Contacts of the strand formed by residues 147 - 152 (chain C) in PDB entry 3SDL
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 THR 147 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 3.5 21.5 - - + +
87C ARG* 4.4 22.8 + - + +
93C SER* 5.2 2.5 + - - +
125C THR 4.4 0.2 - - - +
126C PHE* 3.7 17.8 - - - -
127C GLU 5.1 0.5 + - - -
145C LEU 3.8 2.1 + - - -
146C SER* 1.3 75.6 + - - +
148C VAL* 1.3 68.5 + - - +
149C PHE* 3.7 39.0 - - + -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE* 4.5 13.5 - - + -
85C LEU 2.8 13.4 + - - +
86C VAL* 3.1 10.9 - - + +
87C ARG 2.9 25.5 + - - -
107C LEU* 5.0 1.3 - - + -
124C LEU* 3.5 37.7 - - + -
125C THR 3.3 14.4 - - - +
126C PHE* 4.2 8.1 - - + -
131C LEU* 4.0 12.3 - - + -
142C LEU* 3.7 31.4 - - + -
146C SER 5.2 0.7 - - - +
147C THR* 1.3 75.0 - - - +
149C PHE* 1.3 63.3 + - - +
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Residues in contact with PHE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 3.5 48.9 - - + +
123C TRP 3.8 0.2 - - - +
124C LEU* 3.2 8.6 - - - -
125C THR* 2.8 53.3 + - - +
126C PHE* 5.5 1.3 - - - -
127C GLU 5.6 4.3 - - - -
128C GLY 6.3 0.2 - - - -
147C THR* 3.7 32.3 - - + -
148C VAL* 1.3 75.5 - - - +
150C MET* 1.3 64.0 + - - +
151C ASN* 3.9 5.3 - - - +
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Residues in contact with MET 150 (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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86C VAL* 4.6 3.6 - - + -
87C ARG 2.9 22.3 + - - +
88C ASN* 3.8 21.3 - - - -
89C ASN* 4.4 17.6 - - + +
111C VAL* 3.6 31.4 - - + -
115C GLU* 3.9 24.9 - - + +
117C VAL* 4.3 11.4 - - + -
122C PHE* 3.6 44.6 - - + -
123C TRP 3.8 2.2 - - - -
124C LEU* 4.3 5.4 - - + -
148C VAL 4.1 0.2 + - - -
149C PHE* 1.3 74.1 - - - +
151C ASN* 1.3 70.0 + - - +
152C LEU* 4.3 2.7 - - + -
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Residues in contact with ASN 151 (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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89C ASN* 5.7 0.7 - - - -
122C PHE* 3.0 9.6 - - - +
123C TRP* 2.8 72.3 + - + +
125C THR* 3.0 39.8 + - - +
149C PHE* 3.9 6.1 - - - +
150C MET* 1.3 82.2 + - - +
152C LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 152 (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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89C ASN* 3.8 36.8 + - + +
117C VAL* 4.7 19.1 - - + -
121C LEU* 3.7 15.0 - - + +
122C PHE* 4.7 4.7 - - + -
123C TRP* 3.6 10.8 - - - -
150C MET* 6.0 2.9 - - + -
151C ASN* 1.3 71.4 - - - +
153C ARG* 1.3 72.9 + - - +
154C LEU* 5.1 3.8 - - + +
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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