Contacts of the strand formed by residues 133 - 137 (chain D) in PDB entry 3OX4
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 LEU 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PHE* 4.4 2.4 - - - -
92D VAL* 3.2 22.9 - - + +
94D SER 4.1 1.6 - - - +
104D ALA* 3.9 24.9 - - + +
105D LYS* 3.9 29.8 - - + -
108D ALA* 4.5 4.9 - - + -
130D ALA* 5.9 0.9 - - + -
131D LEU 3.1 8.8 + - - +
132D PRO* 1.3 74.1 - - - +
134D MET* 1.3 74.6 + - - +
135D SER* 3.9 11.7 - - - +
168D VAL* 4.2 4.9 - - - +
170D PRO* 3.6 29.8 - - + +
171D MET* 2.8 38.9 + - - +
172D VAL 3.5 3.1 + - - -
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Residues in contact with MET 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 6.3 0.2 - - - -
22D ALA* 3.7 34.3 - - + +
23D ILE* 4.1 20.9 - - - -
26D LEU* 4.1 22.2 - - + -
91D PHE* 3.7 20.4 - - + -
92D VAL 2.9 6.4 + - - +
93D ILE* 3.1 11.1 - - + +
94D SER 2.9 23.7 + - - -
133D LEU* 1.3 73.8 - - - +
135D SER* 1.3 63.8 + - - +
136D ILE* 4.4 13.5 - - + -
172D VAL* 3.3 29.8 - - + +
174D VAL* 4.1 19.3 - - + -
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Residues in contact with SER 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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94D SER* 2.7 22.2 + - - -
101D HIS* 3.7 8.1 + - - +
105D LYS* 5.3 0.2 - - - -
133D LEU* 3.9 7.8 - - - +
134D MET* 1.3 71.9 - - - +
136D ILE* 1.3 63.6 + - - +
137D ASN 3.7 1.4 + - - -
145D GLU* 3.6 33.0 - - - +
170D PRO* 3.6 17.5 - - - +
172D VAL 3.0 7.9 + - - -
173D SER* 3.6 1.6 - - - -
174D VAL* 2.9 25.6 + - - -
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Residues in contact with ILE 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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19D LEU* 4.1 19.7 - - + -
23D ILE* 5.1 1.8 - - + -
51D VAL* 4.2 21.1 - - + -
93D ILE* 3.6 25.4 - - + -
94D SER* 2.7 15.0 + - - +
95D LEU* 3.4 11.5 - - + +
96D GLY 3.1 26.2 + - - +
101D HIS* 3.4 3.3 - - - -
134D MET* 4.4 9.4 - - + -
135D SER* 1.3 72.5 - - - +
137D ASN* 1.3 60.1 + - - +
174D VAL* 3.8 31.0 - - + +
176D ASP 6.0 0.2 - - - +
179D LEU* 3.5 31.6 - - + -
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Residues in contact with ASN 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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96D GLY 3.5 4.8 - - - +
97D GLY* 4.4 0.9 - - - -
101D HIS* 3.3 17.1 + - - +
135D SER 3.7 1.6 + - - -
136D ILE* 1.3 74.2 - - - +
138D THR* 1.3 67.5 + - - +
139D THR* 2.7 33.0 + - - +
142D THR* 4.7 3.1 + - - -
145D GLU* 3.3 22.8 - - + +
174D VAL 3.0 13.0 + - - +
175D ASN* 2.8 27.3 + - - +
176D ASP 4.6 7.4 + - - +
179D LEU* 4.6 3.3 - - - +
180D MET* 3.5 16.3 - - - +
247D GLN* 3.3 19.2 + - - +
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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