Contacts of the helix formed by residues 471 - 478 (chain B) in PDB entry 1GPU
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 SER 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B HIS 3.4 2.4 + - - -
470B ASP* 1.3 90.8 + - - +
472B ILE* 1.3 61.2 + - - +
473B GLY* 2.8 19.8 + - - +
474B VAL* 2.9 25.2 + - - +
482B GLN* 3.8 9.7 - - - +
483B PRO* 4.2 10.8 - - - -
500B ARG* 4.3 5.1 + - - -
529B GLN* 4.5 2.6 + - - -
617B VAL* 3.6 35.3 - - - +
618B LEU* 4.5 2.2 - - - -
646B PHE* 4.2 4.3 - - - -
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Residues in contact with ILE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B SER* 1.3 73.8 - - - +
473B GLY* 1.3 58.6 + - - +
474B VAL 2.8 5.8 - - - -
475B GLY* 2.8 22.6 + - - -
482B GLN* 3.5 30.6 + - + +
483B PRO 4.9 1.4 + - - +
484B ILE* 5.1 7.2 - - + -
617B VAL* 4.3 10.8 - - + +
633B ILE* 3.7 27.6 - - + -
637B GLY* 4.2 7.0 - - - -
642B ALA* 4.5 1.6 - - - -
645B VAL* 3.7 26.4 - - + +
646B PHE* 3.6 38.1 - - + -
649B PHE* 3.8 26.0 - - + -
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Residues in contact with GLY 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ASP* 5.9 0.2 - - - -
471B SER* 2.8 11.5 + - - -
472B ILE* 1.3 81.4 - - - +
474B VAL* 1.3 50.8 + - - +
475B GLY 3.1 0.6 + - - -
528B ARG* 2.7 30.8 + - - -
529B GLN* 3.9 16.7 - - - +
642B ALA* 3.5 11.6 - - - +
646B PHE* 3.5 27.4 - - - -
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B HIS* 3.5 42.8 - - + +
471B SER 2.9 21.8 + - - +
472B ILE 2.8 0.2 - - - -
473B GLY* 1.3 72.8 - - - +
475B GLY* 1.3 58.7 + - - +
476B GLU* 3.5 4.2 + - - +
477B ASP* 3.7 33.1 + - + +
481B HIS* 3.9 21.5 - - + +
482B GLN* 3.9 10.1 - - + -
528B ARG* 2.3 47.0 + - - +
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Residues in contact with GLY 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE 2.8 14.6 + - - -
473B GLY 3.1 0.4 - - - -
474B VAL* 1.3 78.2 - - - +
476B GLU* 1.3 67.7 + - - -
477B ASP 3.4 0.2 - - - -
478B GLY 3.1 5.2 + - - -
482B GLN* 3.0 20.6 + - - +
638B ALA 3.5 5.2 - - - +
640B GLY 2.8 19.3 - - - +
642B ALA* 3.9 12.8 - - - -
645B VAL* 4.7 1.3 - - - -
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Residues in contact with GLU 476 (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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26A ALA 4.9 1.4 - - - +
27A ASN 5.5 0.2 - - - +
28A SER* 3.4 21.6 + - - +
94A ARG* 3.3 47.6 - - + +
95A GLN* 5.0 2.8 + - - +
102A GLY* 3.5 8.3 - - - -
474B VAL 3.5 5.2 + - - +
475B GLY* 1.3 69.9 - - - -
477B ASP* 1.3 60.5 + - - +
478B GLY 2.9 5.6 - - - -
528B ARG* 5.0 2.3 + - - -
639B SER* 2.6 22.5 + - - -
640B GLY 2.9 18.6 + - - +
641B LYS* 3.7 28.0 + - - +
642B ALA* 4.4 1.7 + - - +
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Residues in contact with ASP 477 (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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30A HIS* 4.0 8.7 + - - -
94A ARG* 3.0 28.9 + - - +
102A GLY* 4.6 0.7 - - - -
103A HIS* 2.8 40.3 + - + +
1682A THD 5.0 2.8 - - - +
442B PHE* 5.1 6.2 - - - -
469B HIS* 5.8 1.6 - - - -
474B VAL* 3.7 22.5 + - + +
475B GLY 3.2 1.6 + - - -
476B GLU* 1.3 76.0 - - - +
478B GLY* 1.3 60.3 + - - +
479B PRO* 4.7 0.2 - - - +
480B THR* 4.1 4.2 + - - -
481B HIS* 3.8 24.3 - - + -
528B ARG* 5.0 4.3 + - - -
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Residues in contact with GLY 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B VAL* 4.7 0.2 - - - +
475B GLY 3.1 7.9 + - - -
476B GLU 2.9 4.2 + - - -
477B ASP* 1.3 78.9 - - - +
479B PRO* 1.3 69.5 - - - +
480B THR 3.3 2.9 - - - -
481B HIS* 2.9 20.3 + - - +
482B GLN* 3.1 20.0 - - - +
638B ALA 3.9 1.1 - - - -
639B SER* 3.7 18.2 - - - -
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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