Contacts of the strand formed by residues 484 - 488 (chain B) in PDB entry 4HXG
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 ALA 484 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B ILE 4.0 2.2 + - - -
461B GLY* 3.1 21.1 - - - -
462B ILE* 3.1 8.1 + - - +
476B LEU* 4.6 6.3 - - - -
482B PHE* 3.4 4.0 + - - +
483B LYS* 1.3 81.3 - - - +
485B GLY* 1.3 58.8 + - - +
536B ALA* 4.2 1.8 - - - -
537B PRO* 3.6 12.8 - - + +
599B PHE* 4.8 3.4 - - + -
600B PHE* 4.7 7.9 - - + -
603B LYS* 3.8 29.8 - - + +
604B LEU* 4.2 13.9 - - + -
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Residues in contact with GLY 485 (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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462B ILE* 3.2 13.7 - - - -
472B THR* 4.5 4.9 - - - -
476B LEU* 4.5 6.1 - - - +
484B ALA* 1.3 78.0 - - - +
486B ILE* 1.3 63.7 + - - -
537B PRO 3.3 7.5 + - - -
538B LEU* 3.2 14.8 - - - +
539B LEU 3.1 23.4 + - - -
599B PHE* 3.6 5.3 - - - -
600B PHE* 4.9 2.2 - - - -
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Residues in contact with ILE 486 (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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462B ILE 3.2 7.3 + - - -
463B THR* 3.0 35.1 + - - +
464B GLY 3.4 5.2 + - - +
472B THR* 4.0 2.5 - - - +
485B GLY* 1.3 75.1 - - - -
487B SER* 1.3 61.5 + - - +
488B GLU* 4.2 10.5 - - + +
539B LEU* 3.4 17.7 - - + +
541B ILE* 4.2 23.6 - - + -
596B PHE* 3.8 24.7 - - + +
599B PHE* 3.6 28.9 - - + -
600B PHE* 3.5 33.9 - - + -
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Residues in contact with SER 487 (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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464B GLY 4.0 2.9 - - - -
469B GLY* 3.3 12.5 + - - -
472B THR* 3.9 15.0 - - - -
473B ASN* 2.9 32.0 + - - -
486B ILE* 1.3 72.5 - - - +
488B GLU* 1.3 63.4 + - - +
489B ASN 4.3 0.4 + - - -
490B GLY 4.9 2.9 + - - -
538B LEU* 4.0 5.1 - - - +
539B LEU 3.0 6.9 + - - -
540B LEU* 3.4 21.8 - - - +
541B ILE 2.9 24.3 + - - +
554B SER* 5.6 0.3 + - - -
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Residues in contact with GLU 488 (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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463B THR* 4.3 4.0 + - - -
464B GLY 3.1 13.2 + - - +
465B ILE* 3.2 18.6 - - + +
466B ALA 2.8 20.1 + - - -
469B GLY* 4.1 1.1 - - - -
486B ILE* 4.2 6.7 - - + +
487B SER* 1.3 77.1 + - - +
489B ASN* 1.3 79.5 + - - +
490B GLY* 3.1 4.6 + - - -
541B ILE* 3.4 38.9 - - + +
580B HIS* 4.9 0.9 - - - -
581B SER* 4.8 1.2 - - - -
592B ARG* 2.6 45.8 + - - -
596B PHE* 3.9 14.7 - - - -
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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