Contacts of the strand formed by residues 148 - 153 (chain C) in PDB entry 1E3S
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 GLY 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ASP* 3.4 13.7 - - - -
136C MET* 4.0 12.3 - - - -
146C GLN* 3.7 10.0 - - - +
147C ARG* 1.3 80.0 - - - +
149C VAL* 1.3 66.9 + - - +
190C GLY 3.4 4.5 + - - +
191C ILE* 3.4 10.7 - - - +
192C ARG 3.2 19.1 + - - -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP 3.3 9.7 + - - +
87C VAL* 3.4 17.5 - - + +
88C ALA 3.1 23.9 + - - +
136C MET* 3.7 3.0 - - - +
146C GLN* 3.7 14.1 - - - +
148C GLY* 1.3 77.0 - - - +
150C ILE* 1.3 66.6 + - - +
151C ILE* 4.2 21.5 - - + -
192C ARG* 3.4 52.5 - - + +
194C VAL* 5.5 1.1 - - + -
240C VAL* 4.6 7.0 - - + +
241C ILE* 4.4 11.0 - - + +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 3.5 11.9 - - + +
90C ASN* 4.3 6.3 - - - +
129C ILE* 4.0 33.7 - - + +
132C VAL* 3.9 19.5 - - + -
133C ALA* 5.0 2.7 - - - -
136C MET* 3.9 17.3 - - + -
149C VAL* 1.3 79.5 - - - +
151C ILE* 1.3 64.5 + - - +
152C ASN* 3.8 21.1 - - - +
186C LEU* 4.3 10.3 - - + -
191C ILE* 3.8 19.5 - - + -
192C ARG 3.0 11.1 + - - +
193C VAL* 3.4 10.9 - - + +
194C VAL 3.0 24.8 + - - +
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Residues in contact with ILE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C VAL* 4.9 2.9 - - + -
88C ALA 3.0 9.3 + - - +
89C VAL* 3.4 16.1 - - + +
90C ASN* 2.8 26.0 + - - -
149C VAL* 4.2 7.4 - - + -
150C ILE* 1.3 76.6 - - - +
152C ASN* 1.3 70.4 + - - +
194C VAL* 3.2 8.3 - - + +
196C ILE* 4.0 27.8 - - + -
233C TYR* 4.6 1.6 - - - +
237C VAL* 3.8 34.1 - - + +
240C VAL* 3.8 32.3 - - + -
241C ILE* 3.9 18.2 - - + -
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Residues in contact with ASN 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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90C ASN* 3.0 31.8 + - - -
125C THR* 3.8 8.5 - - + +
129C ILE* 3.4 19.5 - - - +
150C ILE* 3.8 4.4 - - - +
151C ILE* 1.3 80.8 - - - +
153C THR* 1.3 61.7 + - - +
154C ALA 4.1 0.2 - - - -
175C ILE* 3.9 16.6 - - + +
178C MET* 5.8 1.8 - - - +
179C THR* 4.4 3.6 + - - +
193C VAL* 3.8 25.1 - - - +
194C VAL 2.9 6.9 + - - -
195C THR* 3.3 23.3 + - - +
196C ILE* 2.9 26.5 + - - +
233C TYR* 4.7 0.2 + - - -
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Residues in contact with THR 153 (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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22C LEU* 4.7 0.2 - - + -
90C ASN* 2.8 24.9 + - - +
91C CYS* 3.8 4.9 - - - -
125C THR* 5.7 0.6 + - - +
152C ASN* 1.3 71.5 - - - +
154C ALA* 1.3 64.4 + - - +
172C LYS* 3.0 18.4 + - - -
175C ILE* 3.8 12.9 - - - +
196C ILE* 3.5 2.9 - - - +
198C PRO* 3.8 20.2 - - + -
233C TYR* 2.8 30.7 + - + -
301C NAD 3.5 39.8 + - - +
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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
------------------------------------------------------------
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