Contacts of the helix formed by residues 138 - 147 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ALA 5.3 0.9 - - - -
89B PHE* 5.8 0.7 - - - -
90B ARG* 3.2 50.4 + - + +
93B ASP* 2.6 47.7 + - + +
98B GLY* 3.4 30.4 + - - -
99B TYR 3.8 2.9 - - - -
100B ILE* 3.7 40.2 - - + -
105B LEU* 6.0 0.2 - - + -
136B VAL* 3.1 6.2 + - + -
137B ASN* 1.3 69.2 - - - +
139B GLU* 1.3 75.9 + - + +
141B PHE* 3.8 10.4 - - + +
142B VAL* 2.9 33.0 + - + +
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Residues in contact with GLU 139 (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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88B ALA 4.6 8.5 + - - +
98B GLY 4.7 2.4 + - - +
137B ASN* 3.2 9.1 + - - +
138B TYR* 1.3 90.2 - - + +
140B GLU* 1.4 59.0 + - - +
142B VAL* 3.4 15.9 - - + +
143B GLN* 3.0 48.9 + - + +
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Residues in contact with GLU 140 (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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137B ASN* 3.0 26.4 + - + +
139B GLU* 1.4 74.3 - - - +
141B PHE* 1.3 52.9 + - - +
143B GLN* 3.3 19.0 + - - +
144B MET* 2.7 74.7 + - + +
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Residues in contact with PHE 141 (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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105B LEU* 3.5 35.0 - - + -
109B MET* 4.4 5.8 - - + -
124B MET* 3.2 33.7 - - + -
125B ILE* 3.7 19.3 - - + -
128B ALA* 3.5 25.8 - - + -
136B VAL* 4.3 12.6 - - + -
137B ASN 3.1 19.1 + - - +
138B TYR* 3.8 9.6 - - + +
139B GLU 3.4 0.2 - - - -
140B GLU* 1.3 75.5 - - - +
142B VAL* 1.4 58.7 + - + +
144B MET* 3.5 9.7 + - + +
145B MET* 3.0 61.6 + - + +
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Residues in contact with VAL 142 (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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774A ILE* 4.5 11.7 - - + -
88B ALA* 4.7 14.4 - - + +
90B ARG* 3.3 31.9 - - - +
138B TYR* 2.9 21.3 + - + +
139B GLU* 3.4 26.0 - - - +
141B PHE* 1.4 73.9 - - + +
143B GLN* 1.3 67.6 + - + +
145B MET* 3.2 22.7 - - - +
146B THR* 3.1 28.9 + - + +
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Residues in contact with GLN 143 (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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139B GLU* 3.0 39.3 + - + +
140B GLU* 3.6 18.8 + - - +
142B VAL* 1.3 76.8 - - + +
144B MET* 1.3 57.0 + - - +
146B THR* 4.1 5.2 - - - -
147B ALA* 2.9 42.1 + - + +
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Residues in contact with MET 144 (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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781A TRP* 4.7 0.9 - - - -
127B GLU* 3.7 18.6 - - + +
128B ALA* 5.8 6.5 - - - -
140B GLU* 2.7 56.4 + - + +
141B PHE* 3.9 9.4 - - + +
143B GLN* 1.3 71.4 - - - +
145B MET* 1.3 63.4 + - - +
147B ALA* 5.2 0.9 - - - -
148B LYS* 3.0 56.2 - - - +
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Residues in contact with MET 145 (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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774A ILE* 4.4 5.2 - - - -
778A ILE* 3.3 49.6 - - + -
781A TRP* 2.7 42.2 - - + -
109B MET* 4.0 8.1 - - + -
124B MET* 4.5 9.9 - - + -
141B PHE* 3.0 55.6 + - + +
142B VAL* 3.2 35.2 - - - +
144B MET* 1.3 76.6 - - - +
146B THR* 1.3 62.1 + - + +
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Residues in contact with THR 146 (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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774A ILE* 6.5 0.9 - - + -
777A THR* 3.8 35.2 - - + +
778A ILE* 5.2 1.8 - - + +
781A TRP* 3.2 20.6 - - + +
86B ARG 5.5 2.3 + - - -
142B VAL* 3.1 21.2 + - + +
143B GLN* 3.7 5.0 + - - -
145B MET* 1.3 79.5 - - + +
147B ALA* 1.3 60.2 + - - +
148B LYS 3.0 10.9 + - - -
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Residues in contact with ALA 147 (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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143B GLN* 2.9 28.8 + - + +
144B MET* 5.2 1.1 - - - -
146B THR* 1.3 73.7 + - - +
148B LYS* 1.3 62.1 + - + +
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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