Contacts of the strand formed by residues 370 - 374 (chain D) in PDB entry 4O9U
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 VAL 370 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D MET* 3.6 46.0 - - + +
289D LEU* 4.8 4.3 - - + -
292D ALA* 3.6 9.9 - - + -
294D LYS 3.2 2.6 + - - -
295D VAL* 3.2 11.7 - - + +
296D VAL 3.0 22.2 + - - -
368D VAL* 3.4 4.2 - - - +
369D ASP* 1.3 86.2 - - + +
371D ALA* 1.3 60.7 + - - +
372D VAL* 3.6 18.1 + - + +
404D ASN* 3.2 10.3 - - + +
406D ILE* 3.7 31.4 - - + -
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D VAL* 3.3 9.9 - - + +
298D VAL* 5.3 0.9 - - + -
365D PHE* 4.3 13.2 - - + -
368D VAL* 4.0 4.0 - - + +
369D ASP 4.4 0.2 - - - -
370D VAL* 1.3 70.1 - - - +
372D VAL* 1.3 63.7 + - - +
373D VAL* 3.4 2.0 + - + +
399D VAL* 3.8 24.2 - - + -
402D ALA* 3.9 19.9 - - + +
404D ASN 2.7 10.9 + - - +
405D VAL* 3.3 11.0 - - + +
406D ILE 3.3 18.2 + - - -
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Residues in contact with VAL 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D LEU* 3.9 23.6 - - + -
295D VAL* 4.4 5.2 - - + -
296D VAL 2.8 8.6 + - - +
297D PHE* 3.2 32.3 - - + -
298D VAL* 2.7 31.5 + - - +
370D VAL* 3.6 21.7 + - + -
371D ALA* 1.3 68.8 - - - +
373D VAL* 1.3 58.0 + - - +
374D ILE* 4.2 1.5 + - + +
406D ILE* 3.4 22.0 - - + +
408D ILE* 4.1 22.9 - - + -
440D LEU* 5.5 0.7 - - + -
443D LEU* 5.1 7.4 - - + -
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Residues in contact with VAL 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D VAL* 3.4 28.0 - - + +
371D ALA 3.7 10.8 - - - +
372D VAL* 1.3 77.0 - - - +
374D ILE* 1.3 58.7 + - - +
376D ALA* 3.7 32.5 - - + +
380D VAL* 4.3 10.8 - - + -
399D VAL* 3.9 20.6 - - + -
405D VAL* 4.2 7.6 - - + -
406D ILE 2.5 14.9 + - - +
407D VAL* 4.3 13.2 - - + -
408D ILE* 2.7 35.4 + - - +
423D LEU* 5.0 1.3 - - + -
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Residues in contact with ILE 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D PHE* 5.2 2.9 - - + -
298D VAL 2.9 10.8 + - - +
299D PRO* 3.5 23.9 - - + +
300D GLY 2.9 27.4 + - - -
303D MET* 3.9 19.6 + - + -
308D ALA* 4.5 0.9 - - + -
312D LEU* 4.1 23.3 - - + -
372D VAL* 5.0 2.0 - - + +
373D VAL* 1.3 74.2 - - - +
375D GLY* 1.3 61.5 + - - +
376D ALA 3.2 1.5 + - - -
408D ILE* 3.7 33.0 - - + -
436D ALA* 3.6 32.1 - - + -
440D LEU* 4.2 15.7 - - + -
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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