Contacts of the strand formed by residues 427 - 431 (chain A) in PDB entry 4QGC
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 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A SER* 3.2 7.5 - - - -
426A GLY* 1.3 83.8 - - - +
428A ILE* 1.3 65.4 + - - +
429A ILE* 3.9 2.5 - - + -
448A ALA* 4.0 6.1 - - - -
449A PRO* 3.3 18.6 - - + +
451A ILE* 4.0 16.8 - - + -
503A PHE* 3.6 22.7 - - + -
509A VAL* 3.6 10.6 - - + +
510A ILE 3.1 22.7 + - - -
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Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 3.8 12.6 - - + +
417A VAL* 4.1 3.8 - - - -
420A SER* 3.8 33.4 - - - +
427A ALA* 1.3 74.8 - - - +
429A ILE* 1.3 61.8 + - - +
430A VAL* 3.6 20.0 + - + -
441A VAL* 3.8 26.5 - - + -
446A PRO* 4.0 16.6 - - + -
448A ALA* 4.6 4.5 - - + +
449A PRO 3.0 10.2 + - - +
450A ILE* 3.4 9.6 - - + +
451A ILE 2.9 22.0 + - - -
510A ILE* 3.4 18.2 - - + +
512A LEU* 4.4 12.1 - - + -
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Residues in contact with ILE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ALA* 4.7 2.9 - - + -
428A ILE* 1.3 71.9 - - - +
430A VAL* 1.3 56.1 + - - +
431A LEU* 3.9 20.6 - - + -
451A ILE* 3.6 20.2 - - + +
453A VAL* 4.1 1.6 - - + -
490A VAL* 4.4 7.4 - - + +
493A ALA* 3.7 36.8 - - + -
494A MET* 4.1 22.7 - - + +
503A PHE* 5.0 2.0 - - + -
509A VAL* 4.1 24.5 - - + -
510A ILE 2.5 14.2 + - - +
511A VAL* 3.2 16.2 - - + +
512A LEU* 2.7 32.7 + - - +
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A ILE* 4.0 15.5 - - + -
429A ILE* 1.3 76.1 - - - +
431A LEU* 1.3 68.1 + - - +
432A THR* 3.4 3.3 + - - +
437A SER* 3.3 29.8 - - - +
438A ALA* 3.9 21.3 - - + +
441A VAL* 4.3 6.7 - - + -
450A ILE* 3.9 22.9 - - + -
451A ILE 3.0 9.7 + - - +
452A ALA* 3.4 3.1 - - - -
453A VAL 2.8 27.3 + - - -
512A LEU* 3.7 24.5 - - + +
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ILE* 3.9 21.5 - - + -
430A VAL* 1.3 76.1 - - - +
432A THR* 1.3 58.4 + - - +
453A VAL* 3.6 16.2 - - + -
486A VAL* 3.9 19.5 - - + +
489A ARG* 3.6 57.2 - - + +
490A VAL* 4.4 9.4 - - + -
511A VAL* 4.7 0.9 - - + -
512A LEU 3.0 18.0 + - - +
513A THR* 3.7 28.8 - - + -
522A THR* 4.4 7.8 + - - -
1002A SO4 5.0 1.6 - - - +
1003A SO4 4.3 5.4 + - - -
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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