Contacts of the strand formed by residues 149 - 155 (chain A) 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 ASN 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 2.6 50.9 + - - -
142A LEU* 3.6 7.5 - - + +
143A ASN* 4.0 11.0 + - - -
147A VAL 3.0 23.4 + - - +
148A ARG* 1.3 77.4 - - - +
150A THR* 1.3 74.1 + - - +
163A LEU* 3.7 22.2 - - + +
164A ASN 3.0 17.3 - - - +
165A ILE* 4.0 2.5 - - + -
166A SER* 4.2 2.7 - - - +
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 5.8 0.2 - - - -
149A ASN* 1.3 81.6 - - - +
151A ILE* 1.3 66.3 + - - +
152A HIS* 5.4 1.9 - - - -
162A VAL 3.6 0.9 - - - +
163A LEU* 3.4 2.4 - - - +
164A ASN* 2.7 44.3 + - - +
5B T 5.0 1.5 - - - -
6B G 3.0 26.5 + - - +
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 4.6 16.4 - - + +
135A LEU* 3.5 40.4 - - + +
136A GLU* 3.6 20.2 - - + +
139A SER* 3.9 11.9 - - - +
150A THR* 1.3 81.8 - - - +
152A HIS* 1.3 71.1 + - - +
161A TYR* 4.4 21.3 - - + -
162A VAL 3.3 7.4 - - - +
163A LEU* 4.1 17.7 - - + -
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Residues in contact with HIS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 5.3 2.7 - - - -
151A ILE* 1.3 79.6 - - - +
153A LEU* 1.3 70.1 + - - +
154A ASP* 3.2 18.9 + - - -
161A TYR* 3.3 9.8 - - - +
162A VAL* 2.8 51.8 + - + +
6B G 3.4 64.0 + - + +
7B C 3.1 22.3 + + - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A HIS* 1.3 81.1 + - - +
154A ASP* 1.3 62.1 + - - +
155A ASP 4.1 3.8 - - - +
156A HIS* 3.6 47.6 - - + +
159A GLY* 3.8 34.3 - - - -
160A VAL 3.9 5.2 - - - +
161A TYR* 3.7 33.2 - - + +
7B C 4.4 2.5 + - - -
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 5.2 1.3 + - - -
128A TRP* 2.8 31.1 + - + -
152A HIS* 3.2 12.7 + - - -
153A LEU* 1.3 74.8 - - - +
155A ASP* 1.3 61.5 + - - +
156A HIS* 3.8 5.0 + - - -
160A VAL 2.9 12.4 + - - +
162A VAL* 3.6 26.4 - - + +
7B C 3.8 12.5 + - - +
8B C 2.9 57.9 + - - -
9B G 4.8 1.4 - - - +
16D C 5.0 2.1 + - - -
17D C 4.2 4.0 + - - -
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TRP* 6.3 0.7 - - + -
153A LEU* 4.1 4.3 - - - +
154A ASP* 1.3 76.9 - - + +
156A HIS* 1.3 59.0 + - - +
157A ARG* 2.7 53.0 + - - +
158A HIS* 3.1 15.5 + - - -
159A GLY* 3.0 23.9 + - - -
160A VAL* 2.9 29.7 + - + +
8B C 5.5 1.3 - - - -
9B G 5.6 1.8 - - - +
15D C 2.8 35.9 + - + -
16D C 4.7 5.1 + - - +
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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