Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 4DGX
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 PHE 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 5.3 2.0 - - + -
113A PHE* 3.5 24.5 - + - -
137A VAL* 4.3 8.5 - - + -
138A ARG 3.3 20.2 - - - +
139A GLU* 3.5 29.6 - - + -
140A SER* 3.9 1.9 - - - +
145A GLY 3.4 18.6 - - - -
146A ASP* 1.3 78.7 - - - +
148A VAL* 1.3 67.4 + - - +
171A MET* 3.7 2.6 - - - +
172A ILE* 2.7 48.7 + - + +
174A CYS* 4.6 1.8 - - + -
179A TYR* 4.0 28.3 - + - -
190A LEU* 3.8 21.5 - - + -
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Residues in contact with VAL 148 (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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136A LEU 3.9 0.2 - - - +
137A VAL* 3.3 7.1 - - - +
138A ARG* 2.8 70.9 + - - +
140A SER* 3.8 24.2 - - - +
147A PHE* 1.3 82.0 - - - +
149A LEU* 1.3 69.9 + - - +
150A SER* 4.1 11.6 + - - +
169A HIS* 4.1 15.5 - - + -
170A VAL 3.4 11.7 - - - +
171A MET* 4.9 12.3 - - + -
172A ILE* 4.5 0.9 - - - +
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Residues in contact with LEU 149 (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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135A PHE* 3.9 23.6 - - + -
136A LEU 3.5 15.3 - - - +
137A VAL* 3.6 17.7 - - + +
148A VAL* 1.3 74.3 - - - +
150A SER* 1.3 60.0 + - - +
151A VAL* 4.1 17.7 - - + +
168A THR 3.8 0.9 - - - +
169A HIS* 3.3 1.4 - - - -
170A VAL* 2.6 50.1 + - + +
172A ILE* 3.7 22.4 - - + +
181A VAL* 5.9 0.2 - - + -
193A LEU* 5.7 3.8 - - + -
194A VAL* 4.9 4.9 - - + -
197A TYR* 6.0 0.2 - - + -
202A MET* 3.6 30.7 - - + -
212A LEU* 4.5 13.2 - - + -
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Residues in contact with SER 150 (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* 5.0 3.6 - - - +
126A LEU* 3.6 23.1 - - - +
135A PHE* 3.2 7.1 - - - +
136A LEU* 3.0 45.4 + - - +
138A ARG* 4.3 5.9 + - - -
148A VAL* 4.1 6.4 + - - +
149A LEU* 1.3 73.8 - - - +
151A VAL* 1.3 63.3 + - - +
167A VAL* 4.4 0.4 - - - -
168A THR 3.3 4.5 - - - -
169A HIS* 3.1 30.5 - - - +
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Residues in contact with VAL 151 (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 LEU* 4.3 2.0 - - - +
134A SER 3.4 7.6 - - - +
135A PHE* 4.2 2.7 - - + -
149A LEU* 4.1 25.4 - - + +
150A SER* 1.3 81.1 - - - +
152A ARG* 1.3 70.0 + - - +
153A THR* 3.9 10.4 + - + -
166A LYS 3.6 1.0 - - - +
167A VAL* 3.2 3.0 - - - -
168A THR* 2.8 43.0 + - - +
170A VAL* 5.5 1.6 - - + -
210A LEU* 4.6 22.9 - - + -
211A GLN 3.6 24.5 - - - +
212A LEU* 4.1 15.3 - - + -
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Residues in contact with ARG 152 (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 LEU* 3.1 29.0 + - + +
127A THR* 2.8 36.8 + - - +
130A GLY 3.8 10.7 + - - -
131A LYS 3.3 29.0 - - - +
132A HIS* 4.7 0.4 - - - +
133A GLY* 2.7 32.1 + - - -
134A SER* 2.9 12.8 + - - +
151A VAL* 1.3 72.5 - - - +
153A THR* 1.3 66.0 + - - +
156A ASP 3.2 23.8 + - - -
157A LYS* 3.5 1.0 - - - +
158A GLY 3.2 22.8 + - - +
160A SER* 4.4 6.1 - - - -
165A SER* 3.9 21.9 + - - -
166A LYS 3.4 10.8 - - - +
167A VAL* 4.3 13.2 - - + +
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Residues in contact with THR 153 (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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132A HIS* 3.3 19.3 - - + +
133A GLY 4.6 1.3 - - - +
151A VAL* 4.3 16.1 + - + -
152A ARG* 1.3 81.7 - - - +
154A GLY* 1.3 57.6 + - - +
164A LYS 4.2 0.7 - - - +
165A SER* 3.4 4.0 - - - -
166A LYS* 3.0 52.2 + - - +
168A THR* 4.7 2.4 + - - -
208A THR* 4.1 11.6 - - - +
209A VAL 3.8 22.0 - - - +
210A LEU* 4.5 8.4 - - + +
211A GLN 4.4 4.7 - - - +
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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