Contacts of the strand formed by residues 359 - 367 (chain B) in PDB entry 3H44
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 359 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B ILE 3.7 19.7 - - - +
339B GLY* 4.0 11.2 - - - +
341B GLU* 4.1 3.1 + - + +
346B LEU* 3.7 33.7 - - + -
347B LEU* 3.8 32.8 - - + +
350B LEU* 4.3 3.8 - - + -
358B THR* 1.3 78.6 - - - +
360B VAL* 1.3 81.3 + - - +
361B GLY 4.0 0.4 - - - +
375B ILE* 4.1 12.8 - - + -
376B ASN 3.2 6.7 - - - +
377B VAL* 3.7 20.6 - - + -
394B MET* 5.3 0.2 - - + -
1D ALA* 2.8 25.3 + - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B THR* 6.1 1.3 - - - -
359B LEU* 1.3 83.4 - - - +
361B GLY* 1.3 59.7 + - - +
374B ILE* 3.7 20.7 - - + +
375B ILE* 3.3 1.9 - - - -
376B ASN* 2.7 49.3 + - + +
1D ALA* 3.2 19.1 - - + +
3D LEU* 4.0 21.5 - - + -
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Residues in contact with GLY 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B GLY* 3.8 9.1 - - - +
338B ILE* 4.9 7.6 - - - -
339B GLY* 4.5 4.0 - - - -
359B LEU* 4.0 6.2 - - - +
360B VAL* 1.3 77.0 - - - +
362B GLY* 1.3 55.2 + - - -
374B ILE* 3.0 13.9 - - - -
375B ILE* 4.3 2.2 - - - -
1D ALA 3.1 7.1 + - - +
2D SER* 3.4 8.7 - - - -
3D LEU* 2.8 28.8 + - - -
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Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B GLY* 3.4 22.0 - - - -
338B ILE* 5.3 0.2 - - - +
361B GLY* 1.3 75.3 - - - -
363B GLN* 1.3 62.9 + - - -
373B PHE* 3.5 17.8 - - - -
374B ILE* 2.9 34.3 + - - +
2D SER* 5.4 0.7 - - - -
3D LEU* 4.5 5.8 - - - -
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Residues in contact with GLN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ILE* 4.7 2.7 - - + -
322B LEU* 3.8 6.9 - - - +
329B ASN* 3.5 18.4 + - - +
331B GLY* 3.3 20.9 + - - -
332B HIS* 3.0 33.9 - - - +
362B GLY* 1.3 73.3 - - - -
364B LYS* 1.3 59.9 - - - +
371B MET* 3.2 31.9 - - + +
372B PHE 3.4 8.1 - - - +
373B PHE* 3.9 11.0 - - + -
3D LEU* 3.2 20.7 - - - +
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PHE* 6.3 1.3 - - - -
205B GLU* 2.8 32.7 + - - -
363B GLN* 1.3 74.1 - - - +
365B GLU* 1.3 75.4 + - - +
371B MET* 3.3 9.3 - - - +
372B PHE* 2.8 58.1 + - + +
374B ILE* 4.4 21.8 - - + +
376B ASN* 6.3 0.2 - - - +
2000B DIO 3.5 26.4 + - - +
3D LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B GLN* 4.3 0.4 - - - +
364B LYS* 1.3 85.2 - - - +
366B GLY* 1.3 62.8 + - - +
371B MET* 4.0 10.5 - - + -
372B PHE* 3.5 12.4 - - - -
443B TYR* 5.3 7.3 + - - -
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Residues in contact with GLY 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 5.0 3.5 - - - +
144B GLY* 5.9 1.7 - - - -
145B GLU* 4.6 2.8 - - - +
215B PHE* 5.6 2.2 - - - -
364B LYS 3.8 0.6 + - - -
365B GLU* 1.3 78.9 - - - +
367B ALA* 1.3 63.6 + - - +
370B PHE* 3.3 35.8 + - - -
371B MET* 3.9 1.8 - - - +
372B PHE* 3.9 6.3 - - - -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.7 13.5 - - + -
145B GLU* 3.4 24.7 - - - +
288B PHE* 3.6 13.5 - - + -
321B ASP* 3.4 6.6 - - - +
366B GLY* 1.3 75.4 + - - +
368B ARG* 1.3 65.7 + - - +
369B GLY 3.1 2.1 + - - -
370B PHE* 2.9 42.6 + - + +
371B MET* 5.2 0.5 - - - +
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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