Contacts of the strand formed by residues 86 - 89 (chain A) in PDB entry 3A4T
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ASP 5.3 0.4 - - - +
85A ASP* 1.3 72.4 - - - +
87A ILE* 1.3 62.5 + - - +
110A THR* 3.6 10.8 - - + +
112A VAL* 3.7 15.0 - - + -
155A ILE* 3.5 25.8 - - + -
156A PHE 3.3 27.1 - - - -
157A PHE* 3.3 30.1 - + - +
158A ASP* 2.8 43.7 + - - +
159A LYS 3.6 2.4 + - - -
202A LYS* 5.3 4.7 - - - +
56B SER 4.1 6.3 - - - -
57B THR 4.6 0.4 - - - -
58B PRO* 3.6 53.8 - - + -
61B LEU* 4.0 9.6 - - + -
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Residues in contact with ILE 87 (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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79A LEU* 4.5 8.5 - - + -
81A PRO* 3.9 13.0 - - + -
85A ASP* 3.6 22.0 - - + -
86A PHE* 1.3 77.3 - - - +
88A LEU* 1.3 68.4 + - - +
101A LEU* 4.0 27.1 - - + -
105A MET* 3.7 29.8 - - + -
110A THR 2.8 9.8 + - - +
111A ILE* 3.2 11.6 - - + -
112A VAL* 2.7 30.8 + - - +
157A PHE* 3.5 10.4 - - - -
159A LYS* 3.3 33.2 - - + +
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Residues in contact with LEU 88 (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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87A ILE* 1.3 79.0 - - - +
89A ASP* 1.3 56.5 + - - +
90A MET* 3.7 24.9 - - + -
112A VAL* 3.3 35.7 - - + +
114A VAL* 3.9 15.5 - - + -
143A MET* 4.3 7.2 - - + -
150A LEU* 4.6 3.4 - - + -
157A PHE* 3.6 29.3 - - + -
159A LYS 3.4 4.9 + - - -
160A ILE* 3.3 14.0 - - + +
161A LEU* 2.8 32.7 + - - +
200A LEU* 3.7 31.0 - - + -
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Residues in contact with ASP 89 (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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87A ILE 4.2 0.2 - - - -
88A LEU* 1.3 71.5 - - - +
90A MET* 1.3 61.9 + - - +
91A CYS 3.4 6.6 + - - +
92A ALA* 3.5 22.3 - - + +
97A LYS* 4.3 0.9 - - - +
98A THR* 2.7 36.4 + - - +
101A LEU* 4.4 6.0 - - + +
111A ILE* 4.1 15.7 - - + +
112A VAL 2.8 15.0 + - - +
113A ALA* 4.3 1.3 - - - -
114A VAL* 3.0 27.0 + - - +
161A LEU* 3.6 29.1 - - - +
163A ASP 4.9 1.6 + - - -
500A SFG 4.4 2.8 + - - -
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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