Contacts of the helix formed by residues 145 - 154 (chain G) in PDB entry 2HTN
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 GLY 145 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141G ILE 3.0 17.2 + - - -
142G GLN 3.8 3.9 + - - -
143G LYS 3.6 2.2 - - - -
144G MET* 1.3 80.7 - - - +
146G LEU* 1.3 64.6 + - - -
147G GLN 3.3 3.4 - - - -
148G ASN 3.6 0.4 + - - -
149G TYR* 3.0 22.7 + - - +
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Residues in contact with LEU 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F LYS 5.7 2.0 - - - +
82G ASP* 6.5 0.7 - - + -
83G VAL* 4.8 11.2 - - + -
84G GLU* 5.4 5.4 - - + +
141G ILE* 3.7 27.1 + - + +
145G GLY* 1.3 71.8 - - - -
147G GLN* 1.3 56.1 + - + +
149G TYR* 3.4 9.3 - - + +
150G LEU* 2.7 70.1 + - + +
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Residues in contact with GLN 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F GLN 4.8 2.4 + - - -
143F LYS 3.8 15.8 + - - +
144F MET* 3.2 44.6 + - - +
145F GLY* 3.4 9.1 - - - +
148F ASN* 3.4 14.2 + - - +
145G GLY* 3.3 1.2 - - - -
146G LEU* 1.3 78.0 - - + +
148G ASN* 1.3 62.4 + - - +
150G LEU* 4.7 0.7 - - - -
151G GLN* 3.0 19.9 + - - +
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Residues in contact with ASN 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ASN* 3.0 28.0 + - - +
151F GLN* 5.3 0.3 - - - +
144G MET* 3.4 38.3 + - + +
145G GLY 3.6 2.2 + - - -
147G GLN* 1.3 78.5 - - - +
149G TYR* 1.3 63.8 + - - +
151G GLN* 3.3 11.5 + - - +
152G ALA* 3.1 21.7 + - - +
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Residues in contact with TYR 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU* 3.8 12.8 - - + +
83G VAL* 4.1 17.9 - - + -
87G LEU* 4.0 4.9 - - - +
137G GLU* 2.5 51.2 + - - +
140G LEU* 4.3 13.0 - - + -
141G ILE* 3.8 35.0 - - + -
144G MET* 4.0 17.2 - - + +
145G GLY 3.0 19.4 + - - +
146G LEU* 3.4 9.2 - - + +
148G ASN* 1.3 75.5 - - - +
150G LEU* 1.3 74.3 + - + +
152G ALA* 3.0 9.1 + - + +
153G GLN* 2.9 50.6 + - + -
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Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 6.1 1.1 - - + -
143F LYS* 4.0 40.4 - - + +
144F MET* 4.5 11.4 - - + -
37G LEU* 4.1 19.9 - - + +
83G VAL* 3.7 29.8 - - + -
146G LEU* 2.7 51.7 + - + +
147G GLN 3.9 3.1 - - - +
149G TYR* 1.3 80.9 - - + +
151G GLN* 1.3 62.1 + - - +
153G GLN* 2.9 21.9 + - + +
154G ILE* 3.6 9.0 + - - +
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Residues in contact with GLN 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F MET* 3.7 20.9 - - - -
148F ASN* 2.8 44.2 + - + +
151F GLN* 2.7 41.9 + - - +
152F ALA* 3.7 14.8 - - + +
147G GLN 3.0 13.7 + - - +
148G ASN* 3.3 14.7 + - - +
150G LEU* 1.3 75.6 - - - +
152G ALA* 1.3 62.0 + - - +
154G ILE* 3.3 23.1 - - + +
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Residues in contact with ALA 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ARG* 3.6 16.6 - - - +
144G MET* 5.3 6.5 - - + -
148G ASN 3.1 10.7 + - - +
149G TYR* 3.0 15.6 + - + +
151G GLN* 1.3 78.4 - - - +
153G GLN* 1.3 64.9 + - - +
154G ILE 3.6 0.4 - - - -
155G ARG* 4.6 6.4 + - - +
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Residues in contact with GLN 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LEU* 4.0 21.5 - - + -
38G LYS 3.1 5.7 + - - -
39G ARG* 2.8 68.7 + - + +
40G LEU* 3.1 24.3 - - + +
137G GLU* 4.6 0.2 + - - -
149G TYR* 2.9 61.8 + - + +
150G LEU* 2.9 11.2 + - + +
152G ALA* 1.3 85.6 + - - +
154G ILE* 1.3 60.5 + - - +
155G ARG 3.4 2.0 - - - -
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Residues in contact with ILE 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ARG* 5.2 9.6 - - - +
140F LEU* 4.7 9.9 - - + -
144F MET* 3.8 27.6 - - + -
149F TYR* 6.4 0.2 - - + -
152F ALA* 3.2 37.9 - - + +
153F GLN* 5.0 4.0 - - - +
36G GLY 3.5 16.8 - - - +
37G LEU* 4.4 4.2 - - + +
38G LYS* 2.7 41.9 + - - +
150G LEU 3.6 4.5 + - - +
151G GLN* 3.3 20.0 - - + +
153G GLN* 1.3 77.3 - - - +
155G ARG* 1.3 73.8 + - + +
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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