Contacts of the helix formed by residues 112 - 125 (chain B) in PDB entry 1DI2
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 MET 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B PRO* 1.3 68.1 - - + +
114B VAL* 4.0 2.2 - - + +
115B GLY* 2.9 43.3 - - - +
116B SER* 2.8 39.3 + - - -
119B GLU* 5.4 3.8 - - - +
168B ARG* 4.7 9.2 - - - +
7C C 5.5 0.4 - - - +
8C G 6.1 3.6 - - - +
14D G 4.2 15.5 - - - +
15D C 2.9 68.0 - - - +
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET* 1.3 84.5 - - + +
114B VAL* 1.3 60.3 + - + +
116B SER* 4.3 0.4 - - - -
117B LEU* 2.8 31.5 + - - +
168B ARG* 4.0 28.9 - - + +
171B ALA* 3.8 14.0 - - + +
172B GLU* 3.3 48.2 - - + +
175B LEU* 3.6 17.9 - - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B MET* 3.3 0.9 - - + -
113B PRO* 1.3 77.7 - - + +
115B GLY* 1.3 63.3 + - - +
117B LEU* 3.1 3.3 + - - +
118B GLN* 3.0 23.6 + - + +
129B PRO* 5.7 0.2 - - - +
131B TYR* 3.6 19.8 + - + +
167B LYS* 3.7 31.9 - - + +
168B ARG* 4.3 13.0 - - + -
171B ALA* 3.9 18.8 - - + -
14D G 3.6 29.6 - - - +
15D C 4.1 14.1 - - - +
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Residues in contact with GLY 115 (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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112B MET* 2.9 32.5 - - - +
114B VAL* 1.3 75.9 - - - +
116B SER* 1.3 56.6 + - - +
118B GLN* 3.4 7.0 + - - +
119B GLU* 3.0 40.0 + - - +
8C G 5.8 3.1 + - - -
14D G 3.5 13.5 - - - -
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Residues in contact with SER 116 (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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112B MET* 2.8 27.8 + - - -
113B PRO* 3.7 4.3 - - - -
115B GLY* 1.3 74.3 - - - +
117B LEU* 1.3 66.6 + - - +
119B GLU* 3.5 9.2 + - - +
120B LEU* 3.0 23.9 + - - +
175B LEU* 4.1 16.9 - - - +
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Residues in contact with LEU 117 (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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113B PRO 2.8 16.8 + - - +
114B VAL 3.1 5.6 + - - +
116B SER* 1.3 72.9 - - - +
118B GLN* 1.3 66.8 + - - +
120B LEU* 3.3 12.7 + - + +
121B ALA* 3.1 21.0 + - - +
126B TRP* 5.8 0.6 - - + -
129B PRO* 3.8 13.7 - - + -
131B TYR* 3.5 13.5 - - - +
149B CYS* 3.5 32.5 - - - -
151B VAL* 4.2 19.1 - - + -
171B ALA* 4.1 11.9 - - - -
174B LEU* 3.9 15.7 - - + -
175B LEU* 3.8 25.3 - - + +
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Residues in contact with GLN 118 (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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114B VAL* 3.0 12.9 + - + +
115B GLY* 3.5 9.4 + - - +
117B LEU* 1.3 76.6 - - - +
119B GLU* 1.3 65.3 + - - +
121B ALA* 2.9 5.9 + - - +
122B VAL* 2.9 37.8 + - + +
128B LEU* 4.4 13.2 - - + +
129B PRO* 4.1 16.4 - - + +
8C G 3.5 12.3 - - - +
9C C 4.3 7.4 + - - +
12D G 4.8 1.4 - - - +
13D C 2.6 54.6 + - - -
14D G 3.3 17.9 + - - +
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Residues in contact with GLU 119 (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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112B MET* 5.4 3.1 - - - +
115B GLY* 3.0 23.0 + - - +
116B SER* 3.9 7.1 - - - +
118B GLN* 1.3 81.7 - - + +
120B LEU* 1.3 57.9 + - - +
122B VAL* 3.8 2.9 - - - +
123B GLN* 2.8 31.2 + - - +
8C G 2.6 32.6 + - - +
9C C 3.2 52.5 + - - +
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Residues in contact with LEU 120 (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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116B SER 3.0 14.5 + - - +
117B LEU* 3.4 14.4 - - + +
118B GLN 3.1 0.2 - - - -
119B GLU* 1.3 77.4 - - - +
121B ALA* 1.3 52.8 + - - +
123B GLN* 3.1 11.7 + - + +
124B LYS* 2.8 55.3 + - + +
126B TRP* 3.8 22.9 - - + -
175B LEU* 4.1 17.5 - - + -
178B PHE* 3.8 43.7 - - + -
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Residues in contact with ALA 121 (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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117B LEU 3.1 8.3 + - - +
118B GLN 2.9 8.4 + - - +
120B LEU* 1.3 74.9 - - - +
122B VAL* 1.3 66.5 + - - +
124B LYS 3.2 1.0 + - - -
125B GLY 2.9 4.9 + - - -
126B TRP* 2.8 51.4 + - + +
127B ARG 4.0 12.8 - - - +
128B LEU* 4.4 2.7 - - + -
129B PRO* 4.0 14.6 - - + -
151B VAL* 4.1 11.7 - - + -
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Residues in contact with VAL 122 (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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118B GLN* 2.9 29.6 + - + +
119B GLU* 3.8 4.7 - - - +
121B ALA* 1.3 75.7 - - - +
123B GLN* 1.3 63.6 + - - +
125B GLY* 3.2 10.5 + - - -
126B TRP 4.8 2.5 - - - -
128B LEU* 3.6 24.5 - - + -
9C C 4.2 8.7 - - - +
10C C 3.9 35.4 - - - +
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Residues in contact with GLN 123 (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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119B GLU 2.8 20.0 + - - +
120B LEU* 3.2 12.8 - - + +
122B VAL* 1.3 80.1 - - - +
124B LYS* 1.3 70.0 + - + +
125B GLY* 3.4 1.0 + - - -
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Residues in contact with LYS 124 (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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120B LEU* 2.8 32.6 + - + +
121B ALA 3.2 0.4 + - - +
123B GLN* 1.3 80.0 - - + +
125B GLY* 1.3 60.7 + - - +
126B TRP* 3.5 45.6 + - + +
178B PHE* 4.1 29.5 - - - -
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Residues in contact with GLY 125 (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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121B ALA 2.9 4.5 + - - -
122B VAL* 3.2 7.0 + - - -
123B GLN 3.2 4.6 + - - -
124B LYS* 1.3 79.2 - - - +
126B TRP* 1.3 64.7 + - - +
127B ARG 4.2 0.2 + - - -
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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