Contacts of the strand formed by residues 147 - 152 (chain A) in PDB entry 4FMF
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LYS 4.9 1.2 + - - -
146A PRO* 1.3 72.1 + - - +
148A ASN* 1.3 64.8 + - - +
149A TRP* 3.6 25.9 - - + -
173A THR 3.5 2.1 - - - +
174A SER* 3.5 0.9 - - - -
175A ALA* 2.7 39.7 + - - -
176A ASN* 5.7 1.8 + - - -
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Residues in contact with ASN 148 (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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146A PRO* 3.6 13.3 + - - +
147A THR* 1.3 80.3 - - - +
149A TRP* 1.3 68.1 + - - +
173A THR 3.2 3.8 - - - +
174A SER* 2.6 28.9 + - - -
228A VAL* 3.0 31.0 - - + +
230A TYR* 5.8 0.6 - - - +
235A PHE* 3.6 49.3 - - + +
237A GLU* 4.1 0.9 - - - +
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Residues in contact with TRP 149 (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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147A THR* 3.6 33.4 - - + -
148A ASN* 1.3 82.2 - - - +
150A ILE* 1.3 75.3 + - - +
151A GLU* 3.2 29.7 + - + +
172A CYS* 3.5 4.2 - - - -
173A THR* 2.8 68.2 + - + -
175A ALA* 3.9 13.5 - - + -
226A CYS* 4.6 5.2 - - - -
235A PHE* 4.3 1.5 - - - -
237A GLU* 3.3 13.2 - - - +
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Residues in contact with ILE 150 (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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149A TRP* 1.3 81.6 - - - +
151A GLU* 1.3 69.9 + - - +
170A ALA* 4.2 5.8 - - + -
171A THR 3.3 9.9 - - - +
185A TRP* 3.7 23.8 - - + -
224A LEU 3.5 25.1 - - - +
226A CYS* 4.0 9.2 - - + +
237A GLU* 3.2 53.5 + - + +
238A SER 4.5 6.7 - - - +
239A LEU* 3.9 23.3 - - + +
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Residues in contact with GLU 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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149A TRP* 3.2 29.2 + - + +
150A ILE* 1.3 78.3 - - - +
152A GLY* 1.3 68.8 + - - +
154A GLN* 5.4 7.3 + - - -
170A ALA* 3.4 1.1 - - - -
171A THR* 2.8 53.6 + - + +
173A THR* 5.0 2.1 + - - -
239A LEU* 4.4 3.4 - - - -
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Residues in contact with GLY 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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151A GLU* 1.3 82.4 - - - +
153A THR* 1.3 68.6 + - - +
154A GLN* 3.6 6.2 + - - +
169A VAL 3.3 15.7 - - - -
170A ALA* 4.7 0.2 - - - -
239A LEU* 3.6 24.2 - - - +
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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