Contacts of the helix formed by residues 107 - 120 (chain A) in PDB entry 1DJ9
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.1 2.6 - - - +
106A ILE* 1.3 86.7 - - - +
108A GLY* 1.3 58.5 + - - +
109A PHE* 3.5 6.2 + - - +
110A ALA* 3.0 24.3 + - - +
111A ALA* 2.9 24.4 + - - +
241A SER* 5.8 0.9 - - - -
242A GLY* 3.9 9.0 - - - -
243A ALA* 3.5 11.3 - - - +
400A KAM 3.6 13.4 + - - -
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Residues in contact with GLY 108 (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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107A SER* 1.3 72.1 - - - +
109A PHE* 1.3 57.1 + - - +
111A ALA* 3.1 2.9 + - - +
112A ASN* 2.9 37.1 + - - -
231A VAL* 4.8 3.1 - - - +
233A THR* 3.2 25.1 + - - -
243A ALA* 3.5 8.7 - - - +
400A KAM 2.8 25.0 + - - -
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Residues in contact with PHE 109 (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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107A SER* 3.8 4.9 - - - +
108A GLY* 1.3 77.1 - - - +
110A ALA* 1.3 62.0 + - - +
112A ASN* 3.6 0.3 + - - +
113A GLN* 2.9 66.4 + - + +
133A HIS* 4.0 11.0 - + - -
134A ALA* 4.8 3.8 - - + -
135A SER* 3.3 32.3 - - - -
138A GLU* 3.6 15.9 - - - -
261A HIS* 5.7 2.5 - - - -
400A KAM 3.1 19.9 + - - +
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Residues in contact with ALA 110 (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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105A PHE* 4.2 8.1 - - + -
106A ILE* 4.2 11.9 - - + +
107A SER* 3.0 23.0 + - - +
109A PHE* 1.3 75.0 - - - +
111A ALA* 1.3 66.9 + - - +
114A ALA* 2.9 28.1 + - - +
261A HIS* 3.3 43.5 - - + +
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Residues in contact with ALA 111 (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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105A PHE* 3.7 33.0 - - + -
107A SER 2.9 13.6 + - - +
108A GLY 3.1 7.4 + - - +
110A ALA* 1.3 78.1 - - - +
112A ASN* 1.3 63.0 + - - +
114A ALA* 3.8 1.4 - - - +
115A VAL* 3.1 29.8 + - - +
231A VAL* 4.0 20.6 - - + -
243A ALA* 4.0 6.3 - - + -
244A ALA 5.0 0.7 - - - +
245A VAL* 4.1 6.0 - - + +
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Residues in contact with ASN 112 (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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108A GLY 2.9 17.1 + - - +
109A PHE 4.1 0.9 - - - +
111A ALA* 1.3 77.4 - - - +
113A GLN* 1.3 58.8 + - + +
115A VAL* 3.6 1.2 + - - +
116A ILE* 3.1 34.6 + - - +
135A SER* 3.0 29.4 + - - +
136A LEU* 3.5 27.0 - - + +
139A ALA* 5.2 0.4 - - - -
202A MET* 3.9 5.8 - - - +
204A ASP* 2.9 26.3 + - - +
231A VAL* 3.4 30.4 - - - +
400A KAM 3.9 6.9 - - - -
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Residues in contact with GLN 113 (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 PHE* 2.9 53.8 + - + +
110A ALA* 4.0 3.6 - - - +
112A ASN* 1.3 75.5 - - - +
114A ALA* 1.3 59.4 + - - +
116A ILE* 4.2 0.3 - - - +
117A ALA* 2.8 34.8 + - - +
135A SER* 2.7 32.6 + - - +
138A GLU* 3.4 25.3 + - - +
139A ALA* 3.8 17.2 - - + +
142A LEU* 6.0 1.0 - - - +
261A HIS* 4.9 8.2 + - + -
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Residues in contact with ALA 114 (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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105A PHE* 3.5 26.2 - - + -
110A ALA 2.9 19.5 + - - +
111A ALA 3.8 0.7 - - - +
113A GLN* 1.3 77.0 - - - +
115A VAL* 1.3 56.6 + - - +
117A ALA* 3.9 3.2 - - - +
118A ALA* 2.9 33.3 + - - +
259A ALA* 4.0 16.4 - - + +
260A ARG 5.9 0.2 - - - +
261A HIS* 3.9 18.7 - - + +
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Residues in contact with VAL 115 (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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105A PHE* 5.4 1.6 - - + -
111A ALA 3.1 20.7 + - - +
114A ALA* 1.3 73.9 - - - +
116A ILE* 1.3 69.7 + - - +
118A ALA* 3.2 1.4 + - - +
119A MET* 3.0 33.4 + - + +
171A MET* 5.4 1.8 - - + -
202A MET* 3.6 28.9 - - + -
229A LEU* 4.0 24.5 - - + -
231A VAL* 5.1 1.1 - - + -
245A VAL* 3.7 35.9 - - + -
255A LEU* 4.3 17.0 - - + -
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Residues in contact with ILE 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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112A ASN 3.1 14.8 + - - +
113A GLN 4.2 1.3 - - - +
115A VAL* 1.3 80.2 - - - +
117A ALA* 1.3 64.4 + - - +
120A MET* 3.1 35.3 + - + +
126A ILE* 3.9 22.9 - - + -
136A LEU* 3.6 46.7 - - + +
139A ALA* 3.9 28.3 - - + +
140A ALA* 4.4 6.5 - - + -
143A SER* 4.5 5.1 + - - -
171A MET* 6.1 2.2 - - + -
173A VAL* 4.9 9.9 - - + -
202A MET* 4.0 18.8 - - - -
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Residues in contact with ALA 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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113A GLN 2.8 20.5 + - - +
114A ALA* 3.9 4.5 - - - +
116A ILE* 1.3 78.9 - - - +
118A ALA* 1.3 66.5 + - - +
119A MET 3.2 0.3 + - - -
120A MET 3.7 12.2 - - - +
139A ALA* 6.2 0.7 - - + -
143A SER* 5.8 3.4 - - - +
144A PRO* 6.5 0.9 - - - -
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Residues in contact with ALA 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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114A ALA 2.9 22.3 + - - +
115A VAL 4.0 2.0 - - - +
117A ALA* 1.3 74.1 - - - +
119A MET* 1.3 61.4 + - - +
120A MET 4.8 1.0 - - - +
254A TYR* 3.0 22.8 + - + -
255A LEU* 4.1 19.7 - - + -
258A PHE* 4.0 38.4 - - + +
259A ALA* 4.2 1.8 - - - +
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Residues in contact with MET 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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115A VAL* 3.0 21.9 + - + +
118A ALA* 1.3 81.9 - - - +
120A MET* 1.3 73.0 - - - +
121A ALA* 4.0 0.9 + - - +
124A ASP* 3.9 7.8 - - - +
171A MET* 3.5 17.9 - - + -
200A TRP* 3.3 41.1 - - + -
229A LEU* 3.7 21.3 - - + -
251A VAL* 4.2 19.7 - - + -
254A TYR* 3.5 28.1 + - + -
255A LEU* 4.5 7.6 - - + -
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Residues in contact with MET 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 ILE* 3.1 25.5 + - + +
117A ALA* 3.7 11.3 - - - +
118A ALA 4.8 0.5 - - - +
119A MET* 1.3 84.8 - - - +
121A ALA* 1.3 59.2 + - - +
124A ASP* 3.5 23.6 - - + +
125A ARG 3.5 17.5 - - - +
126A ILE* 3.3 36.3 - - + -
143A SER* 3.7 10.1 + - - +
144A PRO* 4.4 7.8 - - - +
145A SER* 3.7 15.3 - - - +
169A GLN* 4.5 1.8 - - + +
170A GLN 5.1 0.2 - - - -
171A MET* 3.7 35.0 - - + +
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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