Contacts of the strand formed by residues 148 - 153 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ASP* 3.4 13.7 - - - -
136D MET* 4.0 11.0 - - - -
146D GLN* 3.7 9.7 - - - +
147D ARG* 1.3 80.2 - - - +
149D VAL* 1.3 67.7 + - - +
190D GLY 3.4 4.8 + - - +
191D ILE* 3.4 11.3 - - - +
192D ARG 3.3 19.9 + - - -
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ASP 3.3 9.3 + - - +
87D VAL* 3.4 14.3 - - + +
88D ALA 3.1 24.1 + - - +
136D MET* 3.7 2.6 - - - +
146D GLN* 3.6 13.0 - - - +
148D GLY* 1.3 79.4 - - - +
150D ILE* 1.3 69.2 + - - +
151D ILE* 4.2 23.1 - - + -
192D ARG* 3.2 52.7 - - + +
194D VAL* 5.4 1.3 - - + -
240D VAL* 4.6 5.4 - - + +
241D ILE* 4.5 13.0 - - + +
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA* 3.5 10.3 - - + +
90D ASN* 4.3 4.7 - - - +
129D ILE* 4.0 29.6 - - + +
132D VAL* 3.9 22.4 - - + -
133D ALA* 5.0 2.0 - - + -
136D MET* 3.9 16.2 - - + -
149D VAL* 1.3 80.0 - - - +
151D ILE* 1.3 63.2 + - - +
152D ASN* 3.8 20.9 - - - +
186D LEU* 4.3 15.0 - - + -
191D ILE* 3.8 20.2 - - + -
192D ARG 2.9 12.7 + - - +
193D VAL* 3.4 11.0 - - + +
194D VAL 3.0 25.5 + - - +
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D VAL* 4.9 2.2 - - + -
88D ALA 2.9 11.1 + - - +
89D VAL* 3.3 15.5 - - + +
90D ASN* 2.9 25.8 + - - -
149D VAL* 4.2 7.9 - - + -
150D ILE* 1.3 77.0 - - - +
152D ASN* 1.3 71.9 + - - +
194D VAL* 3.2 8.3 - - + +
196D ILE* 4.1 24.0 - - + -
233D TYR* 4.7 1.8 - - - +
237D VAL* 3.9 33.7 - - + +
240D VAL* 3.8 31.6 - - + -
241D ILE* 3.9 18.6 - - + -
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Residues in contact with ASN 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ASN* 3.0 30.7 + - - -
125D THR* 3.7 8.6 - - + +
129D ILE* 3.5 20.1 - - - +
150D ILE* 3.8 4.0 - - - +
151D ILE* 1.3 78.4 - - - +
153D THR* 1.3 64.0 + - - +
154D ALA 4.1 0.2 - - - -
175D ILE* 3.9 16.6 + - + +
178D MET* 5.7 1.8 - - - +
179D THR* 4.4 4.2 + - - +
193D VAL* 3.8 25.3 - - - +
194D VAL 3.0 7.7 + - - -
195D THR* 3.2 23.6 + - - +
196D ILE* 2.8 27.2 + - - +
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Residues in contact with THR 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.7 0.2 - - + -
90D ASN* 2.9 26.3 + - - +
91D CYS* 3.8 5.4 - - - -
125D THR* 5.9 0.4 + - - +
152D ASN* 1.3 74.0 - - - +
154D ALA* 1.3 67.8 + - - +
172D LYS* 3.1 17.3 + - - -
175D ILE* 3.8 12.6 - - - +
196D ILE* 3.5 3.1 - - - +
198D PRO* 3.8 22.0 - - + -
233D TYR* 2.7 29.6 + - + -
301D NAD 3.5 32.9 + - - +
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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