Contacts of the strand formed by residues 151 - 156 (chain A) in PDB entry 3ALQ
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 TYR 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.6 27.8 - + + +
16A VAL 3.5 12.1 - - - +
17A VAL* 4.7 3.6 - - + -
28A TRP* 3.5 6.7 - - - -
59A TYR* 3.9 15.5 - + - -
60A SER* 2.7 26.0 + - - -
61A GLN* 2.6 61.9 + - + +
119A TYR* 3.3 13.6 - + - -
148A GLY* 3.4 26.5 - - - -
150A VAL* 1.3 80.4 - - - +
152A PHE* 1.3 55.7 + - - +
94B LEU* 3.3 17.3 - - + +
120B LEU* 4.1 1.0 - - - +
121B GLY 3.1 36.8 + - - -
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Residues in contact with PHE 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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14A ALA 4.4 0.2 - - - -
15A HIS* 3.6 1.4 - - - -
16A VAL* 2.9 38.0 + - + +
28A TRP* 3.7 33.9 - + + -
46A ASN 5.2 1.1 - - - -
48A LEU* 3.8 25.9 - - + +
58A ILE* 4.2 11.9 - - + -
59A TYR* 3.5 13.7 - - - -
60A SER* 4.0 3.8 - - - +
80A ILE* 3.9 19.1 - - + -
132A LEU* 3.4 42.4 - - + -
133A SER* 4.1 3.6 - - - -
134A ALA* 3.4 29.6 - - + -
151A TYR* 1.3 78.2 - - - +
153A GLY* 1.3 70.6 + - - +
154A ILE* 4.6 0.4 - - + -
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Residues in contact with GLY 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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14A ALA 2.8 14.8 - - - -
15A HIS* 4.2 0.2 - - - -
48A LEU* 4.6 2.2 - - - -
58A ILE* 4.0 0.5 - - - +
59A TYR* 3.0 55.9 + - - +
152A PHE* 1.3 78.2 - - - +
154A ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 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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12A PRO 5.1 0.2 - - - +
13A VAL* 3.9 1.4 - - - +
14A ALA* 2.7 46.3 + - + +
41A VAL* 4.1 24.5 - - + -
48A LEU* 4.1 16.6 - - + -
50A VAL* 4.5 10.8 - - + -
56A TYR* 4.0 26.7 - - + -
57A LEU 3.2 10.1 - - - +
58A ILE* 3.9 12.1 - - + -
59A TYR* 3.9 3.7 - - - -
132A LEU* 3.8 32.1 - - + -
152A PHE* 4.6 1.1 - - + -
153A GLY* 1.3 81.7 - - - +
155A ILE* 1.3 64.0 + - - +
123B VAL* 5.3 0.3 - - - +
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Residues in contact with ILE 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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11A MET* 4.9 4.5 - - + -
12A PRO 3.5 9.9 - - - +
13A VAL* 4.0 11.0 - - + -
56A TYR* 3.4 5.3 - - - -
57A LEU* 3.0 49.1 + - + +
59A TYR* 5.4 0.2 - - + -
154A ILE* 1.3 77.2 - - - +
156A ALA* 1.3 73.4 + - - +
157A LEU* 3.5 5.7 + - + +
55B LEU* 4.2 13.5 - - + -
123B VAL* 3.7 38.6 - - + -
157B LEU* 3.6 38.8 - - + -
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Residues in contact with ALA 156 (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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11A MET* 3.4 23.1 - - + +
12A PRO* 3.0 35.0 + - + -
52A SER* 5.8 0.2 - - - +
53A GLU 6.1 0.4 - - - +
54A GLY* 6.0 1.3 - - - -
55A LEU 3.7 4.0 - - - +
56A TYR* 3.5 33.0 - - + +
155A ILE* 1.3 81.5 - - - +
157A LEU* 1.3 63.6 + - - +
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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