Contacts of the helix formed by residues 138 - 147 (chain F) 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 TYR 138 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88F ALA 5.5 3.4 - - - -
89F PHE* 5.5 2.0 - - - -
90F ARG* 3.5 58.4 + - + +
93F ASP* 2.7 45.6 + - + +
98F GLY* 3.3 24.2 + - - -
99F TYR 3.6 4.3 - - - -
100F ILE* 3.6 27.4 - - + -
136F VAL* 3.1 5.3 + - - -
137F ASN* 1.3 73.7 + - - +
139F GLU* 1.3 72.9 + - + +
140F GLU 3.4 0.2 - - - -
141F PHE* 3.7 6.5 - - - +
142F VAL* 2.9 35.3 + - + +
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Residues in contact with GLU 139 (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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88F ALA 5.2 8.5 + - - +
89F PHE* 6.1 0.7 - - - -
98F GLY 4.8 1.7 + - - +
137F ASN* 3.1 9.3 + - - +
138F TYR* 1.3 90.9 - - + +
140F GLU* 1.3 63.8 + - - +
142F VAL* 3.1 24.8 - - - +
143F GLN* 3.0 43.0 + - - +
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Residues in contact with GLU 140 (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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137F ASN* 3.0 27.4 + - + +
139F GLU* 1.3 76.2 - - - +
141F PHE* 1.4 51.2 + - - +
143F GLN* 3.3 18.0 + - - +
144F MET* 2.7 71.5 + - + +
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Residues in contact with PHE 141 (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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90F ARG* 5.1 4.0 - - - -
105F LEU* 3.8 33.2 - - + -
109F MET* 4.2 11.4 - - + -
124F MET* 3.2 37.5 - - + -
125F ILE* 3.9 9.6 - - + -
128F ALA* 3.6 21.3 - - + -
136F VAL* 3.8 20.2 - - + -
137F ASN 3.1 18.2 + - - +
138F TYR* 3.7 9.6 - - + +
139F GLU 3.4 0.2 - - - -
140F GLU* 1.4 76.3 - - - +
142F VAL* 1.4 60.6 + - - +
144F MET* 3.9 8.7 - - - +
145F MET* 3.1 47.3 + - + +
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Residues in contact with VAL 142 (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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870A ILE* 5.4 9.9 - - + -
88F ALA* 4.9 25.6 - - + +
90F ARG* 4.1 23.1 - - - +
138F TYR* 2.9 24.4 + - + +
139F GLU* 3.1 36.3 - - - +
141F PHE* 1.4 70.3 - - + +
143F GLN* 1.4 63.4 + - + +
145F MET* 3.3 18.2 + - + +
146F THR* 3.0 32.7 + - + +
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Residues in contact with GLN 143 (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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139F GLU* 3.0 40.6 + - - +
140F GLU* 3.6 18.2 + - - +
142F VAL* 1.4 77.6 - - + +
144F MET* 1.3 56.6 + - - +
146F THR* 4.0 5.8 - - - -
147F ALA* 2.8 41.0 + - + +
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Residues in contact with MET 144 (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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127F GLU* 5.0 17.9 - - + +
128F ALA* 5.6 7.2 - - - -
140F GLU* 2.7 54.9 + - + +
141F PHE* 3.9 7.6 - - - +
143F GLN* 1.3 73.6 - - + +
145F MET* 1.3 57.2 + - - +
147F ALA* 5.2 0.9 - - - -
148F LYS* 3.0 50.9 + - - +
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Residues in contact with MET 145 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870A ILE* 4.7 20.2 - - + +
873A HIS* 5.6 1.3 - - + -
874A VAL* 4.3 24.0 - - - -
877A TRP* 3.1 39.8 + - + +
880A ARG* 3.2 10.9 + - - -
90F ARG* 6.1 0.4 - - - +
109F MET* 4.0 16.6 - - + -
124F MET* 4.7 8.3 - - + +
141F PHE* 3.1 46.0 + - + +
142F VAL* 3.5 19.5 - - + +
144F MET* 1.3 78.4 - - - +
146F THR* 1.3 73.7 + - + +
148F LYS* 4.2 1.7 - - - +
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Residues in contact with THR 146 (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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873A HIS* 3.4 41.0 + - + +
877A TRP* 4.8 1.2 + - - +
880A ARG* 4.4 2.9 + - - -
142F VAL* 3.0 20.8 + - + +
143F GLN* 3.6 6.2 + - - -
145F MET* 1.3 85.8 - - + +
147F ALA* 1.3 60.7 + - - +
148F LYS 3.1 16.4 + - - -
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Residues in contact with ALA 147 (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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143F GLN* 2.8 27.7 + - + +
144F MET* 5.2 0.7 - - - -
146F THR* 1.3 71.2 + - - +
148F LYS* 1.3 62.0 + - - +
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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