Contacts of the strand formed by residues 145 - 152 (chain B) in PDB entry 3ABD
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 THR 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 3.9 10.3 - - - -
37B TYR* 5.8 2.0 - - - -
87B ILE* 3.4 8.7 - - - +
88B LEU* 2.8 45.9 + - - +
89B ASP 4.8 3.6 + - - +
90B LYS* 6.3 0.2 - - - -
92B HIS* 5.1 8.4 - - + +
143B GLY 3.8 7.8 + - - +
144B CYS* 1.3 78.7 - - - +
146B PHE* 1.3 66.1 + - - +
1884Y PRO* 5.3 6.5 - - - -
1886Y SER* 5.7 12.3 - - - -
1887Y ARG 6.0 1.3 - - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.4 12.6 - - + -
31B LEU* 3.5 37.7 - - + -
36B VAL* 4.3 2.0 - - + -
37B TYR* 3.6 22.4 - + - -
60B LEU* 4.1 2.5 - - + -
63B TYR* 4.1 18.2 - + - -
64B ILE* 4.3 10.5 - - + -
85B VAL* 4.4 8.3 - - + -
86B VAL 3.1 15.7 - - - +
87B ILE* 4.4 5.4 - - + +
88B LEU* 4.6 6.4 - - - +
145B THR* 1.3 80.8 + - - +
147B THR* 1.3 75.6 + - - +
148B VAL* 4.2 18.8 - - + -
1884Y PRO* 3.4 54.8 - - + +
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 4.7 8.0 + - - -
85B VAL* 3.7 1.2 - - - -
86B VAL* 2.9 48.5 + - + +
88B LEU* 4.3 16.4 - - + -
146B PHE* 1.3 82.9 - - - +
148B VAL* 1.3 79.5 + - - +
149B LEU* 4.1 17.3 - - + -
178B ASP* 5.8 3.8 - - + +
1879Y LYS* 3.7 24.7 + - - -
1880Y PRO* 3.8 9.2 + - - +
1884Y PRO* 5.6 1.1 - - - -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 5.0 9.4 - - + -
63B TYR* 5.6 2.2 + - + -
67B THR* 4.1 32.5 - - + +
68B LEU* 6.0 2.9 - - + -
71B VAL* 5.4 1.1 - - + -
83B VAL* 3.9 24.5 - - + -
84B VAL 3.3 9.9 - - - +
85B VAL* 4.9 11.2 - - + -
146B PHE* 4.2 19.7 - - + -
147B THR* 1.3 81.7 + - - +
149B LEU* 1.3 67.0 + - - +
150B VAL* 4.4 7.6 - - + -
171B TRP* 4.2 1.5 - - + -
1878Y LEU 3.8 0.3 - - - +
1879Y LYS* 3.3 6.8 - - - +
1880Y PRO* 3.0 30.0 - - + +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS 4.0 0.3 - - - +
83B VAL* 3.5 2.4 - - - -
84B VAL* 2.7 47.1 + - + +
86B VAL* 3.8 26.5 - - + -
97B LYS* 5.6 2.9 - - + +
147B THR* 4.1 11.0 - - + -
148B VAL* 1.3 76.7 - - - +
150B VAL* 1.3 62.3 + - - +
151B HIS* 4.1 7.6 - - + +
174B ALA* 4.4 7.0 - - + -
178B ASP* 4.0 12.3 - - + +
179B VAL* 3.6 30.3 - - + -
1877Y ILE* 4.1 11.9 - - + -
1878Y LEU 3.3 3.8 - - - +
1879Y LYS* 3.4 33.7 - - + -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.8 29.4 - - + -
74B LEU* 4.7 9.0 - - + -
80B VAL* 3.9 31.6 - - + -
82B LYS 3.5 2.2 - - - -
83B VAL* 4.7 6.1 - - + -
148B VAL* 4.4 7.0 - - + -
149B LEU* 1.3 78.5 - - - +
151B HIS* 1.3 67.6 + - - +
152B THR* 4.5 9.6 - - + -
163B ILE* 4.8 2.0 - - + -
171B TRP* 3.8 18.6 - - + -
1876Y ASN 3.4 2.4 - - - +
1877Y ILE* 3.4 3.3 - - - -
1878Y LEU* 2.8 39.2 + - + +
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Residues in contact with HIS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.6 4.7 - - - +
81B GLU* 2.8 37.7 + - + +
82B LYS* 2.9 46.8 + - + +
84B VAL* 3.9 28.6 - - + +
149B LEU* 4.6 6.9 - - - +
150B VAL* 1.3 77.9 - - - +
152B THR* 1.3 62.7 + - - +
179B VAL* 5.5 1.7 - - + +
1876Y ASN* 3.8 5.2 - - + -
1877Y ILE* 3.5 39.6 - - + +
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.4 18.2 - - + -
79B ASP* 3.2 13.5 - - - +
80B VAL* 5.5 0.2 - - - -
81B GLU* 4.2 9.6 - - - +
150B VAL* 4.5 5.6 - - + -
151B HIS* 1.3 79.5 - - - +
153B ARG* 1.3 70.4 + - - +
1876Y ASN* 3.0 38.6 + - - +
1878Y LEU* 3.9 25.4 - - + +
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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