Contacts of the strand formed by residues 365 - 369 (chain B) in PDB entry 3HO5
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 365 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ALA* 4.3 12.6 - - + -
300B TYR* 4.6 17.5 - - + -
321B VAL* 4.8 10.3 - - + -
342B PHE* 5.1 2.7 - - + -
357B LEU* 4.5 6.5 - - + -
358B LEU 3.5 11.4 - - - +
359B PHE* 3.6 32.6 - - + -
364B PHE* 1.3 71.5 - - - +
366B TYR* 1.3 66.0 + - - +
367B ILE* 3.9 26.1 - - + +
393B LEU 3.6 0.5 - - - +
394B ARG* 3.2 4.7 - - - -
395B LEU* 2.8 45.0 + - + +
397B VAL* 3.8 27.8 - - + +
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Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLN 3.6 0.7 - - - +
357B LEU* 3.3 7.4 - - - +
358B LEU* 2.7 60.0 + - + +
360B GLY* 3.9 6.1 - - - -
362B ASP* 2.7 38.9 + - - -
364B PHE 3.6 8.1 - - - -
365B LEU* 1.3 77.6 - - - +
367B ILE* 1.3 63.4 + - - +
368B ILE* 4.1 1.6 - - + -
392B VAL* 4.1 23.1 - - + -
393B LEU 3.1 6.7 - - - +
394B ARG* 3.1 39.0 + - + -
425B PHE* 4.9 7.4 - + - -
448B LEU* 3.5 21.2 - - + +
450B ILE* 5.3 6.3 - - + -
466B LEU* 5.3 2.5 - - + -
468B ILE* 3.6 18.3 - - + +
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 4.2 17.5 - - + -
343B LEU* 4.1 9.2 - - + -
355B GLY* 4.8 4.5 - - - -
356B GLN 3.4 2.9 - - - +
357B LEU* 3.6 28.9 - - + -
365B LEU* 3.9 17.7 - - + +
366B TYR* 1.3 76.5 - - - +
368B ILE* 1.3 63.8 + - - +
369B LEU* 3.5 31.9 + - + -
391B SER 3.6 0.7 - - - +
392B VAL* 3.6 1.3 - - - -
393B LEU* 2.9 46.2 + - + +
395B LEU* 3.8 35.0 - - + -
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B GLY* 3.6 2.5 - - - -
355B GLY* 2.7 30.6 + - - -
356B GLN* 2.9 30.4 + - + +
358B LEU* 3.8 26.9 - - + -
366B TYR* 5.4 0.9 - - + -
367B ILE* 1.3 74.0 - - - +
369B LEU* 1.3 54.5 + - - +
391B SER 4.2 1.8 - - - -
392B VAL* 4.4 19.1 - - + +
429B LEU* 3.5 26.2 - - + -
432B PRO* 4.2 14.1 - - + -
433B GLY 5.6 0.7 - - - +
435B CYS* 3.8 28.3 - - - -
450B ILE* 3.9 17.3 - - + -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.7 39.0 - - + -
343B LEU* 5.7 0.4 - - + -
345B VAL* 3.9 20.9 - - + -
347B GLU* 6.1 0.2 - - - +
353B LEU 4.0 4.0 - - - +
355B GLY* 4.3 5.4 - - - +
367B ILE* 3.5 20.8 + - + -
368B ILE* 1.3 72.5 - - - +
370B GLY* 1.3 60.7 + - - +
388B PHE* 3.6 40.4 - - + +
389B THR* 4.2 5.8 - - + +
390B GLY* 3.2 22.0 + - - +
391B SER 3.1 18.6 + - - +
393B LEU* 4.0 11.7 - - + -
429B LEU* 3.9 9.6 - - - +
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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