Contacts of the strand formed by residues 457 - 464 (chain E) in PDB entry 4K4I
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 LEU 457 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448E LEU* 3.7 35.9 - - + +
451E LEU* 3.4 21.4 + - + -
452E ARG* 4.0 30.7 - - + +
455E GLY* 4.4 4.8 - - - -
456E PHE* 1.3 85.1 - - + +
458E THR* 1.3 61.5 + - - +
459E ASP 3.5 0.7 - - - -
460E ASP* 4.7 1.3 - - - +
473E TYR* 3.6 37.0 - - + +
476E VAL 3.5 9.0 - - - +
477E CYS* 4.2 1.6 - - + -
489E LEU* 4.0 25.8 - - + -
491E ILE* 4.9 0.4 - - + -
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Residues in contact with THR 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E GLY 4.4 7.2 - - - +
456E PHE 3.9 11.2 - - - +
457E LEU* 1.3 72.4 - - - +
459E ASP* 1.3 90.8 + - - +
476E VAL* 3.0 21.3 + - - +
478E ARG* 3.3 36.1 - - + +
486E HIS* 3.5 14.4 - - + +
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Residues in contact with ASP 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375E ILE* 4.0 21.8 - - + +
378E LYS* 2.9 30.0 + - - -
379E HIS* 3.1 21.6 + - - -
457E LEU 3.5 1.6 - - - -
458E THR* 1.3 109.7 + - - +
460E ASP* 1.3 65.1 + - - +
473E TYR* 3.0 6.2 + - - -
475E GLY* 3.4 0.5 - - - -
476E VAL* 2.9 40.5 + - + +
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Residues in contact with ASP 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E THR* 5.5 2.1 - - - +
372E GLN* 5.6 0.2 - - - +
375E ILE* 3.6 19.7 - - - +
452E ARG* 2.8 42.8 + - - +
457E LEU* 4.6 3.3 - - - +
459E ASP* 1.3 77.3 + - - +
461E LEU* 1.3 63.7 + - - +
462E VAL 5.2 1.8 - - - +
473E TYR* 2.5 37.0 + - + +
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Residues in contact with LEU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E TRP* 3.9 42.6 - - + -
372E GLN* 2.7 48.1 + - - +
375E ILE* 3.9 24.7 - - + -
376E GLY 5.3 0.4 - - - +
383E PHE* 5.2 1.3 - - + -
460E ASP* 1.3 78.5 - - - +
462E VAL* 1.3 59.9 + - - +
474E LEU* 2.9 11.9 + - + +
475E GLY* 4.2 9.6 - - - -
476E VAL* 4.4 8.3 - - + -
488E ARG* 3.7 38.6 - - - +
10F T 4.0 6.7 + - - +
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Residues in contact with VAL 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E TRP* 4.2 9.4 - - + -
372E GLN* 3.4 15.9 - - - +
460E ASP* 6.0 1.6 - - - -
461E LEU* 1.3 83.1 - - - +
463E SER* 1.3 72.7 + - - +
464E GLN* 4.1 12.6 - - + +
472E LYS* 5.0 1.1 - - + +
473E TYR* 3.6 9.3 - - - -
474E LEU* 3.0 60.5 + - + +
9F C 3.6 27.8 - - - +
10F T 3.4 7.2 - - - -
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Residues in contact with SER 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448E LEU* 5.8 0.9 - - - -
462E VAL* 1.3 74.8 - - - +
464E GLN* 1.3 58.3 + - - +
465E GLU* 3.2 21.5 + - - -
472E LYS 3.5 5.4 - - - -
473E TYR* 5.4 4.0 - - - -
607E CAC 2.4 48.9 + - - +
9F C 3.1 24.7 - - - +
10F T 2.9 16.7 + - - -
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Residues in contact with GLN 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E VAL* 4.1 11.4 - - + +
463E SER* 1.3 69.2 - - - +
465E GLU* 1.3 56.5 + - - +
466E GLU 3.0 10.6 + - - -
467E ASN* 3.7 8.0 + - - +
470E GLN 3.7 2.4 - - - +
471E GLN* 3.1 4.3 - - - -
472E LYS* 2.8 67.5 + - + +
474E LEU* 5.6 3.8 - - - +
7F T 5.9 0.2 + - - -
8F A 2.9 60.8 + - - +
9F C 3.1 22.8 + - - +
5G A 5.8 2.4 + - - -
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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