Contacts of the helix formed by residues 132 - 140 (chain W) in PDB entry 5FYW
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 132 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121W GLY* 5.3 7.9 - - - +
122W TYR* 5.5 2.5 - - - +
131W TYR* 1.3 77.8 - - - +
133W GLN* 1.3 55.6 + - - +
134W LEU* 3.4 6.3 - - - -
135W GLU* 3.2 9.3 + - - +
136W ALA* 2.8 31.7 + - - +
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Residues in contact with GLN 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G ILE* 4.2 18.6 - - + +
121W GLY 5.5 2.0 - - - +
132W THR* 1.3 75.9 - - - +
134W LEU* 1.3 59.4 + - - +
136W ALA* 2.8 28.2 + - - +
137W VAL 3.2 5.0 + - - -
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Residues in contact with LEU 134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188B LYS* 5.4 6.1 - - - +
151G ILE* 2.4 58.3 - - + +
160G ILE* 5.0 2.0 - - - +
132W THR* 3.4 3.6 - - - -
133W GLN* 1.3 78.4 - - - +
135W GLU* 1.3 62.0 + - - +
137W VAL* 3.2 17.0 + - - +
138W GLN* 3.3 10.2 + - - +
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Residues in contact with GLU 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131W TYR* 3.8 15.0 - - + -
132W THR* 3.2 27.3 + - - +
134W LEU* 1.3 76.2 - - - +
136W ALA* 1.3 59.9 + - - +
138W GLN* 3.3 8.8 + - - +
139W LEU* 2.8 32.7 + - + +
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Residues in contact with ALA 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PHE* 6.1 6.7 - - + -
160G ILE* 6.2 1.6 - - + -
131W TYR* 6.1 0.2 - - - -
132W THR 2.8 13.1 + - - +
133W GLN* 2.8 18.5 + - - +
135W GLU* 1.3 75.0 - - - +
137W VAL* 1.3 64.8 + - - +
139W LEU* 3.1 14.6 + - - +
140W LEU* 3.1 15.4 + - - +
147W PHE* 5.6 4.0 - - - +
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Residues in contact with VAL 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PHE* 5.9 7.2 - - + -
151G ILE* 5.1 1.1 - - + -
158G HIS* 3.2 41.6 + - + -
159G ALA* 3.9 13.5 - - - +
160G ILE* 4.4 14.8 - - + +
133W GLN 3.2 2.4 + - - -
134W LEU* 3.2 10.1 + - - +
136W ALA* 1.3 79.4 - - - +
138W GLN* 1.3 63.0 + - - +
140W LEU* 3.8 13.7 + - - +
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Residues in contact with GLN 138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179B GLN* 4.6 17.9 - - - +
151G ILE* 6.2 2.2 - - + -
158G HIS* 4.3 15.8 + - + -
134W LEU 3.3 9.2 + - - +
135W GLU* 3.7 11.0 - - - +
136W ALA 3.1 0.4 - - - -
137W VAL* 1.3 81.4 - - - +
139W LEU* 1.3 60.9 + - - +
140W LEU 3.3 6.4 + - - +
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Residues in contact with LEU 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135W GLU* 2.8 21.5 + - + +
136W ALA* 3.1 4.0 + - - +
138W GLN* 1.3 71.4 - - - +
140W LEU* 1.3 63.1 + - - +
141W ASN* 3.5 2.8 + - - +
147W PHE* 4.4 11.4 - - + -
148W LEU* 3.2 49.7 + - - +
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Residues in contact with LEU 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLU* 5.7 8.3 - - - +
109G PHE* 6.3 4.5 - - + -
136W ALA 3.1 14.3 + - - +
137W VAL* 4.0 10.9 - - - +
138W GLN 3.2 8.4 - - - +
139W LEU* 1.3 78.3 - - - +
141W ASN* 1.3 61.5 + - - +
146W GLU 4.0 8.7 - - - +
147W PHE* 5.0 1.6 - - - +
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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