Contacts of the helix formed by residues 115 - 125 (chain A) in PDB entry 1DWQ
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 SER 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A SER* 2.9 16.5 + - - -
114A PRO* 1.3 76.4 - - - +
116A TYR* 1.3 63.3 + - - +
117A THR 3.5 0.7 - - - -
118A VAL* 2.9 21.8 + - - +
119A GLU* 2.9 34.6 + - - -
181A GLN* 3.8 18.2 - - - -
184A LEU* 3.9 7.9 - - - +
185A ALA* 3.3 24.5 - - - +
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 4.0 6.7 - - - +
112A HIS* 3.5 56.3 + + + -
113A SER* 3.1 22.9 + - - +
114A PRO 3.3 0.4 - - - -
115A SER* 1.3 77.7 + - - +
117A THR* 1.3 66.2 + - + +
119A GLU* 3.1 19.8 + - + +
120A LYS* 3.0 51.1 + - + +
218A TRP* 3.3 39.3 + + - -
222A ASN* 3.9 6.5 + - - -
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 5.1 0.3 - - - +
106A LEU* 3.5 19.8 - - - +
107A LEU 3.5 23.3 - - - +
108A PRO* 4.3 15.4 - - + +
109A ASP 5.1 0.9 - - - +
114A PRO 4.5 7.4 + - - -
116A TYR* 1.3 83.2 - - + +
118A VAL* 1.3 60.1 + - - +
120A LYS* 4.2 6.5 - - - -
121A LEU* 2.8 25.1 + - - +
215A PHE* 3.5 10.4 - - - -
218A TRP* 4.0 15.9 - - + -
219A GLN* 3.7 20.6 - - + +
222A ASN* 4.8 4.5 - - - +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A CSA 4.6 2.7 - - + -
84A LEU* 3.9 28.3 - - + -
106A LEU* 4.0 12.3 - - + -
114A PRO 4.7 1.3 - - - +
115A SER* 2.9 16.7 + - - +
117A THR* 1.3 76.3 + - - +
119A GLU* 1.4 55.3 + - - +
121A LEU* 3.1 7.5 + - - +
122A LEU* 2.9 36.6 + - + +
179A LEU* 4.0 31.4 - - + -
181A GLN* 3.8 28.0 - - + +
184A LEU* 4.2 13.2 - - + -
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER* 5.8 1.2 - - - -
115A SER* 2.9 38.5 + - - +
116A TYR* 3.2 22.7 - - + +
118A VAL* 1.4 75.5 - - - +
120A LYS* 1.3 60.8 + - + +
122A LEU* 3.3 5.8 + - - +
123A GLU* 3.0 32.8 + - - +
181A GLN* 3.1 25.8 + - - +
185A ALA* 4.7 4.9 - - - +
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.0 43.3 + - + +
117A THR 3.8 0.7 - - - +
119A GLU* 1.3 76.8 - - + +
121A LEU* 1.3 64.9 + - - +
123A GLU* 3.3 32.4 + - - +
124A SER* 3.0 23.6 + - - -
215A PHE* 3.7 8.8 - - + -
218A TRP* 3.5 45.9 - - + +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A CSA 3.3 33.2 - - + -
106A LEU* 4.5 1.6 - - + -
117A THR 2.8 21.6 + - - +
118A VAL 3.6 3.8 - - - +
120A LYS* 1.3 72.7 - - - +
122A LEU* 1.3 55.3 + - + +
124A SER* 3.0 4.5 + - - +
125A PHE* 2.6 40.0 + - + -
128A TRP* 3.7 22.0 - - + -
210A ILE* 3.9 13.9 - - + +
211A PHE* 3.8 28.3 - - + -
215A PHE* 3.4 36.5 - - + -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A CSA 4.9 0.4 - - + -
118A VAL* 2.9 24.9 + - + +
119A GLU* 3.8 5.6 - - - +
120A LYS 3.3 0.2 - - - -
121A LEU* 1.3 81.0 - - + +
123A GLU* 1.3 59.4 + - - +
125A PHE 3.7 3.6 - - - +
126A PRO* 3.1 31.1 - - + +
128A TRP* 3.8 37.7 - - + +
179A LEU* 4.3 13.2 - - + -
181A GLN* 3.4 31.4 - - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 3.0 19.2 + - - +
120A LYS* 3.3 43.1 + - + +
122A LEU* 1.3 76.0 - - - +
124A SER* 1.3 64.3 + - - +
126A PRO* 3.7 10.5 - - - +
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS 3.0 10.3 + - - -
121A LEU* 3.3 8.5 - - - +
123A GLU* 1.3 81.4 - - - +
125A PHE* 1.3 58.2 + - - +
126A PRO* 3.3 7.4 - - - +
212A LEU* 3.9 27.0 + - - +
214A ASP* 6.0 0.5 - - - +
215A PHE* 3.4 31.4 + - - +
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 2.6 20.9 + - + +
122A LEU* 3.4 10.3 - - - +
124A SER* 1.3 73.3 - - - +
126A PRO* 1.3 60.0 - - + +
127A ASP 3.2 24.7 - - - -
128A TRP* 3.0 32.7 + + - -
129A ARG* 5.3 1.8 - - + -
153A LEU* 3.7 17.7 - - + -
157A ASN* 3.4 26.9 - - - -
209A LYS 3.4 19.3 - - - -
210A ILE* 3.7 38.1 - - + +
212A LEU* 3.8 17.7 - - + -
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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