Contacts of the strand formed by residues 149 - 155 (chain A) in PDB entry 3AB0
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A VAL 3.0 10.1 + - - -
148A LEU* 1.3 74.5 - - - +
150A GLY* 1.3 57.2 + - - -
166A SER* 4.7 3.1 - - - -
167A LEU* 3.1 30.0 + - - +
194A THR 3.5 6.3 - - - -
195A GLY* 3.8 7.6 - - - -
197A GLY 3.2 19.1 - - - -
198A LEU* 3.5 10.0 - - - +
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Residues in contact with GLY 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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149A GLY* 1.3 74.3 - - - -
151A LEU* 1.3 68.8 + - - +
165A SER 3.2 14.1 - - - -
166A SER* 3.9 6.9 + - - -
167A LEU 4.3 0.2 - - - -
174A ILE* 4.9 1.6 - - - -
193A VAL* 3.5 3.3 - - - +
194A THR* 2.7 48.9 + - - +
195A GLY* 4.0 0.8 - - - +
198A LEU* 4.4 4.5 - - - +
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Residues in contact with LEU 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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105A VAL* 3.7 24.0 - - + -
138A VAL* 5.3 3.1 - - + -
140A ALA* 3.6 31.6 - - + -
150A GLY* 1.3 82.4 - - - +
152A THR* 1.3 62.5 + - - +
163A THR 3.1 2.3 - - - +
164A GLY* 3.6 1.2 - - - -
165A SER* 2.8 33.6 + - - +
174A ILE* 4.4 13.7 - - + -
176A ILE* 3.9 15.3 - - + -
191A VAL* 4.3 9.4 - - + -
192A ILE 3.4 6.1 - - - +
193A VAL* 3.7 29.2 - - + -
194A THR* 3.3 5.1 + - - -
198A LEU* 4.2 15.0 - - + -
200A LEU* 5.3 1.8 - - + -
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Residues in contact with THR 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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151A LEU* 1.3 78.5 - - - +
153A ILE* 1.3 62.0 + - - +
154A GLN* 3.7 27.1 - - + +
159A PRO* 3.9 10.2 - - + +
163A THR* 2.7 35.0 + - - -
164A GLY* 3.7 4.2 + - - -
176A ILE* 4.4 1.3 - - - -
191A VAL* 3.3 6.5 - - - -
192A ILE 2.8 45.4 + - - +
194A THR* 3.9 4.9 - - + -
69F THR* 3.5 23.5 + - - +
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Residues in contact with ILE 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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136A ILE* 3.9 55.4 - - + +
138A VAL* 3.9 21.8 - - + -
152A THR* 1.3 76.7 + - - +
154A GLN* 1.3 62.5 + - - +
155A VAL* 5.1 0.4 - - + +
159A PRO* 3.4 4.7 - - - +
160A VAL* 2.8 37.2 + - + -
163A THR* 3.4 17.9 + - + -
176A ILE* 3.7 27.8 - - + -
178A ALA* 4.5 5.2 - - + -
189A VAL* 4.1 11.9 - - + -
190A GLU 3.8 3.4 - - - +
191A VAL* 4.5 6.3 - - + +
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Residues in contact with GLN 154 (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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102A ASN* 4.8 0.6 + - - -
152A THR* 3.7 15.8 - - + +
153A ILE* 1.3 78.8 - - - +
155A VAL* 1.3 63.9 + - - +
156A ASN 3.5 0.7 + - - -
157A GLY* 3.5 15.3 + - - +
158A VAL 3.3 8.3 - - - +
159A PRO* 3.8 24.5 - - + +
188A LEU 3.1 12.6 - - - +
189A VAL* 4.7 0.7 - - - -
190A GLU* 2.8 33.5 + - + +
192A ILE* 3.3 31.1 - - + +
194A THR* 5.5 0.6 - - - +
32C TYR* 2.7 40.6 + - - -
67F SER 5.2 4.6 + - - -
68F GLY* 5.3 1.0 - - - -
69F THR* 4.8 1.8 + - - -
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Residues in contact with VAL 155 (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 ILE* 4.6 2.9 - - + -
153A ILE* 5.3 0.7 - - + -
154A GLN* 1.3 67.6 - - - +
156A ASN* 1.3 81.0 + - - +
157A GLY 3.0 2.9 - - - -
158A VAL* 2.9 31.4 + - - +
160A VAL* 3.7 22.3 - - + +
180A THR* 4.0 24.2 - - + +
182A ILE* 3.6 24.0 - - + -
187A SER* 4.1 5.8 - - - -
188A LEU 3.4 4.7 - - - +
189A VAL* 4.1 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