Contacts of the helix formed by residues 474 - 483 (chain B) in PDB entry 5IYB
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 THR 474 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B ARG 2.8 2.8 + - - -
473B LEU* 1.3 73.7 - - - +
475B PHE* 1.3 70.2 + - - +
476B ALA* 3.9 7.4 + - + +
477B SER* 2.8 38.3 + - - +
478B THR* 3.4 6.1 + - - -
729B GLY 3.8 10.5 - - - +
730B LYS 3.5 12.6 - - - +
732B ALA 3.1 27.4 + - - +
734B GLY* 4.3 10.8 + - - +
736B TYR* 3.6 11.2 - - - +
769B PHE* 5.9 0.2 - - - -
773B PRO 4.6 3.6 + - - -
774B ALA* 4.3 14.7 - - - +
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Residues in contact with PHE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.8 1.1 - - + -
179B LEU* 3.3 28.0 - - + -
180B ASP* 4.6 1.1 - - - -
181B PRO* 3.4 27.8 - - + -
472B ARG* 5.7 0.2 - - - -
474B THR* 1.3 73.4 + - - +
476B ALA* 1.3 62.8 + - - +
478B THR* 3.6 7.2 + - - -
479B LEU* 3.3 48.6 + - + +
735B VAL 4.6 0.8 + - - -
736B TYR* 3.4 31.0 - - - +
737B ILE* 4.9 4.0 - - + -
767B LEU* 3.5 23.1 - - + -
768B ARG* 4.6 12.3 - - + -
769B PHE* 5.9 2.7 - + - -
772B LEU* 4.2 32.3 - - + +
773B PRO 5.9 0.6 + - - -
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B THR* 3.2 12.4 + - + +
475B PHE* 1.3 79.9 - - - +
477B SER* 1.3 56.3 + - - +
479B LEU* 3.4 7.2 + - - +
480B SER* 2.8 32.0 + - - -
706B VAL* 4.4 7.8 - - + +
707B CYS* 5.2 6.7 - - - -
710B ILE* 3.5 31.9 - - + -
729B GLY 5.0 6.7 - - - +
769B PHE* 4.7 10.6 - - + -
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Residues in contact with SER 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASN* 3.2 36.0 + - - +
473B LEU 4.0 0.9 - - - -
474B THR* 2.8 35.6 + - - +
476B ALA* 1.3 75.5 - - - +
478B THR* 1.3 64.3 + - - -
480B SER* 3.4 6.4 + - - -
481B HIS* 3.0 23.0 + - - +
484B ARG* 5.1 1.0 + - - -
730B LYS* 3.9 23.1 + - - +
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Residues in contact with THR 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 4.7 0.2 - - - +
181B PRO* 4.5 9.2 - - + -
470B LEU* 3.4 30.7 - - + -
471B ASN 3.2 11.0 + - - +
472B ARG* 3.4 42.4 + - - +
474B THR 3.4 7.7 + - - -
475B PHE* 3.9 12.2 + - - -
476B ALA 3.4 0.2 - - - -
477B SER* 1.3 76.4 - - - +
479B LEU* 1.3 64.1 + - - +
481B HIS* 3.3 2.9 + - - +
482B LEU* 3.1 32.7 + - + +
736B TYR 4.9 2.3 + - - -
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 3.7 30.7 - - + -
40B VAL* 3.9 23.7 - - + +
181B PRO* 4.2 19.5 - - + +
475B PHE* 3.3 40.8 + - + +
476B ALA* 3.6 5.8 - - - +
478B THR* 1.3 81.3 - - - +
480B SER* 1.3 60.7 + - - +
482B LEU* 3.8 5.3 + - - +
483B ARG* 3.5 20.0 + - - +
706B VAL* 4.2 15.7 - - + +
767B LEU* 3.9 19.5 - - + +
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Residues in contact with SER 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B ALA 2.8 21.9 + - - -
477B SER 3.6 4.5 - - - -
479B LEU* 1.3 72.7 - - - +
481B HIS* 1.3 65.3 + - - +
483B ARG* 3.1 15.9 + - - +
484B ARG* 3.1 14.7 + - - -
513B GLU* 3.3 11.0 + - - -
525B ASN* 3.8 4.2 + - - +
706B VAL* 4.7 9.3 - - - +
707B CYS* 4.2 8.1 - - - -
730B LYS* 3.0 37.5 + - - -
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Residues in contact with HIS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 3.7 26.8 - - + +
194B LEU 4.8 1.7 - - - +
195B ILE* 3.3 20.4 - - + +
468B GLN* 2.4 32.6 + - + -
469B VAL 3.8 13.5 - - - -
470B LEU* 3.6 14.4 - - + -
471B ASN* 3.4 27.2 + - + +
477B SER 3.0 16.5 + - - +
478B THR 3.3 0.4 + - - -
480B SER* 1.3 76.6 - - - +
482B LEU* 1.3 62.3 + - - +
484B ARG* 3.3 35.9 + - - +
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 4.2 17.7 - - + +
42B GLN* 5.4 2.4 - - - +
43B GLN* 3.6 29.8 + - + +
181B PRO* 3.5 35.4 - - + -
182B GLY 3.3 23.6 - - - +
183B GLY* 4.0 18.6 - - - +
184B TYR* 4.3 7.4 - - + -
193B VAL* 4.0 18.2 - - + -
470B LEU* 4.4 7.9 - - + -
478B THR* 3.1 24.1 + - + +
479B LEU* 4.0 7.2 - - - +
480B SER 3.2 0.2 - - - -
481B HIS* 1.3 75.9 - - - +
483B ARG* 1.3 56.9 + - - +
484B ARG 3.8 1.7 + - - +
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 5.0 0.2 - - - -
39B LEU* 3.3 33.0 + - - +
40B VAL* 4.9 5.8 - - + +
42B GLN* 4.0 17.7 - - - +
479B LEU 3.5 11.8 + - - +
480B SER* 3.1 10.5 + - - +
482B LEU* 1.3 79.0 - - - +
484B ARG* 1.3 61.8 + - - -
525B ASN* 3.7 7.9 - - + +
526B LEU* 3.0 70.2 + - + +
527B ALA 2.8 26.5 + - - -
528B LEU* 2.9 28.3 + - - +
530B ALA* 4.5 2.2 - - - +
706B VAL* 3.9 28.1 - - - +
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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