Contacts of the strand formed by residues 153 - 159 (chain C) in PDB entry 2P4K
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 ILE 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C GLY* 3.1 3.6 - - - -
128C PHE* 2.8 35.4 + - + +
130C LYS* 3.3 48.7 - - + +
146C LEU* 4.0 0.9 - - - -
147C GLN* 3.5 31.0 - - + +
151C GLY 4.0 1.1 - - - +
152C LEU* 1.3 73.7 - - - +
154C PRO* 1.3 77.0 - - + +
155C LEU* 3.9 1.8 - - + +
192C ARG* 5.3 1.3 - - + +
196C CYS* 3.7 28.5 - - - -
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Residues in contact with PRO 154 (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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72C ILE* 5.9 0.9 - - + -
76C ILE* 3.6 25.4 - - + -
125C TRP* 3.5 29.8 - - + -
126C LEU 4.1 0.4 - - - +
146C LEU* 3.6 17.7 - - + -
147C GLN* 4.0 18.8 - - + +
152C LEU 3.6 8.0 - - - +
153C ILE* 1.3 94.2 - - + +
155C LEU* 1.3 67.6 + - - +
192C ARG* 3.8 19.2 + - - +
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Residues in contact with LEU 155 (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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76C ILE* 5.3 0.4 - - - -
80C ASN* 3.2 19.4 + - - -
93C LEU* 5.1 2.0 - - + -
125C TRP* 5.1 0.9 - - - -
126C LEU* 2.9 22.9 + - + +
127C GLY 4.0 9.2 - - - +
128C PHE* 4.2 2.2 - - + +
135C LEU* 3.4 33.2 - - + -
153C ILE* 3.9 9.6 - - + +
154C PRO* 1.3 85.5 - - - +
156C LEU* 1.3 64.7 + - - +
189C VAL* 3.7 21.9 - - + +
192C ARG* 3.4 21.6 - - + +
193C TYR* 3.6 41.7 - - + +
196C CYS* 4.2 10.8 - - - -
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Residues in contact with LEU 156 (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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80C ASN* 3.4 24.0 - - + +
107C PHE* 4.5 2.7 - - + -
111C LEU* 3.9 21.7 - - + +
124C GLY 4.0 0.2 - - - +
125C TRP* 3.3 7.9 - - - -
126C LEU* 2.8 40.6 + - + -
155C LEU* 1.3 80.0 - - - +
157C GLY* 1.3 69.5 + - - +
158C ILE* 4.0 9.4 - - + -
181C TRP* 4.3 9.9 - - + -
184C ILE* 4.0 32.1 - - + -
186C TRP* 4.0 26.2 - - + -
189C VAL* 4.1 10.5 - - + -
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Residues in contact with GLY 157 (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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77C PHE* 3.3 22.9 - - - -
80C ASN* 2.9 11.7 + - - +
81C LEU* 5.7 0.2 - - - +
123C TRP* 4.3 2.0 - - - -
124C GLY 3.4 4.0 - - - -
125C TRP* 3.3 29.4 - - - -
156C LEU* 1.3 77.2 - - - +
158C ILE* 1.3 72.5 + - - +
159C ASP 4.1 0.4 - - - -
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Residues in contact with ILE 158 (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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77C PHE* 4.1 2.0 - - - -
111C LEU* 4.0 21.1 - - + -
115C SER* 3.9 14.1 - - - +
123C TRP* 3.4 6.2 - - - -
124C GLY 2.8 32.5 + - - +
156C LEU* 4.0 22.2 - - + -
157C GLY* 1.3 85.0 - - - +
159C ASP* 1.3 67.3 + - - +
160C VAL* 3.4 11.1 + - + +
176C TYR* 4.4 2.5 - - + +
177C LEU* 3.5 29.8 - - + -
180C ILE* 4.3 24.5 - - + -
181C TRP* 5.7 5.4 - - + -
184C ILE* 4.4 13.9 - - + -
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Residues in contact with ASP 159 (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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26C HIS* 2.9 10.9 + - - -
74C HIS* 3.5 1.2 + - - -
77C PHE* 3.7 19.5 - - + -
123C TRP* 3.5 32.9 - - + -
158C ILE* 1.3 72.0 - - - +
160C VAL* 1.3 58.7 + - - +
161C TRP* 3.1 31.9 + - - +
164C ALA* 3.5 11.5 - - + +
176C TYR* 2.8 31.4 + - - -
199C MN 2.0 34.7 + - - -
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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