Contacts of the strand formed by residues 86 - 93 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36I LYS* 3.8 22.4 - - + -
37I GLN 3.3 23.3 - - - +
38I PRO* 3.8 4.7 - - + -
39I PRO* 4.6 3.4 - - - -
84I ASP 3.1 10.0 + - - +
85I SER* 1.3 76.8 - - - +
87I VAL* 1.3 64.7 + - - +
88I TYR* 3.7 8.6 - - + -
111I ARG* 4.6 3.1 - - - +
112I LEU 2.8 31.2 + - - +
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Residues in contact with VAL 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I TYR 4.1 0.3 - - - +
36I LYS* 3.7 1.0 - - - -
37I GLN* 2.8 48.4 + - - +
86I ALA* 1.3 76.3 - - - +
88I TYR* 1.3 63.5 + - - +
89I PHE* 3.7 32.4 + - + -
108I THR 5.3 0.4 - - - +
109I GLY* 4.2 3.6 - - - -
110I THR 3.3 21.8 - - - +
111I ARG* 4.1 26.9 - - + +
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Residues in contact with TYR 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLN* 2.9 19.6 + - - -
20I LEU* 3.6 25.6 - - + -
34I TRP* 3.7 9.4 - + + -
35I TYR 3.4 1.8 - - - -
36I LYS* 3.6 32.6 - - + -
46I LEU* 3.8 14.6 - - + -
62I TYR* 4.5 5.3 + - - -
75I PHE* 3.6 26.0 - + - -
77I ILE* 3.8 8.9 - - + +
84I ASP* 2.5 45.0 + - - +
86I ALA* 3.7 18.6 - - + -
87I VAL* 1.3 73.4 - - - +
89I PHE* 1.3 62.5 + - - +
109I GLY* 3.3 1.9 - - - -
110I THR* 2.9 24.7 + - - +
112I LEU* 3.9 15.5 - - + -
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Residues in contact with PHE 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLN* 3.7 0.9 - - - -
34I TRP* 3.3 10.6 - - - -
35I TYR* 2.8 47.8 + - + +
37I GLN* 3.8 21.5 - - + -
43I LEU* 4.0 19.3 - - + -
87I VAL* 3.7 28.3 - - + -
88I TYR* 1.3 74.5 - - - +
90I CYS* 1.3 59.3 + - - +
91I ALA* 5.4 0.6 - - - +
106I PHE* 4.1 23.5 - + + -
107I GLY 3.6 20.2 - - - -
108I THR 3.9 8.1 - - - -
109I GLY* 3.7 18.2 - - - -
37J GLN* 3.4 23.1 - - - -
42J GLY* 4.0 11.9 - - - -
43J LEU* 4.6 7.2 - - + -
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Residues in contact with CYS 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 3.9 4.4 - - + +
5I GLN* 3.0 21.4 + - + +
22I CYS* 2.0 51.6 - - + -
32I LEU* 4.3 12.1 - - - -
33I PHE 3.5 7.9 - - - -
34I TRP* 4.0 17.9 - - + -
73I PHE* 4.7 2.7 - - - -
89I PHE* 1.3 75.6 - - - +
91I ALA* 1.3 65.6 + - - +
106I PHE* 3.6 2.6 - - - -
107I GLY 2.9 26.7 + - - -
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Residues in contact with ALA 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.4 2.2 - - - -
32I LEU* 3.1 13.1 - - - +
33I PHE* 2.8 48.0 + - + -
35I TYR* 5.7 0.2 - - + -
89I PHE 5.4 0.4 - - - +
90I CYS* 1.3 77.0 - - - +
92I LEU* 1.3 60.4 + - - +
104I LEU* 4.0 12.8 - - + -
105I ILE 3.2 13.0 - - - +
106I PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I GLN* 4.3 13.0 - - + +
2I LYS 4.2 12.1 - - - +
3I VAL* 3.6 15.0 - - + +
24I TYR* 4.3 9.0 - - + -
25I GLU 3.4 26.7 - - - +
26I THR* 4.0 11.7 - - - -
30I TYR* 3.5 39.7 - - + -
31I TYR* 3.6 8.1 - - - +
32I LEU* 4.0 13.9 - - + -
91I ALA* 1.3 75.1 - - - +
93I SER* 1.3 67.8 + - - +
103I LYS 3.8 0.7 - - - +
104I LEU* 3.5 1.7 - - - +
105I ILE* 2.7 41.5 + - + +
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Residues in contact with SER 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLN* 3.2 19.9 + - - -
1I GLN* 5.1 3.1 - - - -
30I TYR* 3.8 5.1 - - - +
31I TYR* 3.0 40.4 + - - -
92I LEU* 1.3 81.0 - - - +
94I GLY* 1.3 75.7 + - - +
102I ASP* 4.5 0.9 - - - +
103I LYS 4.0 6.7 - - - -
104I LEU* 3.6 31.6 + - - -
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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