Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 3A46
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.6 27.7 - - + +
30A SER* 2.9 18.4 + - - -
92A GLU* 3.5 14.9 - - + -
93A ALA 2.6 35.6 + - - -
94A LYS 3.2 1.6 - - - -
95A TYR* 1.3 76.6 - - - +
97A ARG* 1.3 60.3 + - - +
98A ALA 3.8 18.8 - - - +
99A VAL* 3.9 10.1 - - + -
109A TYR* 4.1 9.0 - - + +
110A PHE 3.7 6.5 - - - +
111A SER* 3.7 6.0 - - - -
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Residues in contact with ARG 97 (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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28A PHE* 3.2 11.5 - - + +
29A ILE* 3.0 28.1 + - - -
30A SER* 3.0 43.5 + - - +
31A GLY* 4.0 3.6 - - - +
33A TYR* 6.3 2.0 - - + -
95A TYR* 3.3 34.0 + - - +
96A THR* 1.3 74.6 + - - +
98A ALA* 1.3 60.0 + - + +
110A PHE* 2.8 20.3 + - + +
112A ASP* 2.9 28.1 + - + +
113A MET* 3.1 30.3 + - - +
115A ASN* 2.8 32.2 + - - +
119A PHE* 5.8 1.1 - - + -
8C T 4.2 6.7 + - - -
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Residues in contact with ALA 98 (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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26A ILE* 5.0 1.8 - - + -
27A ASP 3.3 4.7 - - - +
28A PHE* 3.6 28.3 - - + -
96A THR* 3.8 1.7 - - - +
97A ARG* 1.3 81.1 - - - +
99A VAL* 1.3 64.0 + - - +
100A LEU* 4.2 11.2 - - + +
108A ALA 4.0 0.3 - - - +
109A TYR* 3.5 4.7 - - - -
110A PHE* 3.1 33.5 + - + +
119A PHE* 4.0 20.2 - - + -
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Residues in contact with VAL 99 (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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25A TYR 3.8 0.7 - - - +
26A ILE* 3.3 2.1 - - - -
27A ASP* 2.8 45.2 + - + +
29A ILE* 4.1 23.3 - - + -
92A GLU* 4.4 4.5 - - - +
96A THR* 3.9 18.6 - - + -
98A ALA* 1.3 77.4 - - - +
100A LEU* 1.3 62.2 + - - +
101A SER* 3.9 5.6 + - - +
107A MET* 3.5 32.1 - - + -
108A ALA 3.7 3.1 - - - +
109A TYR* 3.9 17.9 - - + -
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Residues in contact with LEU 100 (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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23A LEU* 3.8 13.9 - - + -
25A TYR 3.5 3.4 - - - -
26A ILE* 4.0 29.2 - - + -
64A PHE* 4.6 12.1 - - + -
78A ILE* 4.9 7.9 - - + -
88A TRP* 3.8 39.9 - - + -
98A ALA* 4.4 7.4 - - + -
99A VAL* 1.3 81.7 - - - +
101A SER* 1.3 61.8 + - - +
102A PHE* 3.8 29.7 - - + -
107A MET* 3.5 8.7 - - - +
108A ALA* 2.9 37.9 + - + +
119A PHE* 5.5 0.2 - - + -
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Residues in contact with SER 101 (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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23A LEU* 3.6 2.6 - - - +
24A GLU* 2.8 30.1 + - - -
25A TYR* 2.6 31.4 + - - +
99A VAL* 4.5 5.2 + - - +
100A LEU* 1.3 70.3 - - - +
102A PHE* 1.3 65.0 + - - +
106A LEU 3.8 4.5 - - - -
107A MET* 3.7 23.3 - - - +
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Residues in contact with PHE 102 (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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18A PHE* 3.6 40.4 - + + -
21A LYS* 3.7 20.2 - - + -
22A THR 3.2 24.7 - - - +
23A LEU* 3.7 19.3 - - + -
24A GLU* 3.5 9.2 - - - +
52A VAL* 3.6 28.7 - - + -
64A PHE* 5.1 5.8 - + - -
100A LEU* 3.8 37.7 - - + -
101A SER* 1.3 79.2 - - - +
103A ASP* 1.3 67.9 + - - +
105A GLU* 3.7 5.4 + - - -
106A LEU* 2.8 36.0 + - + +
107A MET* 5.5 0.2 - - - +
108A ALA* 3.9 6.5 - - + -
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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