Contacts of the helix formed by residues 120 - 128 (chain M) in PDB entry 2DFS
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 120 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117M PRO 4.9 1.2 + - - -
118M ILE 4.8 0.4 - - - +
119M TYR* 1.3 79.7 - - - +
121M GLU* 1.3 70.9 + - - -
122M ASP* 3.4 12.3 - - - -
123M ILE* 3.3 12.1 + - - +
124M ILE* 3.1 27.7 + - - +
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Residues in contact with GLU 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M TYR 4.7 1.4 - - - +
120M GLY* 1.3 82.0 - - - -
122M ASP* 1.3 58.6 + - - +
124M ILE* 3.4 14.9 + - - +
125M ASN* 2.9 39.7 + - - +
178M ARG* 4.9 16.5 + - - -
182M THR* 5.2 10.5 + - + +
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Residues in contact with ASP 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M GLY* 3.6 2.9 - - - -
121M GLU* 1.3 79.1 + - - +
123M ILE* 1.3 89.4 + - - +
125M ASN* 3.4 8.8 + - - +
126M ALA* 3.2 21.1 + - - +
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Residues in contact with ILE 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M PRO 3.5 24.0 - - - +
118M ILE* 3.7 25.8 - - + +
120M GLY* 3.3 24.6 + - - +
122M ASP* 1.3 96.8 - - - +
124M ILE* 1.4 65.3 + - - +
126M ALA* 3.2 15.8 + - + +
127M TYR* 3.2 38.1 + - + -
138M HIS* 4.8 2.2 - - + +
140M PHE* 4.1 4.7 - - + -
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Residues in contact with ILE 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M TYR 4.3 6.7 - - - +
120M GLY 3.1 18.1 + - - +
121M GLU* 3.6 15.5 - - - +
122M ASP 3.4 0.2 - - - -
123M ILE* 1.4 75.3 - - - +
125M ASN* 1.3 63.3 + - - +
127M TYR 3.5 0.9 + - - -
128M SER* 3.1 20.1 + - - -
140M PHE* 3.6 32.8 - - + -
178M ARG* 4.5 22.0 - - + -
179M TYR* 3.8 29.2 - - + -
182M THR* 4.1 30.3 - - + +
183M VAL* 4.3 11.2 - - + -
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Residues in contact with ASN 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M GLU* 2.9 31.1 + - - +
122M ASP* 3.4 10.0 + - - +
124M ILE* 1.3 80.4 - - - +
126M ALA* 1.3 61.5 + - - +
128M SER* 3.3 25.8 + - - +
130M GLN* 5.1 0.7 + - - -
182M THR* 5.4 6.5 - - - +
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Residues in contact with ALA 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M ASP 3.2 12.9 + - - +
123M ILE* 3.2 13.6 + - + +
125M ASN* 1.3 77.2 - - - +
127M TYR* 1.4 56.7 + - + +
130M GLN* 3.1 25.1 + - - +
135M MET* 3.6 20.1 - - + +
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Residues in contact with TYR 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M ILE* 3.2 44.0 + - + -
124M ILE 4.0 3.4 - - - +
125M ASN 3.4 0.2 - - - -
126M ALA* 1.4 74.1 - - + +
128M SER* 1.4 64.8 + - - +
129M GLY 3.2 0.9 + - - -
130M GLN* 3.1 20.7 + - + +
135M MET* 3.6 33.6 - - + +
136M ASP* 2.7 40.3 + - - +
138M HIS* 3.4 25.4 - - + +
140M PHE* 3.8 17.5 - - + +
141M ALA* 4.0 23.8 - - + -
144M GLU* 3.7 7.6 - - + +
179M TYR* 3.3 22.0 + - + +
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Residues in contact with SER 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124M ILE* 3.1 13.8 + - - -
125M ASN* 3.3 23.1 + - - +
127M TYR* 1.4 72.4 - - - +
129M GLY* 1.3 58.7 + - - +
130M GLN* 2.9 19.8 + - - -
144M GLU* 3.6 2.0 + - - -
179M TYR* 3.2 10.5 + - - -
183M VAL* 4.3 17.3 - - - +
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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