Contacts of the strand formed by residues 88 - 93 (chain P) 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 SER 88 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ARG* 3.5 13.6 - - - +
37P GLN 2.6 33.9 + - - -
38P ASP* 2.8 13.4 + - - -
86P GLN 3.1 10.4 + - - -
87P THR* 1.3 77.3 - - - +
89P VAL* 1.3 65.7 + - - +
90P TYR* 3.8 14.2 - - - -
112P THR 3.8 0.7 - - - +
113P ARG* 3.9 5.4 + - - +
114P LEU* 3.0 31.1 + - - +
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Residues in contact with VAL 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P ARG* 3.3 2.6 - - - -
37P GLN* 2.7 51.6 + - + +
88P SER* 1.3 81.4 + - - +
90P TYR* 1.3 65.1 + - - +
91P PHE* 3.6 28.1 + - + -
110P PRO 5.8 0.4 - - - +
111P GLY* 4.6 1.8 - - - -
112P THR 3.4 15.3 - - - +
113P ARG* 3.8 35.4 - - + +
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Residues in contact with TYR 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLN* 3.2 4.3 - - - +
21P LEU* 3.7 24.9 - - + -
34P TRP* 4.0 6.7 - - + -
35P TYR 3.4 13.7 - - - +
36P ARG* 3.9 13.2 - - + -
46P ILE* 4.9 2.7 - - + -
65P TYR* 2.5 45.5 + + - -
77P LEU* 3.7 19.1 - - + -
79P LEU* 4.3 2.9 - - + +
86P GLN* 2.6 31.7 + - - +
88P SER* 3.8 20.8 - - - -
89P VAL* 1.3 75.7 - - - +
91P PHE* 1.3 61.6 + - - +
111P GLY* 3.0 8.0 - - - -
112P THR* 2.9 38.9 + - - +
114P LEU* 3.9 20.9 - - + +
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Residues in contact with PHE 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N GLN* 4.0 4.0 - - - -
41N GLY 3.7 22.7 - - - -
42N GLU* 5.2 0.7 - - - -
43N LEU* 3.9 25.8 - - + -
6P GLN* 3.7 1.1 - - - +
33P TYR 3.7 0.7 - - - +
34P TRP* 3.6 5.0 - - - -
35P TYR* 2.8 51.8 + - + +
37P GLN* 3.3 24.5 - - + -
43P LEU* 3.8 19.5 - - + -
89P VAL* 3.6 25.1 - - + -
90P TYR* 1.3 75.5 - - - +
92P CYS* 1.3 60.6 + - - +
108P PHE* 4.4 14.1 - + + -
109P GLY 3.5 22.4 - - - -
110P PRO* 3.9 5.8 - - + -
111P GLY* 3.6 18.2 - - - -
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Residues in contact with CYS 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 4.0 4.3 - - + +
6P GLN* 3.0 22.0 - - + +
23P CYS* 2.0 52.9 - - + -
32P MET* 4.4 5.8 - - - -
33P TYR 3.3 12.1 - - - -
34P TRP* 4.0 13.7 - - + -
75P PHE* 4.9 2.2 - - - -
91P PHE* 1.3 74.2 - - - +
93P ALA* 1.3 67.5 + - - +
108P PHE* 3.3 6.3 - - - -
109P GLY 3.0 25.5 + - - -
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Residues in contact with ALA 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104N LEU* 5.0 1.8 - - + -
4P VAL* 4.8 0.9 - - - -
32P MET* 3.5 2.6 - - - +
33P TYR* 2.8 36.9 + - + -
35P TYR* 3.7 20.2 - - + -
92P CYS* 1.3 77.8 - - - +
94P SER* 1.3 64.2 + - - +
95P PRO* 4.0 7.2 - - + -
107P TYR 3.2 7.0 - - - +
108P PHE* 3.5 32.3 - - + -
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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