Contacts of the strand formed by residues 150 - 156 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125G VAL* 5.4 0.4 - - - -
126G VAL* 3.4 18.2 - - + +
128G ALA* 4.2 9.9 - - + -
139G LEU* 3.7 15.9 - - + -
140G ALA* 3.2 45.3 - - + +
143G LEU* 3.2 29.4 - - + -
148G ILE 3.5 2.6 + - - +
149G PRO* 1.3 75.4 - - - +
151G LEU* 1.3 63.1 + - - +
152G ILE* 3.9 20.2 - - + -
163G ARG 4.2 0.4 - - - +
164G ILE* 3.6 4.0 - - - +
165G ILE* 2.7 50.9 + - + +
508G ILE* 6.1 0.7 - - - -
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G VAL* 5.0 5.4 - - + -
126G VAL 2.9 13.0 + - - +
127G VAL* 3.4 14.2 - - + +
128G ALA 2.9 26.7 + - - +
150G LEU* 1.3 74.8 - - - +
152G ILE* 1.3 60.0 + - - +
153G CYS* 3.6 19.4 + - - -
162G MET* 4.1 14.1 - - + -
163G ARG 3.5 18.4 - - - +
164G ILE* 3.8 23.1 - - + -
501G ALA* 3.9 16.8 - - + +
504G GLU* 4.4 7.4 - - + -
505G VAL* 3.7 27.8 - - + +
508G ILE* 5.5 4.3 - - + -
516G PHE* 4.3 5.2 - - + -
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Residues in contact with ILE 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ALA* 3.3 15.3 - - + +
131G LEU* 5.2 7.4 - - + +
136G SER* 4.0 29.2 - - - +
139G LEU* 5.9 0.2 - - + -
140G ALA* 4.5 0.9 - - + -
150G LEU* 3.9 30.7 - - + -
151G LEU* 1.3 71.9 - - - +
153G CYS* 1.3 67.4 + - - +
154G ARG* 5.4 2.2 - - + -
161G TYR* 4.5 17.7 - - + +
162G MET* 3.3 2.9 - - - +
163G ARG* 2.8 48.7 + - + +
165G ILE* 4.4 6.1 - - + -
398G LEU* 4.0 24.2 - - + -
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Residues in contact with CYS 153 (chain G).
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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41G THR* 4.4 7.6 - - + -
45G ILE* 3.8 21.3 - - + -
127G VAL* 4.6 1.3 - - - -
128G ALA 2.7 9.7 + - - +
129G THR* 3.2 9.0 - - + -
130G GLN 3.1 21.7 + - - -
151G LEU* 3.8 16.6 - - - -
152G ILE* 1.3 79.3 - - - +
154G ARG* 1.3 63.6 + - - +
161G TYR 3.5 6.3 - - - +
162G MET* 3.7 16.2 - - - -
497G LEU* 4.6 3.1 - - + -
501G ALA* 3.7 30.5 - - - -
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Residues in contact with ARG 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G THR* 5.2 0.4 - - - -
130G GLN* 3.1 20.9 - - - +
131G LEU 4.3 18.0 + - - +
152G ILE* 5.4 3.4 - - + -
153G CYS* 1.3 77.9 - - - +
155G THR* 1.3 66.0 + - - +
156G TYR* 4.1 22.3 + - + +
159G VAL 3.8 1.0 - - - +
160G GLY* 3.7 0.2 - - - -
161G TYR* 2.7 64.7 + - + +
429G LEU* 4.3 26.8 + - - +
432G VAL* 4.7 4.0 - - - +
433G ASP* 2.7 43.2 + - - -
442G TYR* 3.6 25.7 + - - -
497G LEU* 3.1 8.6 - - - +
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Residues in contact with THR 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G THR* 2.7 25.7 + - - -
130G GLN* 2.5 30.8 + - - +
154G ARG* 1.3 72.6 - - - +
156G TYR* 1.3 67.9 + - - +
157G GLY 4.3 0.2 - - - +
159G VAL 3.7 3.1 - - - -
487G ALA 5.3 1.0 - - - +
488G ALA 4.4 3.3 - - - +
489G GLU* 3.9 29.2 - - + +
490G PRO* 4.1 3.4 - - + -
493G ILE* 3.4 28.4 - - + +
494G ALA* 3.4 14.8 + - - +
497G LEU* 3.5 12.7 - - - +
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Residues in contact with TYR 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ARG* 4.1 21.3 - - + +
155G THR* 1.3 77.1 - - - +
157G GLY* 1.3 58.1 + - - +
158G LEU 3.0 0.3 + - - -
159G VAL* 2.7 43.9 + - + +
429G LEU* 4.0 19.1 - - + -
432G VAL* 3.3 25.4 - - + +
442G TYR* 3.5 20.3 - + - +
443G PRO* 3.4 18.0 + - - +
482G PHE* 3.7 47.6 + + - -
485G TYR* 4.0 6.3 - + + -
487G ALA* 3.3 36.2 + - + -
488G ALA 3.9 2.0 - - - -
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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