Contacts of the strand formed by residues 148 - 151 (chain A) in PDB entry 3SDE
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 ARG 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.7 24.9 - - - +
86A VAL* 3.3 3.1 - - - -
87A GLY* 2.7 45.0 + - - +
88A ASN* 5.0 4.7 - - + -
138A ASP* 3.5 3.1 - - - -
146A PRO 3.7 1.3 + - - +
147A LEU* 1.4 71.0 - - - +
149A ILE* 1.3 60.9 + - - +
150A ARG* 3.8 30.5 - - + +
239A ASP* 5.5 1.4 + - - -
242A ASP* 2.6 42.8 + - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.0 24.5 - - + -
85A PHE 3.3 8.5 - - - +
86A VAL* 4.0 19.7 - - + -
102A PHE* 4.1 15.9 - - + -
133A ALA 4.7 1.1 - - - +
134A LYS* 3.5 33.6 - - + +
137A LEU* 3.5 44.6 - - + +
138A ASP* 2.9 18.1 + - + +
147A LEU* 4.6 10.3 - - + -
148A ARG* 1.3 77.6 - - - +
150A ARG* 1.3 83.7 + - - +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.5 7.5 - - - -
85A PHE* 2.7 40.0 + - + +
134A LYS* 4.1 4.9 - - - +
138A ASP* 3.1 29.1 + - - -
148A ARG* 3.8 36.5 - - + +
149A ILE* 1.3 100.8 + - - +
151A PHE* 1.3 68.5 + - - +
241A GLU* 3.7 35.1 + - - +
242A ASP* 2.6 41.7 + - - -
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLN 5.5 0.2 - - - -
81A ARG* 3.4 20.9 - - - -
83A ARG 3.6 8.5 - - - -
84A LEU* 3.8 8.7 - - + -
85A PHE* 4.7 0.7 - - - +
127A ARG* 3.3 36.8 - - - +
130A ALA* 3.5 20.9 - - + -
131A GLU* 3.6 47.3 - - - -
134A LYS* 3.7 25.2 - - + +
150A ARG* 1.3 79.0 - - - +
152A ALA* 1.3 68.0 + - - +
153A THR* 3.6 2.3 + - - -
241A GLU* 5.8 0.4 + - - -
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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