Contacts of the strand formed by residues 365 - 370 (chain A) in PDB entry 4OI0
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 HIS 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ASP 3.2 27.9 + - - -
362A ILE* 3.0 16.1 + - - +
363A LYS 3.2 7.6 - - - -
364A HIS* 1.3 78.7 - - - +
366A LEU* 1.3 65.7 + - - +
367A PHE* 4.1 9.4 - - + -
389A LEU* 3.6 2.5 - - - +
390A VAL* 3.1 29.8 + - - +
416A PHE* 3.3 24.7 - + + -
417A SER 2.8 22.4 + - - +
418A ASP* 3.4 17.8 - - - -
419A ILE 3.6 2.9 - - - -
420A THR* 3.4 24.9 - - + +
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Residues in contact with LEU 366 (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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159A VAL* 4.0 35.7 - - + -
160A PRO 4.7 1.3 - - - +
301A VAL* 4.0 11.0 - - + -
305A PHE* 3.8 28.5 - - + -
364A HIS 3.9 0.2 + - - -
365A HIS* 1.3 74.4 - - - +
367A PHE* 1.3 64.3 + - - +
387A PHE* 4.2 10.3 - - + -
388A CYS 3.3 13.2 - - - +
389A LEU* 3.9 14.4 - - + -
417A SER* 3.0 36.9 + - - +
419A ILE* 3.0 42.9 + - + +
420A THR* 5.7 0.4 - - - -
421A HIS* 5.4 0.4 - - + -
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Residues in contact with PHE 367 (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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327A LEU* 3.9 26.2 - - + -
328A CYS 4.6 0.2 - - - -
356A MET* 4.3 3.8 - - - -
362A ILE* 3.9 28.7 - - + -
365A HIS* 4.0 10.8 - - + -
366A LEU* 1.3 80.2 - - - +
368A ALA* 1.3 60.8 + - - +
369A PHE* 3.9 0.5 + - - -
387A PHE* 3.3 6.4 - - - -
388A CYS* 3.0 47.6 + - - -
390A VAL* 3.7 29.2 - - + -
414A LEU* 3.6 27.8 - - + -
415A VAL 3.2 7.0 - - - -
416A PHE* 3.6 42.6 - + + -
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Residues in contact with ALA 368 (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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187A ASN* 3.8 11.9 - - + +
367A PHE* 1.3 73.0 - - - +
369A PHE* 1.3 62.7 + - - +
370A SER 3.4 1.6 + - - -
384A VAL* 3.7 25.8 - - + -
386A GLY 3.3 7.6 - - - +
387A PHE* 3.5 24.0 - - + -
414A LEU* 3.3 4.4 - - - -
415A VAL* 2.7 42.1 + - + +
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Residues in contact with PHE 369 (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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368A ALA* 1.3 69.9 - - - +
370A SER* 1.3 58.8 + - - +
384A VAL* 3.4 3.0 - - - -
385A PHE* 2.8 35.1 + - + +
386A GLY* 2.8 25.3 + - - +
387A PHE 3.8 10.1 - - - -
388A CYS* 3.7 34.8 - - + -
402A ILE* 4.3 0.7 - - + -
404A CYS* 3.9 12.6 - - - -
405A PRO* 5.2 0.4 - - + -
409A ILE* 3.6 32.1 - - + -
410A PRO* 3.5 39.5 - - + -
411A SER* 3.4 23.3 - - - -
413A VAL 3.8 3.1 - - - -
414A LEU* 3.7 22.7 - - + -
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Residues in contact with SER 370 (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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368A ALA 3.4 2.2 + - - -
369A PHE* 1.3 72.4 - - - +
371A ARG* 1.3 65.1 + - - +
372A SER* 3.2 21.9 + - - +
379A VAL* 4.0 9.6 + - - +
382A SER* 4.0 9.2 + - - -
383A PRO 4.3 4.5 + - - -
384A VAL* 4.4 6.6 - - - +
385A PHE* 3.5 1.2 - - - -
411A SER* 2.8 30.8 + - - -
413A VAL* 2.9 30.5 + - - -
415A VAL* 3.8 18.6 - - - -
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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