Contacts of the strand formed by residues 150 - 156 (chain C) in PDB entry 1R4N
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 LEU 150 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL* 5.4 0.7 - - - -
126C VAL* 3.4 18.8 - - + +
128C ALA* 4.2 9.6 - - + -
139C LEU* 3.7 14.6 - - + -
140C ALA* 3.2 44.6 - - + +
143C LEU* 3.2 29.8 - - + -
148C ILE 3.4 2.6 + - - +
149C PRO* 1.3 75.2 - - - +
151C LEU* 1.3 63.5 + - - +
152C ILE* 3.8 21.3 - - + -
163C ARG 4.2 0.4 - - - +
164C ILE* 3.7 4.3 - - - +
165C ILE* 2.8 48.0 + - + +
166C ILE* 5.2 0.2 - - - +
508C ILE* 6.1 0.7 - - - -
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Residues in contact with LEU 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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125C VAL* 5.0 5.6 - - + -
126C VAL 2.9 13.0 + - - +
127C VAL* 3.4 13.1 - - + +
128C ALA 2.9 25.8 + - - +
150C LEU* 1.3 74.2 - - - +
152C ILE* 1.3 59.4 - - - +
153C CYS* 3.5 18.5 + - - -
162C MET* 4.1 15.3 - - + -
163C ARG 3.5 18.4 - - - +
164C ILE* 3.7 23.6 - - + -
501C ALA* 3.9 17.9 - - + +
504C GLU* 4.4 7.9 - - + -
505C VAL* 3.7 26.7 - - + +
508C ILE* 5.5 4.0 - - + -
516C PHE* 4.2 4.3 - - + -
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Residues in contact with ILE 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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128C ALA* 3.3 16.6 - - + +
131C LEU* 5.2 7.4 - - + +
136C SER* 4.1 26.0 - - - +
140C ALA* 4.5 0.9 - - + -
150C LEU* 3.8 33.2 - - + -
151C LEU* 1.3 70.1 - - - +
153C CYS* 1.3 67.5 + - - +
154C ARG* 5.4 2.5 - - + -
161C TYR* 4.1 17.5 - - + +
162C MET* 3.3 2.3 - - - +
163C ARG* 2.8 48.2 + - + +
165C ILE* 4.4 5.8 - - + -
398C LEU* 4.0 26.5 - - + -
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Residues in contact with CYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C THR* 4.3 7.0 - - + -
45C ILE* 3.8 21.5 - - + -
127C VAL* 4.6 2.2 - - - -
128C ALA 2.7 9.1 + - - +
129C THR* 3.2 8.9 - - + -
130C GLN 3.1 21.8 + - - -
151C LEU* 3.8 16.2 - - - -
152C ILE* 1.3 79.4 - - - +
154C ARG* 1.3 64.3 + - - +
161C TYR 3.5 6.3 - - - +
162C MET* 3.8 16.8 - - - +
497C LEU* 4.6 3.8 - - + -
501C ALA* 3.7 30.3 - - - -
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Residues in contact with ARG 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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41C THR* 5.2 0.7 - - - -
130C GLN* 3.1 20.0 - - - +
131C LEU 4.2 17.7 + - - +
152C ILE* 5.4 3.1 - - + -
153C CYS* 1.3 79.4 - - - +
155C THR* 1.3 66.3 + - - +
156C TYR* 4.1 22.3 + - + +
159C VAL 3.8 0.7 - - - +
160C GLY* 3.8 0.2 - - - -
161C TYR* 2.7 65.3 + - + +
429C LEU* 4.3 27.1 + - - +
432C VAL* 4.7 3.8 - - - +
433C ASP* 2.7 43.3 + - - -
442C TYR* 3.6 25.7 + - - -
497C LEU* 3.1 7.5 - - - +
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Residues in contact with THR 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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41C THR* 2.7 25.9 + - - -
130C GLN* 2.4 33.2 + - - +
154C ARG* 1.3 72.7 - - - +
156C TYR* 1.3 67.8 + - - +
159C VAL 3.8 3.4 - - - -
487C ALA 5.4 1.0 - - - +
488C ALA 4.4 3.3 - - - +
489C GLU* 3.9 29.8 - - + +
490C PRO* 4.1 4.3 - - + +
493C ILE* 3.4 27.9 - - + +
494C ALA* 3.5 14.7 + - - +
497C LEU* 3.5 12.5 - - - +
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Residues in contact with TYR 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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130C GLN* 6.1 0.2 - - - -
154C ARG* 4.1 21.5 - - + +
155C THR* 1.3 76.7 - - - +
157C GLY* 1.3 58.4 + - - +
158C LEU 3.0 0.3 + - - -
159C VAL* 2.7 42.8 + - + +
429C LEU* 4.0 19.3 - - + -
432C VAL* 3.3 25.2 - - + +
442C TYR* 3.5 20.0 - + - +
443C PRO* 3.4 16.3 - - - +
482C PHE* 3.7 48.7 + + - -
485C TYR* 4.0 6.4 - + + -
487C ALA* 3.3 38.0 + - + -
488C ALA 4.0 1.6 - - - -
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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