Contacts of the strand formed by residues 450 - 453 (chain I) in PDB entry 1ZUM
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 450 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427I LEU 3.1 8.7 + - - -
428I ALA* 3.1 8.4 - - - -
429I ALA 2.9 25.2 + - - +
448I ALA* 3.2 1.1 - - - +
449I GLY* 1.3 80.6 + - - +
451I VAL* 1.3 69.3 + - - +
452I TRP* 3.7 39.5 - - + +
458I VAL 5.4 0.7 - - - +
464I PRO 3.9 10.8 + - - +
465I PHE* 3.4 25.3 - - + -
466I GLY 4.8 0.2 + - - -
490J THR* 3.1 15.6 - - + +
492J THR* 4.8 4.9 - - - +
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Residues in contact with VAL 451 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429I ALA* 3.2 8.3 - - + +
431I VAL* 5.0 3.4 - - + -
443I SER* 3.8 39.0 - - - +
446I LEU* 4.2 31.2 - - + +
448I ALA* 4.2 16.4 - - + +
450I THR* 1.3 78.5 - - - +
452I TRP* 1.3 73.4 + - - +
453I VAL* 4.6 3.6 - - + -
489J LYS* 4.5 4.3 - - + -
490J THR 2.8 11.4 + - - +
491J VAL* 3.3 13.4 - - + +
492J THR 2.9 23.3 + - - -
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Residues in contact with TRP 452 (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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303I CYS* 4.1 3.6 - - + -
428I ALA* 3.5 30.1 - - + -
429I ALA 2.8 21.5 + - - -
430I ALA* 3.1 4.8 - - + -
431I VAL 2.8 25.9 + - - -
450I THR* 3.7 18.8 - - + +
451I VAL* 1.3 75.6 - - - +
453I VAL* 1.3 63.6 + - - +
454I ASN 4.1 0.4 - - - -
455I CYS* 3.2 22.7 - - - +
456I TYR* 3.8 29.4 - + - -
457I ASP* 3.5 39.3 - - - -
458I VAL* 2.9 41.5 + - + +
459I PHE* 4.0 20.4 - + - -
465I PHE* 4.8 0.7 - + - -
492J THR* 3.3 25.2 - - - -
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Residues in contact with VAL 453 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431I VAL* 3.3 13.7 - - + +
433I THR* 5.1 1.8 - - + -
439I ALA* 3.9 20.0 - - + +
443I SER* 4.6 8.3 - - - -
451I VAL* 4.6 7.2 - - + +
452I TRP* 1.3 79.2 - - - +
454I ASN* 1.3 71.2 + - - +
455I CYS* 3.3 1.2 + - - -
491J VAL* 4.4 11.9 - - + -
492J THR 3.0 6.9 + - - -
493J VAL* 3.7 28.3 - - + +
494J LYS 3.0 22.0 + - - -
436L LEU* 3.7 30.3 - - + -
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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