Contacts of the strand formed by residues 428 - 433 (chain I) in PDB entry 5IIO
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 VAL 428 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387I MET* 3.7 23.3 - - - -
392I ALA* 3.9 26.9 - - + +
395I ILE* 4.2 21.8 - - + -
396I GLU 4.8 0.9 - - - +
414I ALA* 4.4 14.6 - - + -
415I CYS 6.0 0.4 - - - -
418I TYR* 5.9 3.4 - - + -
427I ASP* 1.3 80.5 - - - +
429I ASP* 1.3 64.2 + - - +
430I VAL* 4.0 22.2 - - + -
488I ARG 3.0 7.8 + - - +
489I LEU* 3.4 11.0 - - + +
490I ASP* 2.8 30.4 + - - -
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Residues in contact with ASP 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413I VAL 3.6 0.3 - - - +
414I ALA* 3.3 3.0 - - - +
415I CYS* 2.8 47.2 + - + +
416I GLY* 3.9 18.2 + - - -
427I ASP* 3.5 21.7 - - - +
428I VAL* 1.3 82.2 - - - +
430I VAL* 1.3 63.0 + - - +
431I LEU 3.8 0.7 + - - -
490I ASP* 3.0 34.9 - - + +
492I ILE* 4.4 10.8 - - + -
506I PHE* 4.2 12.4 - - + +
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Residues in contact with VAL 430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I GLU* 4.3 17.3 - - + +
399I VAL* 3.7 46.0 - - + -
412I CYS* 4.3 11.2 - - + -
413I VAL 3.6 8.3 - - - +
414I ALA* 4.8 0.7 - - - -
428I VAL* 4.0 18.6 - - + -
429I ASP* 1.3 73.9 - - - +
431I LEU* 1.3 59.7 + - - +
432I ILE* 4.0 14.5 + - + -
489I LEU* 4.0 5.2 - - + -
490I ASP 2.8 13.0 + - - +
491I ILE* 3.4 5.4 - - + +
492I ILE* 2.8 33.6 + - - +
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Residues in contact with LEU 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411I LEU 3.5 1.0 - - - +
412I CYS* 3.3 4.2 - - - -
413I VAL* 2.8 42.8 + - + +
415I CYS* 3.9 11.2 - - - -
429I ASP 3.8 1.0 + - - -
430I VAL* 1.3 72.9 - - - +
432I ILE* 1.3 63.0 + - - +
492I ILE* 3.4 26.5 - - + +
494I VAL* 3.6 28.9 - - + -
499I PHE* 3.7 21.2 - - + -
502I ALA* 3.8 11.7 - - + +
503I LEU* 3.5 48.2 - - + +
506I PHE* 4.4 5.4 - - + -
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Residues in contact with ILE 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399I VAL* 4.1 15.5 - - + -
403I ALA* 4.2 9.2 - - + -
410I LEU* 4.2 26.9 - - + -
411I LEU 3.2 7.4 - - - +
412I CYS* 3.8 17.3 - - - -
430I VAL* 4.0 6.5 - - + +
431I LEU* 1.3 82.2 - - - +
433I THR* 1.3 62.9 + - - +
443I ILE* 5.0 3.6 - - + -
447I LEU* 3.5 32.1 - - + -
491I ILE* 4.1 11.2 - - + -
492I ILE 2.7 13.8 + - - +
493I VAL* 3.2 18.3 - - + +
494I VAL* 2.9 28.0 + - - +
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Residues in contact with THR 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410I LEU* 3.4 12.2 - - - +
411I LEU* 2.9 40.8 + - + -
432I ILE* 1.3 73.7 - - - +
434I HIS* 1.3 65.9 + - - +
440I HIS* 4.5 3.8 - - - -
494I VAL* 2.7 32.5 + - - -
496I TYR* 3.2 33.1 + - + -
499I PHE* 3.5 37.0 - - + -
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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