Contacts of the strand formed by residues 86 - 93 (chain T) in PDB entry 2AK4
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 ALA 86 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36T LYS* 3.8 22.7 - - + -
37T GLN 3.3 23.1 - - - +
38T PRO* 3.9 4.9 - - + -
39T PRO* 4.7 3.1 - - - -
84T ASP 3.0 10.4 + - - +
85T SER* 1.3 76.3 - - - +
87T VAL* 1.3 64.2 + - - +
88T TYR* 3.7 8.8 - - + -
111T ARG* 3.7 2.9 - - - -
112T LEU 2.8 31.0 + - - +
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Residues in contact with VAL 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T TYR 4.1 0.2 - - - +
36T LYS* 3.7 1.2 - - - -
37T GLN* 2.8 49.6 + - - +
86T ALA* 1.3 75.6 - - - +
88T TYR* 1.3 63.4 + - - +
89T PHE* 3.7 31.4 + - + -
108T THR 5.3 0.7 - - - +
109T GLY* 4.2 3.8 - - - -
110T THR 3.3 22.2 - - - +
111T ARG* 4.2 22.7 - - + +
37U GLN* 5.6 0.7 - - - +
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Residues in contact with TYR 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLN* 2.9 20.1 + - - +
20T LEU* 3.6 26.2 - - + -
34T TRP* 3.7 8.5 - - + -
35T TYR 3.4 4.0 - - - +
36T LYS* 3.6 29.5 - - + -
46T LEU* 3.8 16.8 - - + -
62T TYR* 4.4 5.1 + - - -
75T PHE* 3.6 26.7 - + - -
77T ILE* 3.8 8.4 - - + +
84T ASP* 2.5 45.2 + - - +
86T ALA* 3.7 17.5 - - + -
87T VAL* 1.3 73.0 - - - +
89T PHE* 1.3 62.1 + - - +
109T GLY* 3.3 2.0 - - - -
110T THR 2.9 24.1 + - - +
112T LEU* 3.9 16.4 - - + -
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Residues in contact with PHE 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLN* 3.7 0.9 - - - -
33T PHE 3.9 0.2 - - - +
34T TRP* 3.2 10.9 - - - -
35T TYR* 2.8 47.1 + - + +
37T GLN* 3.8 14.4 - - + -
43T LEU* 4.1 19.3 - - + -
87T VAL* 3.7 26.2 - - + -
88T TYR* 1.3 74.7 - - - +
90T CYS* 1.3 60.3 + - - +
91T ALA* 5.5 0.2 - - - +
106T PHE* 4.2 21.8 - + + -
107T GLY 3.7 11.7 - - - -
108T THR 3.9 1.1 - - - -
109T GLY* 3.6 20.6 - - - -
37U GLN* 3.5 29.4 - - - -
42U GLY* 3.5 28.9 - - - -
43U LEU* 4.2 10.1 - - + -
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Residues in contact with CYS 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T VAL* 3.8 4.8 - - + +
5T GLN* 2.9 21.1 + - + +
22T CYS* 2.0 50.9 - - + -
32T LEU* 4.4 11.9 - - - -
33T PHE 3.5 6.5 - - - -
34T TRP* 4.0 20.4 - - + -
73T PHE* 4.7 2.0 - - - -
89T PHE* 1.3 73.9 - - - +
91T ALA* 1.3 65.3 + - - +
106T PHE* 3.7 2.3 - - - -
107T GLY 2.9 26.5 + - - -
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Residues in contact with ALA 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T VAL* 4.4 2.0 - - - -
32T LEU* 3.1 13.7 - - - +
33T PHE* 2.9 47.5 + - + -
35T TYR* 5.7 0.7 - - + -
89T PHE 5.5 0.2 - - - +
90T CYS* 1.3 78.3 - - - +
92T LEU* 1.3 60.4 + - - +
104T LEU* 4.0 12.8 - - + -
105T ILE 3.2 11.7 - - - +
106T PHE* 3.8 25.4 - - + -
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Residues in contact with LEU 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T GLN* 4.3 14.1 - - + +
2T LYS 4.3 7.4 - - - +
3T VAL* 3.6 15.7 - - + +
24T TYR* 4.3 15.7 - - + -
25T GLU 3.8 22.7 - - - +
26T THR* 3.8 15.7 - - - +
30T TYR* 3.5 33.4 - - + -
31T TYR 3.5 17.3 - - - +
32T LEU* 4.0 14.4 - - + -
91T ALA* 1.3 74.9 - - - +
93T SER* 1.3 64.8 + - - +
103T LYS 3.6 1.9 - - - +
104T LEU* 3.6 1.7 - - - -
105T ILE* 2.8 40.0 + - + +
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Residues in contact with SER 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S GLN* 3.4 17.3 + - - -
1T GLN* 5.3 3.1 - - - -
30T TYR* 3.5 7.0 - - - +
31T TYR* 2.9 46.8 + - - +
92T LEU* 1.3 79.6 - - - +
94T GLY* 1.3 82.3 + - - +
102T ASP* 4.5 0.5 - - - +
103T LYS 3.8 9.0 + - - -
104T LEU* 3.7 25.6 - - - -
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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