Contacts of the strand formed by residues 149 - 155 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I SER* 2.6 49.2 + - - -
142I LEU* 3.5 8.4 - - + +
143I ASN* 3.9 11.1 + - - -
147I VAL 2.9 24.9 + - - -
148I ARG* 1.3 75.8 - - - +
150I THR* 1.3 72.6 + - - +
163I LEU* 3.7 21.7 - - + +
164I ASN 3.0 16.6 - - - +
165I ILE* 4.0 4.3 - - + -
166I SER* 4.2 2.2 - - - +
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Residues in contact with THR 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149I ASN* 1.3 80.6 - - - +
151I ILE* 1.3 69.1 + - - +
152I HIS* 4.9 1.3 + - - -
162I VAL 3.6 0.3 - - - +
163I LEU* 3.3 5.0 - - - +
164I ASN* 2.8 48.4 + - - +
5J T 6.2 0.9 - - - -
6J G 2.7 28.8 + - - +
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Residues in contact with ILE 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I LYS* 4.6 14.2 - - + -
135I LEU* 3.7 40.2 - - + +
136I GLU* 3.8 16.2 - - + +
139I SER* 3.9 15.7 - - - +
150I THR* 1.3 84.5 - - - +
152I HIS* 1.3 68.7 + - - +
161I TYR* 4.1 26.7 - - + -
162I VAL 3.4 9.9 - - - +
163I LEU* 4.1 13.2 - - + -
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Residues in contact with HIS 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I LYS* 6.4 0.2 - - - +
150I THR* 4.9 1.6 + - - -
151I ILE* 1.3 78.7 - - - +
153I LEU* 1.3 71.6 + - - +
154I ASP* 3.2 13.1 + - - -
161I TYR* 3.4 10.5 - - - +
162I VAL* 2.9 52.7 + - + +
164I ASN* 5.2 0.9 - - + -
6J G 3.1 55.1 + + + +
7J C 3.1 28.5 - + - +
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Residues in contact with LEU 153 (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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152I HIS* 1.3 82.0 - - - +
154I ASP* 1.3 61.0 + - - +
155I ASP 4.2 2.7 - - - +
156I HIS* 3.6 50.8 - - + +
159I GLY* 3.5 30.1 - - - +
160I VAL 3.5 20.2 - - - +
161I TYR* 3.8 31.5 - - + +
7J C 4.4 3.1 + - - -
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Residues in contact with ASP 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I ARG* 5.2 1.9 + - - -
128I TRP* 3.0 27.9 + - + +
152I HIS* 3.2 13.7 + - - -
153I LEU* 1.3 74.8 - - - +
155I ASP* 1.3 60.2 + - + +
156I HIS* 3.8 6.1 + - - -
160I VAL 2.9 12.5 + - - +
161I TYR 4.4 0.2 - - - -
162I VAL* 3.5 27.9 - - + +
7J C 3.8 12.3 - - - +
8J C 3.2 50.9 + - - +
9J G 5.0 0.5 - - - +
16L C 5.2 1.6 + - - -
17L C 4.2 2.9 + - - -
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Residues in contact with ASP 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I TRP* 6.3 0.7 - - + -
153I LEU* 4.2 2.6 - - - +
154I ASP* 1.3 75.5 - - + +
156I HIS* 1.3 58.1 + - - +
157I ARG* 2.7 52.1 + - - +
158I HIS* 3.5 10.5 - - - -
159I GLY* 3.0 24.4 + - - -
160I VAL* 2.9 32.5 + - + -
8J C 5.6 1.8 - - - -
9J G 5.6 3.6 - - - +
15L C 2.9 37.0 + - + -
16L C 4.4 4.8 + - - +
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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
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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