Contacts of the strand formed by residues 150 - 156 (chain A) in PDB entry 4FYT
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 ILE 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A HIS* 3.4 43.9 + - + +
137A VAL* 3.3 40.4 - - + +
138A VAL* 4.4 0.4 - - - -
139A LEU* 4.0 26.0 - - + +
148A PRO 3.9 0.4 + - - +
149A ASP* 1.3 75.6 - - - +
151A ASP* 1.3 63.5 + - - +
152A LYS 3.7 18.8 - - - +
153A THR* 4.3 1.3 - - + -
164A VAL* 3.9 20.9 - - + -
165A HIS 3.9 8.1 - - - +
166A LEU* 4.2 8.3 - - + -
167A LYS* 4.0 9.8 - - - -
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Residues in contact with ASP 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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135A HIS* 3.4 16.3 - - - -
149A ASP 3.6 3.4 + - - -
150A ILE* 1.3 72.5 - - - +
152A LYS* 1.3 82.7 + - - +
165A HIS* 2.8 25.6 + - + +
166A LEU 4.4 3.8 - - - +
167A LYS* 4.0 28.0 - - + +
1013A SO4 4.5 0.3 + - - -
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Residues in contact with LYS 152 (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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150A ILE* 3.7 3.2 - - - +
151A ASP* 1.3 99.7 + - - +
153A THR* 1.3 71.0 + - - +
154A GLU* 6.5 0.2 - - - -
164A VAL 3.9 0.2 - - - -
165A HIS* 3.0 48.2 + - + +
1013A SO4 3.6 16.2 - - - +
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Residues in contact with THR 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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135A HIS* 4.9 0.2 - - + -
136A ARG* 3.0 34.6 + - + +
137A VAL* 4.4 6.7 - - + -
150A ILE* 4.3 6.1 - - + -
152A LYS* 1.3 84.3 - - - +
154A GLU* 1.3 63.9 + - - +
162A LEU* 4.0 10.3 - - + -
163A VAL 3.2 9.6 - - - +
164A VAL* 3.9 29.8 - - + -
165A HIS* 4.9 0.4 - - - -
1013A SO4 2.6 36.2 + - - +
1014A SO4 3.2 11.8 + - - -
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Residues in contact with GLU 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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71A TRP* 3.8 16.0 + - - -
136A ARG* 3.7 1.6 - - - +
152A LYS* 6.4 0.4 - - + -
153A THR* 1.3 76.1 - - - +
155A LEU* 1.3 64.4 + - - +
156A VAL* 4.0 18.6 - - + +
162A LEU* 3.6 4.5 - - - +
163A VAL* 2.8 48.5 + - + +
165A HIS* 2.7 30.1 + - + +
1014A SO4 3.5 18.5 + - - +
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Residues in contact with LEU 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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124A SER* 4.2 9.2 - - - +
127A LEU 4.0 16.8 - - - +
129A TYR* 4.1 13.0 - - + -
136A ARG* 3.9 15.9 - - - +
154A GLU* 1.3 73.8 - - - +
156A VAL* 1.3 64.0 + - - +
157A GLU* 3.8 12.5 + - + +
161A TYR 3.4 12.1 - - - +
162A LEU* 3.9 27.8 - - + -
1014A SO4 2.8 20.7 + - - +
1019A SO4 3.5 26.0 - - - +
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Residues in contact with VAL 156 (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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71A TRP* 3.5 25.4 - - + +
72A ASN* 3.9 12.8 - - - +
154A GLU* 4.0 15.7 - - - +
155A LEU* 1.3 73.0 - - - +
157A GLU* 1.3 61.5 + - - +
158A PRO* 4.0 11.0 - - + -
159A THR* 3.2 22.4 - - + +
160A GLU* 3.0 22.3 + - - -
161A TYR* 2.9 22.5 + - + +
163A VAL* 3.8 22.0 - - + -
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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