Contacts of the strand formed by residues 125 - 129 (chain E) in PDB entry 5AK9
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 LEU 125 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 3.3 17.3 - - + +
122E LEU* 3.8 28.5 - - + +
124E ARG* 1.3 75.6 - - - +
126E ARG* 1.3 63.4 + - - +
164E ASN* 3.7 1.8 + - - +
165E ILE* 2.7 67.5 + - + +
166E SER 4.9 0.2 - - - +
167E LEU* 3.9 16.4 - - + +
170E ARG* 3.8 38.6 - - + +
173E PHE* 4.2 20.6 - - + -
174E VAL* 4.4 5.8 - - + -
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Residues in contact with ARG 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E TYR* 3.3 9.2 + - - -
118E GLY* 3.2 4.0 - - - -
119E ASP* 2.9 47.7 + - + +
124E ARG* 3.8 31.0 + - + +
125E LEU* 1.3 84.0 - - - +
127E ILE* 1.3 64.4 + - - +
128E TRP* 3.4 34.9 - - + +
154E ASP* 5.3 2.0 + - - -
162E VAL* 3.7 19.1 - - + -
163E LEU 3.2 4.9 - - - -
164E ASN* 3.5 18.6 - - - +
7F C 3.8 12.3 - - - +
8F C 4.6 2.6 - - - +
17H C 3.9 4.6 - - - +
18H G 2.9 51.3 + - - -
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Residues in contact with ILE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ILE* 4.6 9.9 - - + -
113E LEU* 4.3 24.0 - - + +
114E TYR* 3.4 39.3 - - + +
117E GLU* 3.8 22.0 - - + +
118E GLY* 4.7 0.4 - - - -
126E ARG* 1.3 73.4 - - - +
128E TRP* 1.3 68.2 + - - +
129E ASN* 5.6 0.7 - - + -
135E LEU* 4.3 10.6 - - + +
138E VAL* 4.6 20.9 - - + -
161E TYR 4.0 0.2 - - - +
162E VAL* 3.3 2.3 - - - -
163E LEU* 2.7 53.2 + - + +
165E ILE* 4.7 11.9 - - + -
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Residues in contact with TRP 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E GLU* 3.1 51.4 + - - +
118E GLY 3.8 0.9 - - - -
119E ASP* 3.5 25.6 - - + -
126E ARG* 3.4 52.7 - - + -
127E ILE* 1.3 76.0 - - - +
129E ASN* 1.3 65.9 + - - +
135E LEU* 4.9 0.2 - - - -
154E ASP* 3.0 28.7 + - + -
160E VAL* 4.2 8.3 - - + -
161E TYR 3.4 6.1 - - - +
162E VAL* 3.5 21.7 - - + +
15H C 3.5 23.5 - - + +
16H C 3.5 51.5 - + + -
17H C 3.7 11.0 - + - -
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Residues in contact with ASN 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ILE* 4.9 6.7 + - - +
113E LEU* 4.9 3.8 - - + +
117E GLU* 2.7 29.1 + - + +
127E ILE* 4.1 1.0 + - + -
128E TRP* 1.3 73.1 + - - +
130E LYS* 1.3 63.8 + - - +
131E ASN* 2.8 37.4 + - - +
134E LEU* 4.3 15.3 - - + +
135E LEU* 3.9 23.4 - - + +
160E VAL* 3.9 4.1 - - - +
161E TYR* 2.9 36.5 + - - +
1189E MN 4.1 2.2 + - - -
15H C 3.5 15.8 + - - -
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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
------------------------------------------------------------
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