Contacts of the strand formed by residues 398 - 405 (chain A) in PDB entry 2OIV
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 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A PO4 4.2 1.6 - - - +
363A LEU* 3.0 22.6 + - + +
364A LEU* 3.4 5.4 - - + -
365A HIS 2.8 26.0 + - - +
396A PRO 3.5 0.2 - - - -
397A PRO* 1.3 76.5 - - - +
399A VAL* 1.3 59.8 + - - +
400A PHE* 3.6 29.4 - - + -
414A VAL* 4.5 4.3 - - + -
415A VAL 3.3 5.8 - - - +
416A ASP* 3.8 16.2 - - + +
418A ARG* 3.7 33.0 - - + +
485A VAL* 3.9 31.2 - - + -
490A PHE* 4.4 17.9 - - + -
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Residues in contact with VAL 399 (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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365A HIS* 3.4 28.0 - - + +
367A ALA* 4.4 1.8 - - + -
390A LEU* 4.5 8.1 - - + +
395A ILE* 4.7 0.2 - - + -
396A PRO 3.3 24.9 - - - +
397A PRO 4.1 2.9 - - - -
398A ILE* 1.3 72.5 - - - +
400A PHE* 1.3 64.6 + - - +
401A LEU* 3.8 31.2 + - + +
413A LEU 3.6 1.6 - - - +
414A VAL* 3.3 5.9 - - - +
415A VAL* 2.7 45.7 + - + +
417A ARG* 3.4 26.7 - - - +
449A LEU* 5.9 0.9 - - + -
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Residues in contact with PHE 400 (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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364A LEU* 3.5 30.5 - - + -
365A HIS 2.9 19.4 + - - +
366A PHE* 3.7 21.7 - + + -
367A ALA* 2.9 30.9 + - - +
398A ILE* 3.6 25.1 - - + -
399A VAL* 1.3 72.0 - - - +
401A LEU* 1.3 60.1 + - - +
402A PRO* 3.4 5.6 - - - +
412A LEU* 4.2 2.7 - - + -
413A LEU 3.7 3.4 - - - -
414A VAL* 3.7 19.7 - - + -
478A ILE* 4.1 35.1 - - + +
481A LEU* 3.6 39.3 - - + -
482A ALA* 4.3 9.0 - - - -
485A VAL* 4.8 2.2 - - + -
490A PHE* 5.1 1.1 - + - -
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Residues in contact with LEU 401 (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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367A ALA* 4.0 2.0 - - + -
372A VAL* 4.0 22.2 - - + -
375A LEU* 4.9 0.4 - - + -
390A LEU* 3.9 27.8 - - + -
399A VAL* 3.8 25.4 - - + +
400A PHE* 1.3 74.1 - - - +
402A PRO* 1.4 66.4 - - - +
403A ILE* 3.4 4.3 + - + +
412A LEU* 3.7 4.1 - - - +
413A LEU* 2.7 60.3 + - + +
415A VAL* 3.5 31.9 - - + -
445A ALA* 5.8 0.7 - - + -
449A LEU* 3.9 20.0 - - + -
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Residues in contact with PRO 402 (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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344A LEU* 3.7 22.4 - - + -
348A THR* 5.7 2.9 - - + -
367A ALA 3.5 20.0 - - - +
369A SER* 3.9 14.2 - - - +
372A VAL* 3.6 27.1 - - + +
400A PHE 3.4 11.9 - - - +
401A LEU* 1.4 83.2 - - - +
403A ILE* 1.3 60.7 + - - +
404A ASN 4.0 1.7 + - - -
410A TRP* 3.6 21.3 - - + -
411A SER 3.7 6.5 - - - +
412A LEU* 4.3 0.6 - - + -
474A VAL* 4.4 6.3 - - + -
478A ILE* 4.5 14.6 - - + -
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Residues in contact with ILE 403 (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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372A VAL* 3.8 23.3 - - + -
401A LEU* 3.7 15.5 - - + +
402A PRO* 1.3 70.9 - - - +
404A ASN* 1.3 60.2 + - - +
410A TRP* 3.3 7.9 - - - -
411A SER* 2.8 46.9 + - - +
413A LEU* 4.1 22.0 - - + +
427A HIS* 4.5 0.2 - - - +
438A GLN* 3.2 20.8 + - - +
441A LEU* 3.6 31.9 - - + +
442A ALA* 4.3 13.7 - - + +
445A ALA* 4.2 15.3 - - + -
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Residues in contact with ASN 404 (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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338A TRP* 6.2 0.2 - - - -
341A ASP* 3.4 29.8 + - - +
369A SER* 5.3 1.6 - - - +
373A THR* 4.4 17.9 + - - +
402A PRO 4.0 0.8 + - - -
403A ILE* 1.3 71.7 - - - +
405A GLN* 1.3 77.9 + - - +
406A PRO* 3.2 22.6 - - + +
407A ASN 4.3 1.2 + - - -
409A HIS 3.9 1.4 - - - +
410A TRP* 3.5 33.4 + - + -
441A LEU* 3.6 14.9 - - - +
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Residues in contact with GLN 405 (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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403A ILE 3.9 0.4 + - - -
404A ASN* 1.3 76.5 - - - +
406A PRO* 1.3 63.1 - - + +
407A ASN 3.3 0.5 + - - -
408A ALA* 2.9 45.3 + - + +
409A HIS* 2.7 28.2 + - - +
435A ASP* 4.8 7.1 + - - +
437A GLN* 3.3 42.8 + - + +
438A GLN* 2.8 41.8 + - - +
441A LEU* 4.2 3.1 - - + -
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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