Contacts of the strand formed by residues 133 - 137 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C PHE* 5.7 0.4 - - - -
92C VAL* 3.4 29.4 - - + +
94C SER 4.4 0.7 - - - +
104C ALA* 3.9 15.3 - - + +
105C LYS* 3.8 37.7 - - + -
108C ALA* 4.4 6.5 - - + -
130C ALA* 6.1 0.2 - - + -
131C LEU 3.2 7.6 + - - +
132C PRO* 1.3 75.9 - - - +
134C MET* 1.3 74.2 + - - +
135C SER* 4.0 9.2 - - - +
168C VAL* 4.1 5.2 - - - +
169C THR 5.2 0.7 - - - +
170C PRO* 3.6 23.5 - - + +
171C MET* 2.7 37.5 + - - +
172C VAL* 3.4 4.9 + - - -
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Residues in contact with MET 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA* 4.0 24.9 - - + +
23C ILE* 4.8 8.1 - - - -
26C LEU* 3.9 38.4 - - + -
91C PHE* 5.0 5.5 - - + -
92C VAL 2.8 10.2 + - - +
93C ILE* 3.2 20.3 - - + -
94C SER 2.9 24.1 + - - +
133C LEU* 1.3 77.7 - - - +
135C SER* 1.3 64.0 + - - +
136C ILE* 3.9 27.6 - - + -
172C VAL* 3.4 29.8 - - + +
174C VAL* 4.3 4.0 - - + -
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Residues in contact with SER 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C SER* 3.0 19.4 + - - -
101C HIS* 3.8 5.8 + - - +
105C LYS* 5.4 0.2 - - - -
133C LEU* 4.0 7.1 - - - +
134C MET* 1.3 73.2 - - - +
136C ILE* 1.3 59.2 + - - +
137C ASN 3.7 0.9 + - - -
145C GLU* 3.4 34.1 - - - +
170C PRO* 3.4 20.8 - - - +
172C VAL 3.0 9.9 + - - -
173C SER* 3.5 0.9 - - - -
174C VAL 2.8 31.7 + - - +
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.6 24.5 - - + -
22C ALA* 5.2 0.2 - - + -
23C ILE* 5.9 0.2 - - + -
51C VAL* 5.4 2.2 - - + -
93C ILE* 4.0 14.8 - - + -
94C SER 2.9 17.1 + - - +
95C LEU* 3.5 15.1 - - + -
96C GLY 3.1 15.9 + - - -
101C HIS* 3.0 14.3 - - - -
134C MET* 3.9 18.2 - - + -
135C SER* 1.3 70.5 - - - +
137C ASN* 1.3 61.0 - - - +
174C VAL* 3.3 39.5 - - + +
176C ASP 5.9 0.9 - - - +
179C LEU* 3.5 32.1 - - + -
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Residues in contact with ASN 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLY 3.5 3.5 - - - +
97C GLY* 4.4 0.7 - - - -
101C HIS* 3.2 16.1 + - - +
135C SER 3.7 0.8 + - - -
136C ILE* 1.3 75.9 - - - +
138C THR* 1.3 67.8 + - - +
139C THR* 2.7 32.5 + - - +
142C THR* 4.6 3.1 + - - -
143C ALA 5.0 0.4 - - - +
145C GLU* 3.3 24.5 - - + +
174C VAL 2.9 15.2 + - - +
175C ASN* 3.0 27.6 + - - +
176C ASP 4.6 1.6 + - - +
179C LEU* 4.6 5.2 - - - +
180C MET* 3.6 17.2 - - - +
247C GLN* 3.4 18.4 + - - +
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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
------------------------------------------------------------
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