Contacts of the strand formed by residues 160 - 165 (chain E) in PDB entry 5AKF
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 VAL 160 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E TRP* 4.3 11.7 - - + -
129E ASN 3.8 9.2 - - - +
130E LYS* 3.5 20.9 - - + -
153E LEU* 3.2 3.2 - - - +
154E ASP* 3.0 5.7 + - - +
155E ASP* 2.9 42.4 + - + +
158E HIS* 3.7 23.1 - - + -
159E GLY* 1.3 77.2 - - - +
161E TYR* 1.3 72.5 + - - +
14H A 3.9 12.8 - - + -
15H C 3.8 35.0 - - + +
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Residues in contact with TYR 161 (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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128E TRP* 3.5 3.5 - - - -
129E ASN 2.9 37.5 + - - +
130E LYS 3.8 18.8 - - - -
132E LYS* 3.7 49.7 + - + +
135E LEU* 3.9 13.4 - - + +
151E ILE* 4.3 10.1 - - + -
152E HIS* 3.4 6.5 - - - +
153E LEU* 3.5 44.7 - - + +
154E ASP* 4.3 1.3 - - - -
159E GLY* 3.8 12.8 - - - -
160E VAL* 1.3 76.5 - - - +
162E VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 162 (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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126E ARG* 3.9 29.6 - - + -
127E ILE 3.3 9.6 - - - +
128E TRP* 3.8 19.3 - - + +
135E LEU* 4.2 3.8 - - - -
150E THR 3.8 0.3 - - - +
151E ILE* 3.2 6.9 - - - +
152E HIS* 2.9 62.3 + - + +
154E ASP* 3.6 21.3 - - + +
161E TYR* 1.3 75.6 - - - +
163E LEU* 1.3 67.4 + - - +
164E ASN* 4.6 4.5 - - + +
6F G 5.2 0.4 - - - +
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Residues in contact with LEU 163 (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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126E ARG* 3.3 5.4 - - - -
127E ILE* 2.8 42.2 + - + +
135E LEU* 3.6 39.9 - - + +
138E VAL* 4.3 14.6 - - + -
139E SER* 3.9 20.9 - - - +
142E LEU* 4.2 4.7 - - + -
149E ASN* 3.6 18.6 - - + +
150E THR 3.2 10.3 - - - +
151E ILE* 4.3 6.1 - - + -
162E VAL* 1.3 72.4 - - - +
164E ASN* 1.3 60.6 + - - +
165E ILE* 3.6 29.3 + - + -
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Residues in contact with ASN 164 (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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124E ARG* 5.2 4.3 + - - +
125E LEU 3.4 15.3 + - - +
126E ARG* 3.7 16.9 - - + +
149E ASN* 3.0 6.8 - - - +
150E THR* 2.8 39.8 + - - +
152E HIS* 5.6 0.4 - - + +
162E VAL* 3.9 7.8 + - + -
163E LEU* 1.3 74.7 - - - +
165E ILE* 1.3 66.6 + - - +
166E SER* 3.7 1.5 + - - +
167E LEU* 5.7 1.6 - - - +
5F T 3.3 49.8 + - - +
6F G 3.7 19.3 - - - +
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Residues in contact with ILE 165 (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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114E TYR* 4.5 3.6 - - + -
125E LEU* 2.8 53.0 + - + +
127E ILE* 4.4 14.4 - - + -
142E LEU* 4.0 15.9 - - + -
147E VAL* 3.6 23.3 - - + -
148E ARG 3.8 3.1 - - - -
149E ASN* 4.5 1.6 - - + -
163E LEU* 3.6 18.8 + - + -
164E ASN* 1.3 77.5 + - - +
166E SER* 1.3 69.6 + - - +
167E LEU* 3.3 6.4 + - - +
169E ASP 5.2 0.4 - - - +
173E PHE* 3.6 42.4 - - + -
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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