Contacts of the helix formed by residues 111 - 126 (chain A) in PDB entry 1DGD
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 GLY 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 1.3 71.0 - - - +
112A ALA* 1.3 59.9 - - - +
114A SER* 2.6 24.7 + - - -
115A ASN* 2.9 19.5 + - - -
245A ALA* 5.5 0.2 - - - -
271A SER* 3.5 22.7 - - - -
437A PLP 3.2 29.9 + - - -
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Residues in contact with ALA 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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110A THR* 4.2 3.4 - - - +
111A GLY* 1.3 73.1 - - - +
113A GLU* 1.3 66.1 + - - +
115A ASN* 3.3 1.9 + - - +
116A GLU* 3.0 28.9 + - - +
139A HIS 3.9 9.0 - - - -
140A GLY* 4.2 9.9 - - - -
141A MET 4.3 0.9 - - - +
142A THR* 3.5 38.6 - - + +
145A ALA* 4.1 3.9 - - + +
437A PLP 3.0 19.1 + - - +
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Residues in contact with GLU 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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108A LEU* 4.1 11.0 - - + -
109A SER* 2.6 39.9 + - - -
110A THR* 2.9 24.4 + - - +
112A ALA* 1.3 76.8 - - - +
114A SER* 1.3 64.8 + - - +
116A GLU* 3.2 8.7 + - - +
117A ALA* 2.9 25.6 + - - +
142A THR* 4.9 0.9 + - - -
300A PHE* 3.8 12.1 - - + -
302A THR* 3.3 33.5 + - + +
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Residues in contact with SER 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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108A LEU* 4.0 5.8 - - - +
110A THR 2.9 13.0 + - - -
111A GLY* 2.6 25.6 + - - -
113A GLU* 1.3 78.6 - - - +
115A ASN* 1.3 61.9 + - - +
117A ALA 3.4 0.2 + - - -
118A ALA* 3.1 19.2 + - - +
243A ASP* 5.5 0.2 + - - -
269A THR* 3.7 13.7 + - - -
270A LEU 4.0 10.1 + - - -
271A SER* 4.6 0.5 + - - -
281A ALA* 4.1 5.2 - - - -
282A ALA 3.9 23.8 - - - -
283A ILE* 3.2 19.1 - - - +
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Residues in contact with ASN 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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111A GLY 2.9 13.3 + - - +
112A ALA 3.9 3.1 - - - +
113A GLU 3.3 0.2 - - - -
114A SER* 1.3 82.1 + - - +
116A GLU* 1.3 57.1 + - - +
118A ALA* 3.5 4.5 + - - +
119A ILE* 2.9 35.3 + - + +
139A HIS* 3.0 22.6 + - - +
145A ALA* 4.0 14.6 - - + -
208A ILE* 3.5 24.8 - - + +
243A ASP* 2.9 29.1 + - - +
269A THR* 3.1 23.0 + - - +
437A PLP 3.4 3.8 - - - -
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Residues in contact with GLU 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 ALA 3.0 21.7 + - - +
113A GLU* 3.2 6.5 + - - +
115A ASN* 1.3 73.7 - - - +
117A ALA* 1.3 56.4 - - - +
119A ILE* 3.1 6.1 + - - +
120A ARG* 2.8 41.6 + - - +
142A THR* 2.9 23.1 + - - +
143A GLY* 3.1 6.2 - - - -
144A ALA* 2.5 46.4 + - - +
145A ALA 4.2 2.9 - - - +
300A PHE* 4.3 15.2 - - + -
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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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106A LEU* 4.0 9.2 - - + -
108A LEU* 3.9 19.1 - - + -
113A GLU 2.9 15.9 + - - +
114A SER 3.7 4.3 - - - +
116A GLU* 1.3 76.7 - - - +
118A ALA* 1.3 56.9 + - - +
120A ARG* 3.5 0.6 + - - -
121A MET* 3.1 21.1 + - - +
283A ILE* 4.3 6.7 - - + +
298A TYR* 2.8 30.3 + - - +
300A PHE* 3.7 18.8 - - + -
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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 SER 3.1 13.6 + - - +
115A ASN* 3.5 8.7 - - - +
116A GLU 3.1 0.2 - - - -
117A ALA* 1.3 74.5 - - - +
119A ILE* 1.3 65.7 + - - +
121A MET* 3.4 1.3 + - - -
122A ALA* 3.1 23.2 + - - +
241A ILE* 3.9 17.5 - - + -
267A ILE* 3.6 20.2 - - + +
269A THR* 3.8 21.1 - - + -
283A ILE* 4.2 11.4 - - + +
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Residues in contact with ILE 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 ASN 2.9 22.8 + - - +
116A GLU* 3.7 4.0 - - - +
118A ALA* 1.3 76.6 - - - +
120A ARG* 1.3 62.8 + - - +
122A ALA* 3.4 3.6 + - - +
123A LYS* 3.1 37.7 + - + +
131A ILE* 3.7 37.9 - - + +
144A ALA* 4.0 39.9 - - + +
145A ALA* 4.5 4.5 - - - +
148A ALA* 4.7 3.6 - - + -
208A ILE* 4.3 17.0 - - + -
241A ILE* 4.0 17.9 - - + -
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Residues in contact with ARG 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 GLU* 2.8 24.8 + - - +
117A ALA 4.0 2.0 - - - +
119A ILE* 1.3 70.9 - - - +
121A MET* 1.3 64.9 + - - +
123A LYS* 3.1 10.8 + - + +
124A LEU* 2.9 23.6 + - + +
298A TYR* 3.6 17.0 - - + -
299A LEU* 3.3 31.8 + - - +
300A PHE* 3.9 20.1 - - - -
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Residues in contact with MET 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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106A LEU* 5.7 1.8 - - + -
117A ALA 3.1 13.9 + - - +
118A ALA* 3.6 5.4 - - - +
120A ARG* 1.3 74.5 - - - +
122A ALA* 1.3 58.6 + - - +
124A LEU* 3.2 2.6 + - - +
125A VAL* 2.9 33.8 + - + +
239A LEU* 5.2 0.2 - - - -
267A ILE* 4.4 6.7 - - + -
283A ILE* 4.0 19.3 - - + -
285A THR* 3.9 27.4 - - + -
289A ILE* 3.9 18.8 - - + +
290A GLU* 5.1 9.4 - - + -
293A ALA* 3.7 23.3 - - + -
298A TYR* 3.5 46.5 - - + +
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Residues in contact with ALA 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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118A ALA 3.1 14.3 + - - +
119A ILE* 3.7 4.7 - - - +
120A ARG 3.2 0.2 - - - -
121A MET* 1.3 76.8 - - - +
123A LYS* 1.3 54.6 + - + +
125A VAL 4.1 0.2 - - - -
126A THR* 2.5 40.2 + - - +
131A ILE* 5.4 0.4 - - + -
205A ALA* 4.1 2.9 - - + +
206A ALA* 4.1 25.1 - - + -
239A LEU* 3.7 29.4 - - + -
241A ILE* 4.4 6.5 - - + -
267A ILE* 4.4 0.6 - - + +
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Residues in contact with LYS 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 ILE* 3.1 29.6 + - + +
120A ARG* 3.1 9.4 + - - +
122A ALA* 1.3 75.2 - - - +
124A LEU* 1.3 61.8 + - - +
127A GLY* 2.8 30.8 + - - -
128A LYS 3.4 22.2 - - - +
129A TYR* 3.3 33.9 + - + +
131A ILE* 4.1 16.7 - - + +
144A ALA* 5.3 6.1 - - - +
161A ALA* 6.0 4.0 - - - +
162A VAL 5.8 1.0 + - - -
205A ALA* 4.5 5.8 - - + -
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Residues in contact with LEU 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 ARG* 2.9 14.0 + - + +
121A MET* 3.5 8.3 - - - +
123A LYS* 1.3 80.9 - - - +
125A VAL* 1.3 63.4 + - - +
126A THR 3.2 0.3 + - - -
127A GLY* 3.2 8.7 + - - -
293A ALA* 3.5 11.9 - - - +
296A LEU* 3.7 34.4 - - + +
297A GLY 4.2 0.7 - - - -
298A TYR* 3.4 50.9 - - + +
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Residues in contact with VAL 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 MET 2.9 21.7 + - - +
122A ALA* 4.4 2.9 - - - +
124A LEU* 1.3 73.1 - - - +
126A THR* 1.3 67.7 + - + +
239A LEU* 4.6 13.2 - - + -
289A ILE* 4.0 22.4 - - + +
292A ARG* 4.1 27.5 + - + +
293A ALA* 3.8 37.0 - - + +
296A LEU* 4.4 6.0 - - - +
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Residues in contact with THR 126 (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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122A ALA 2.5 24.8 + - - +
123A LYS 3.5 0.9 + - - -
125A VAL* 1.3 82.7 - - + +
127A GLY* 1.3 64.3 + - - +
128A LYS* 3.0 35.0 + - - +
205A ALA* 3.5 26.1 - - - +
237A GLY 3.9 15.9 - - - +
239A LEU* 4.2 16.8 - - + -
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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