Contacts of the strand formed by residues 133 - 139 (chain D) in PDB entry 5FLX
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 GLY 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D MET* 4.7 4.0 - - - -
131D ALA* 3.1 11.5 - - - +
132D LYS* 1.3 81.3 - - - +
134D CYS* 1.3 62.2 + - - +
154D ASP 3.3 11.7 - - - -
155D GLY* 3.7 1.3 - - - -
156D LEU 3.2 22.4 + - - -
157D MET* 4.3 2.2 - - - -
188D ILE* 4.1 1.0 - - - -
189D MET* 3.7 22.8 + - - +
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Residues in contact with CYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 3.6 29.3 - - + +
126D ILE* 3.7 39.0 - - + -
127D MET* 5.1 5.1 - - + +
133D GLY* 1.3 74.4 - - - +
135D GLU* 1.3 63.8 + - - +
136D VAL* 4.3 11.4 - - - -
152D PHE 4.3 0.2 - - - +
153D VAL 3.9 0.3 - - - -
154D ASP* 2.9 37.6 + - + +
157D MET* 4.2 2.4 - - - +
186D VAL* 4.6 1.8 - - - -
187D LYS 3.7 6.5 - - - -
188D ILE* 3.8 14.1 - - + -
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14851 U 4.1 13.2 + - - -
134D CYS* 1.3 75.9 - - - +
136D VAL* 1.3 65.6 + - - +
137D VAL* 4.2 20.8 - - + +
151D LYS* 5.3 6.2 - - + +
152D PHE 3.2 18.4 - - - +
153D VAL* 4.4 18.0 - - + +
157D MET* 3.9 9.0 - - + +
159D HIS* 2.9 32.5 + - - -
185D LYS 3.5 2.0 - - - +
187D LYS* 3.1 52.9 + - + +
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Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 5.2 7.4 - - + -
119D CYS* 4.5 13.5 - - + -
122D VAL* 5.2 10.5 - - + -
123D LEU* 4.4 14.3 - - + +
126D ILE* 5.8 0.4 - - + -
134D CYS* 4.3 15.7 - - - -
135D GLU* 1.3 78.5 - - - +
137D VAL* 1.3 65.5 + - - +
138D VAL* 3.9 23.3 - - + -
151D LYS* 3.5 2.4 - - - -
152D PHE* 2.8 47.6 + - + +
184D ILE* 5.5 1.1 - - + -
185D LYS 3.3 7.0 - - - +
186D VAL* 4.2 23.3 - - + -
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13351 G 5.2 1.6 + - - +
135D GLU* 4.2 22.0 - - + +
136D VAL* 1.3 75.9 - - - +
138D VAL* 1.3 62.6 + - - +
139D SER* 4.0 17.4 + - - +
149D SER* 5.6 0.2 - - - -
151D LYS* 4.0 36.8 - - + -
183D GLY 3.8 0.9 - - - +
184D ILE* 3.3 6.1 - - - +
185D LYS* 2.8 62.1 + - + +
187D LYS* 5.4 6.3 - - - +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 6.0 2.2 - - + -
109D LEU* 6.1 2.7 - - + -
115D VAL* 4.0 28.9 - - + -
119D CYS* 4.6 3.8 - - - -
136D VAL* 3.9 19.7 - - + -
137D VAL* 1.3 76.3 - - - +
139D SER* 1.3 65.6 + - - +
142D LEU* 3.8 24.9 - - + +
148D LYS 4.1 1.9 - - - +
149D SER* 3.5 3.1 - - - -
150D MET* 2.9 46.9 + - + +
152D PHE* 4.9 0.9 - - + -
182D LEU* 5.0 8.5 - - + -
183D GLY 3.8 2.9 - - - +
184D ILE* 4.1 20.2 - - + -
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13341 G 3.8 10.3 - - - +
13351 G 3.3 36.0 + - - -
137D VAL* 4.0 14.3 + - - +
138D VAL* 1.3 77.1 + - - +
140D GLY* 1.3 58.3 + - - +
142D LEU* 5.7 0.7 - - - -
148D LYS 5.1 0.2 - - - -
149D SER* 4.3 9.6 - - - +
182D LEU* 3.4 6.3 - - - +
183D GLY 3.0 32.6 + - - +
301D MG 3.5 16.4 - - - -
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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