Contacts of the strand formed by residues 350 - 355 (chain A) in PDB entry 1B0K
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 ILE 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A LEU 4.1 1.6 - - - +
349A ASP* 1.3 73.2 - - - +
351A ARG* 1.3 59.8 + - - +
352A VAL 3.4 24.5 - - - +
353A GLY* 4.7 0.7 - - - +
384A LYS* 2.7 26.3 + - - -
385A SER* 2.8 24.7 + - - +
440A THR* 3.4 20.6 - - + +
442A VAL* 3.8 25.1 - - + +
472A LEU* 3.8 27.4 - - + +
473A ALA* 5.6 1.1 - - - -
476A GLY 2.9 11.9 + - - +
477A THR 3.6 30.1 - - - +
478A LEU* 3.9 10.5 - - + +
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Residues in contact with ARG 351 (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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347A PRO* 5.9 0.8 - - - +
349A ASP* 2.8 41.3 + - - +
350A ILE* 1.3 76.1 - - - +
352A VAL* 1.4 61.0 + - - +
384A LYS* 5.9 0.7 - - - +
385A SER* 3.8 1.5 - - - -
386A GLN* 3.1 28.3 + - - +
430A ARG* 4.3 2.0 - - - +
432A ASP* 3.8 23.2 + - - +
433A ILE* 4.3 10.3 - - - +
437A GLU* 2.9 30.5 + - - -
438A LYS 4.3 7.5 + - - -
439A ASN* 3.7 39.0 - - + +
440A THR 3.0 10.9 + - - +
441A ILE* 5.0 0.2 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ILE* 3.4 8.6 - - - +
351A ARG* 1.4 82.4 - - - +
353A GLY* 1.4 70.1 + - - +
354A LEU* 3.9 22.9 - - + -
385A SER* 4.7 0.4 - - - -
386A GLN* 3.2 31.4 - - + +
388A THR* 4.3 10.3 - - + -
428A TRP* 3.8 20.6 - - + -
430A ARG* 3.8 23.6 - - - +
432A ASP* 4.1 6.5 - - - +
440A THR 4.1 1.4 + - - -
441A ILE* 3.4 9.5 - - + +
442A VAL 3.2 22.7 + - - +
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Residues in contact with GLY 353 (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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350A ILE* 5.0 0.2 - - - -
352A VAL* 1.4 72.6 - - - +
354A LEU* 1.3 63.2 + - - +
355A ILE 4.3 0.2 - - - -
385A SER* 4.6 1.2 - - - -
386A GLN 2.8 10.1 + - - -
387A PHE* 3.4 8.0 - - - -
388A THR 3.0 25.1 + - - +
442A VAL* 3.4 13.9 - - - -
469A VAL* 3.9 16.2 - - - -
473A ALA* 4.7 10.1 - - - -
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Residues in contact with LEU 354 (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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352A VAL* 3.9 16.2 - - + -
353A GLY* 1.3 74.3 - - - +
355A ILE* 1.4 61.0 + - - +
388A THR* 3.3 24.9 - - + +
423A PRO* 3.6 24.9 - - + -
428A TRP* 3.9 31.4 - - + -
441A ILE* 4.3 10.1 - - + -
442A VAL 3.1 11.8 + - - +
443A THR* 3.5 20.4 - - + -
444A SER 3.2 22.7 + - - -
445A TYR* 3.4 33.5 - - + +
469A VAL* 3.7 2.5 - - - +
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY 4.3 0.2 - - - -
354A LEU* 1.4 70.6 - - - +
356A GLY* 1.3 58.3 + - - +
366A MET* 4.4 11.2 - - + -
369A SER* 3.9 23.6 - - - +
387A PHE* 3.9 17.9 - - + -
388A THR 3.2 10.3 + - - +
389A ILE* 3.6 36.2 - - + -
390A THR* 2.9 26.1 + - - -
409A LEU* 4.6 3.4 - - + -
444A SER* 3.3 6.5 - - - +
445A TYR* 4.3 1.8 + - - -
466A PRO* 3.8 30.1 - - + +
469A VAL* 3.7 24.7 - - + -
470A THR* 4.3 2.0 - - - +
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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