Contacts of the strand formed by residues 126 - 131 (chain C) in PDB entry 5ODS
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 ALA 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LEU 4.0 0.3 - - - +
122C VAL* 3.8 1.7 - - - -
123C THR* 3.0 34.6 + - - +
125C ASN* 1.3 82.4 - - + +
127C VAL* 1.3 66.5 + - - +
128C TYR* 4.0 22.2 - - + +
140C LYS* 4.0 14.6 - - + -
142C PHE 3.4 13.9 - - - +
143C ASP* 3.9 11.2 - - - +
144C ARG* 3.9 5.1 - - - +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA* 5.1 5.2 - - + -
121C LEU 3.4 7.4 - - - +
122C VAL* 4.2 25.6 - - + -
126C ALA* 1.3 81.2 - - - +
128C TYR* 1.3 71.7 + - - +
129C HIS* 4.6 11.4 - - + +
140C LYS* 3.7 2.6 - - - +
141C MET* 2.8 28.8 + - + +
142C PHE* 3.0 50.8 + - + +
144C ARG* 4.6 6.5 - - + -
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Residues in contact with TYR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C MET* 4.6 18.9 - - + +
105C THR* 5.5 0.7 + - - -
106C ASP* 4.4 11.1 + - - -
120C ALA* 3.2 1.6 - - - +
121C LEU* 2.7 56.6 + - + +
123C THR* 3.5 35.3 + - + -
125C ASN* 6.1 0.2 - - - +
126C ALA* 4.0 17.9 - - + +
127C VAL* 1.3 73.6 - - - +
129C HIS* 1.3 73.2 + - - +
130C TRP 4.1 0.2 - - - -
138C PRO* 4.2 23.6 - - + -
139C VAL 3.3 7.0 - - - +
140C LYS* 3.4 41.4 - - + +
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Residues in contact with HIS 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ILE* 4.2 25.3 - - + +
118C THR* 4.7 17.2 - - + +
119C VAL 4.0 2.2 - - - -
120C ALA* 4.0 13.2 - - + +
127C VAL* 4.6 6.5 - - + +
128C TYR* 1.3 85.2 - - - +
130C TRP* 1.3 60.2 + - - +
131C SER 4.0 1.4 + - - -
137C GLN 4.4 0.2 - - - +
138C PRO* 3.8 0.8 - - - +
139C VAL* 2.8 38.1 + - - +
141C MET* 3.4 41.4 - - + +
142C PHE* 6.1 1.0 - - - -
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Residues in contact with TRP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 3.6 39.3 - - + -
89C GLN 4.2 2.5 - - - -
90C ILE* 3.9 30.7 - - + -
100C LYS* 3.3 16.4 - - + +
101C ALA* 3.7 32.8 - - - -
102C HIS* 3.7 20.4 - - + +
111C TRP* 5.1 4.5 - + - -
118C THR* 4.4 2.0 - - - -
119C VAL* 2.9 58.6 + - + +
121C LEU* 4.1 8.1 - - + -
128C TYR 4.1 0.2 - - - -
129C HIS* 1.3 72.9 - - - +
131C SER* 1.3 63.3 + - - +
132C MET 3.7 0.2 + - - -
136C SER 3.2 27.0 + - - -
137C GLN* 3.8 1.0 + - - +
138C PRO* 3.5 36.4 - - + +
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ILE* 4.3 1.4 - - - +
100C LYS* 3.2 26.7 - - - +
117C ASN 3.2 14.9 + - - -
118C THR* 4.3 8.0 - - - +
129C HIS 4.0 2.6 + - - -
130C TRP* 1.3 80.2 - - - +
132C MET* 1.3 62.8 + - - +
133C GLU* 3.4 19.0 + - - +
136C SER* 3.6 19.4 + - - -
137C GLN 5.4 0.8 + - - -
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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