Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 1DT0
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A THR* 3.7 6.8 - - - +
119A GLY 3.9 2.8 + - - -
120A SER* 1.3 74.4 - - - +
122A TRP* 1.3 70.0 + - - -
138A THR 3.0 13.2 - - - -
140A GLY 3.6 7.0 - - - -
157A VAL* 3.0 29.6 + - - +
158A TRP* 3.3 16.1 - - - +
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Residues in contact with TRP 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLN* 2.8 27.4 + - - -
72A ASN* 3.5 38.4 + - + -
73A HIS* 3.3 43.5 - + - -
76A TYR* 3.9 10.5 - - + -
117A THR* 4.2 1.9 - - - +
121A GLY* 1.3 76.6 - - - -
123A GLY* 1.3 59.7 + - - +
124A TRP* 3.6 23.2 - + + +
137A SER* 3.4 7.4 + - - -
138A THR* 2.8 40.2 + - - +
140A GLY 3.0 14.9 + - - -
142A GLY 4.3 0.7 - - - -
154A THR* 3.9 13.0 - - + +
155A CYS 3.4 4.9 - - - +
156A ASP* 3.2 48.0 - - + -
157A VAL* 3.8 5.1 - - - +
158A TRP* 3.6 2.6 - + - +
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Residues in contact with GLY 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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110A PHE* 3.7 7.8 - - - -
113A THR* 4.6 4.3 - - - -
114A SER* 3.5 28.0 + - - -
122A TRP* 1.3 74.7 - - - +
124A TRP* 1.3 60.4 + - - -
136A ALA 3.7 3.6 - - - -
154A THR* 3.1 7.3 + - - -
155A CYS 2.8 34.2 + - - -
157A VAL* 4.6 1.4 - - - +
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Residues in contact with TRP 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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71A TRP* 4.1 4.9 - + - -
72A ASN* 3.1 34.8 - - + -
75A PHE* 4.1 9.0 - + - -
110A PHE* 3.6 7.1 - - - -
113A THR* 4.8 1.5 - - - +
122A TRP* 3.6 15.5 - + + +
123A GLY* 1.3 75.9 - - - -
125A LEU* 1.3 59.2 + - - +
126A VAL* 4.1 14.4 - - + -
135A LEU* 3.2 13.2 - - - +
136A ALA* 2.7 46.2 + - + +
138A THR* 2.9 33.3 + - + +
142A GLY 3.5 14.1 - - - -
144A PRO* 3.3 33.4 - - + -
151A PRO* 4.0 22.7 - - + -
153A LEU 3.3 7.0 - - - -
154A THR* 3.0 34.8 - - - -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 5.1 1.1 - - + -
96A ILE* 4.8 9.9 - - + -
100A PHE* 4.2 8.5 - - + -
106A PHE* 3.6 34.8 - - + -
110A PHE* 3.9 14.4 - - + -
124A TRP* 1.3 72.8 - - - +
126A VAL* 1.3 65.6 + - - +
133A LEU* 4.2 20.6 - - + -
134A ALA 3.6 8.7 - - - +
135A LEU* 4.1 2.7 - - + -
151A PRO* 3.9 0.3 - - - +
152A LEU* 2.8 48.3 + - + +
153A LEU* 2.8 19.3 + - + +
183A TRP* 4.7 5.4 - - + -
186A VAL* 4.3 13.5 - - + -
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A TRP* 4.1 9.6 - - + -
125A LEU* 1.3 78.6 - - - +
127A LYS* 1.3 62.4 + - - +
128A LYS* 4.4 1.8 - - - -
133A LEU* 3.4 8.8 - - - +
134A ALA* 2.7 61.2 + - + +
135A LEU 5.1 0.2 - - - -
136A ALA* 4.6 11.2 - - + -
144A PRO* 3.7 36.3 - - + -
149A ASP* 3.9 23.1 - - + +
150A THR 3.1 14.1 - - - +
151A PRO* 4.2 2.9 - - + -
152A LEU* 3.9 5.0 - - - +
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Residues in contact with LYS 127 (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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126A VAL* 1.3 75.2 - - - +
128A LYS* 1.3 77.5 + - - +
131A GLY* 3.7 24.0 - - - +
132A SER 3.4 3.6 - - - +
133A LEU* 4.2 2.7 - - + -
149A ASP 3.8 0.2 - - - -
150A THR* 2.8 57.0 + - - +
152A LEU* 4.1 13.9 - - + -
189A GLN 4.9 0.4 + - - -
190A PHE* 3.1 49.6 + - + +
191A GLU* 3.1 22.8 + - - +
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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