Contacts of the strand formed by residues 130 - 134 (chain C) in PDB entry 1T9G
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 MET 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C TYR* 3.4 27.8 - - + +
53C ILE* 3.8 20.6 - - + -
62C MET* 3.7 20.4 - - + -
97C ALA 3.4 27.8 - - - +
101C ASN* 3.3 11.2 - - - +
124C MET* 3.7 2.5 - - - +
128C PRO 4.4 6.1 - - - +
129C LEU* 1.3 86.2 - - - +
131C CYS* 1.3 61.0 + - - +
169C ASN* 3.7 8.1 - - - +
172C LYS* 3.2 32.4 + - + +
173C ALA* 3.8 1.6 - - - -
174C ASN* 2.7 35.9 + - - +
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Residues in contact with CYS 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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100C GLY 4.0 4.5 - - - +
101C ASN* 3.1 36.4 + - - +
104C GLY* 4.0 2.9 - - - -
105C GLN* 3.8 31.4 - - - -
124C MET* 3.7 4.2 - - + +
130C MET* 1.3 75.0 - - - +
132C ALA* 1.3 61.7 + - - +
169C ASN* 3.6 20.8 + - - +
173C ALA* 3.8 4.0 - - - -
175C TRP* 3.4 41.7 - - + +
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Residues in contact with ALA 132 (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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100C GLY* 4.8 2.7 - - - -
104C GLY* 3.7 10.9 - - - -
131C CYS* 1.3 77.2 - - - +
133C TYR* 1.3 59.7 + - - +
134C CYS 3.9 0.2 - - - -
167C ILE* 4.0 11.2 - - + -
168C THR 3.6 22.0 - - - +
169C ASN 4.5 1.8 - - - +
173C ALA* 4.0 6.3 - - + -
175C TRP* 3.1 4.7 + - - -
176C TYR* 3.5 26.1 - - + -
177C PHE 2.9 26.2 + - - -
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Residues in contact with TYR 133 (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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100C GLY 4.9 1.2 + - - -
103C LEU* 3.4 45.3 - - + -
104C GLY* 4.0 11.4 - - - +
107C PRO* 4.2 9.4 - - + -
132C ALA* 1.3 72.5 - - - +
134C CYS* 1.3 58.8 + - - +
135C VAL* 3.3 25.8 + - + +
167C ILE* 3.4 9.3 - - - +
168C THR 5.0 1.4 + - - -
177C PHE* 3.8 26.2 - + - -
248C ALA* 3.5 21.4 + - + +
251C ALA* 4.9 4.3 - - + -
252C PHE* 3.1 37.0 - + - -
399C FAD 3.0 42.3 + + - +
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Residues in contact with CYS 134 (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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132C ALA 3.8 0.4 + - - -
133C TYR* 1.3 71.8 - - - +
135C VAL* 1.3 60.0 + - - +
164C LYS* 3.3 20.5 - - + -
167C ILE* 3.7 30.1 - - - -
176C TYR* 3.8 27.4 - - + -
177C PHE 2.7 22.3 + - - +
178C LEU* 3.7 14.9 - - + -
179C LEU 3.5 13.9 + - - -
225C ILE* 4.0 15.7 - - - -
227C PHE* 4.5 5.8 - - - -
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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