Contacts of the strand formed by residues 147 - 153 (chain C) in PDB entry 3I5D
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 VAL 147 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.6 4.0 - - + +
75A ALA 6.4 0.2 - - - -
76A LEU* 4.8 12.3 - - + -
86A ILE* 3.4 10.2 - - + +
138C GLY* 5.5 2.7 - - - -
141C ASP* 3.0 14.6 - - + -
146C GLY* 1.3 71.7 - - - -
148C ARG* 1.3 63.0 + - - +
164C VAL* 3.7 1.1 - - - -
165C LEU* 2.6 62.5 + - + +
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Residues in contact with ARG 148 (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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401A NAG 6.0 1.9 - - - +
135C CYS* 5.8 0.2 - - + -
136C LYS 3.8 8.3 - - - +
137C ARG* 3.3 1.6 - - - +
138C GLY* 2.8 27.5 + - - -
140C ASN* 3.6 20.4 - - + -
141C ASP* 2.9 28.6 - - - +
146C GLY 3.7 0.4 + - - -
147C VAL* 1.3 71.4 - - - +
149C THR* 1.3 63.9 + - - +
162C CYS* 4.9 5.6 - - + -
163C GLU 3.3 13.2 - - - +
164C VAL* 3.6 8.1 - - + -
165C LEU* 5.7 0.4 - - - -
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Residues in contact with THR 149 (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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401A NAG 6.2 4.5 - - - -
118C LYS* 4.9 3.6 - - + -
135C CYS* 4.1 5.4 - - - +
136C LYS 4.9 0.2 - - - -
137C ARG* 4.2 4.5 - - - -
147C VAL 3.5 2.4 + - - -
148C ARG* 1.3 76.6 - - - +
150C GLY* 1.3 66.6 + - - +
151C ARG* 2.8 20.2 + - - +
163C GLU* 2.9 52.0 + - + +
164C VAL* 4.4 2.7 - - - +
165C LEU* 4.8 14.8 - - + +
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Residues in contact with GLY 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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132C HIS* 3.6 12.1 - - - +
135C CYS* 2.9 38.5 - - - +
137C ARG* 3.6 22.6 - - - +
149C THR* 1.3 74.5 + - - +
151C ARG* 1.3 56.8 + - - +
152C CYS 3.6 0.3 + - - -
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Residues in contact with ARG 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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132C HIS* 4.6 10.8 - - + -
135C CYS* 3.3 3.6 - - - -
149C THR* 2.8 18.5 + - - +
150C GLY* 1.3 77.7 - - - +
152C CYS* 1.3 60.2 + - - +
153C VAL* 4.2 3.6 - - + -
163C GLU* 3.1 43.5 + - + +
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Residues in contact with CYS 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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129C CYS* 2.0 46.0 - - - -
130C THR 4.6 1.3 - - - -
131C SER* 3.6 35.9 - - - +
132C HIS* 3.8 20.2 + - + +
135C CYS* 3.7 8.1 - - - -
150C GLY 3.6 1.0 + - - -
151C ARG* 1.3 73.7 - - - +
153C VAL* 1.3 71.2 + - - +
160C LYS* 4.5 6.3 - - - -
161C THR 4.4 0.2 - - - -
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Residues in contact with VAL 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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119C CYS* 4.6 0.7 - - - -
120C ALA* 4.0 21.3 - - + +
151C ARG* 5.1 2.9 - - + -
152C CYS* 1.3 81.4 - - - +
154C SER* 1.3 57.1 + - - +
160C LYS* 3.5 6.1 - - - +
161C THR 2.5 47.9 + - - +
163C GLU* 3.5 42.8 - - + +
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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