6 - - - -
2163H ILE* 3.6 31.0 - - - -
2178H LEU* 2.9 22.3 + - - +
2179H MET* 3.6 7.2 - - - -
2181H GLN* 1.3 78.1 - - - +
2183H ILE* 1.3 57.9 + - - +
2185H ASN* 3.1 5.9 + - - +
2186H ILE* 2.9 36.6 + - - +
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Residues in contact with ILE2183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2163H ILE* 5.0 6.7 - - + -
2179H MET* 2.9 50.3 + - + +
2180H ILE* 3.8 6.3 - - - +
2182H SER* 1.3 75.2 - - - +
2184H GLY* 1.3 61.7 + - - +
2186H ILE* 3.2 33.4 - - + +
2187H MET* 3.3 18.8 - - - +
2208H VAL* 5.3 8.7 - - + -
2232H SER* 3.8 37.2 - - - +
2233H CYS* 5.5 2.9 - - + +
2235H ARG* 5.8 1.6 - - - +
2236H PHE* 3.8 24.2 - - + -
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Residues in contact with GLY2184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2180H ILE 2.9 15.1 + - - -
2181H GLN* 3.7 4.3 - - - -
2183H ILE* 1.3 79.3 - - - +
2185H ASN* 1.3 58.4 + - - +
2187H MET* 3.7 11.9 + - - +
2188H ASN* 2.9 24.8 + - - +
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Residues in contact with ASN2185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2155H SER* 5.3 4.9 + - - +
2156H LEU* 5.9 0.5 - - - +
2159H CYS* 4.3 20.4 - - + +
2181H GLN 2.9 18.2 + - - +
2182H SER* 3.1 8.2 + - - +
2184H GLY* 1.3 74.6 - - - +
2186H ILE* 1.3 65.0 + - + +
2187H MET 3.1 2.7 + - - -
2188H ASN* 3.4 16.0 + - - +
2189H ASN* 4.0 7.3 + - - +
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Residues in contact with ILE2186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2156H LEU* 4.3 16.4 - - + +
2159H CYS* 3.5 28.9 - - - -
2160H LEU* 5.8 1.1 - - + -
2163H ILE* 4.0 16.6 - - + -
2182H SER 2.9 16.7 + - - +
2183H ILE* 3.2 42.4 - - + +
2185H ASN* 1.3 76.4 - - - +
2187H MET* 1.3 60.4 + - - +
2189H ASN* 3.8 14.7 - - - +
2192H PHE* 4.4 14.4 - - + +
2204H MET* 6.4 0.2 - - - -
2208H VAL* 6.0 0.4 - - + -
2236H PHE* 3.5 35.6 - - + -
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Residues in contact with MET2187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2183H ILE* 3.3 28.2 + - - +
2184H GLY* 4.0 9.2 - - - +
2185H ASN 3.1 1.0 - - - -
2186H ILE* 1.3 76.0 - - - +
2188H ASN* 1.3 61.6 + - - +
2189H ASN 3.2 13.2 + - - +
2192H PHE* 5.1 6.6 - - + -
2193H TYR* 4.0 22.4 + - - +
2235H ARG* 4.1 24.5 - - - +
2236H PHE* 4.0 29.6 - - + -
2239H TYR* 3.7 48.5 - - + -
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Residues in contact with ASN2188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2184H GLY 2.9 19.8 - - - +
2185H ASN* 3.4 11.7 + - - +
2187H MET* 1.3 79.5 + - - +
2189H ASN* 1.3 62.6 + - - +
2190H 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
------------------------------------------------------------
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