Contacts of the strand formed by residues 317 - 322 (chain A) in PDB entry 4BBZ
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.9 20.0 - - + -
220A ALA* 3.3 14.1 - - + +
222A LEU* 4.7 3.4 - - + -
315A THR* 3.8 0.6 + - + -
316A GLN* 1.3 79.8 - - - +
318A LEU* 1.3 60.1 + - - +
319A VAL* 3.7 16.2 - - + -
405A PHE* 3.5 25.6 - - + -
406A THR* 4.6 3.8 - - - -
409A PHE* 3.5 46.2 - - + -
415A ASN 3.3 3.4 + - - -
416A ALA* 3.3 22.7 - - + -
417A PHE* 2.9 28.4 + - - -
474A PHE* 3.7 3.8 - - - -
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Residues in contact with LEU 318 (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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220A ALA 2.9 6.1 + - - -
221A ILE* 3.2 13.4 - - + +
222A LEU* 2.7 32.6 + - - +
317A ILE* 1.3 72.9 - - - +
319A VAL* 1.3 59.4 + - - +
417A PHE* 3.4 10.3 - - + +
419A TYR* 3.6 31.4 - - + -
471A TRP* 4.0 23.8 - - + -
474A PHE* 3.7 46.0 - - + -
480A PRO* 3.8 15.7 - - + -
490A TRP* 3.7 16.2 - - + -
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Residues in contact with VAL 319 (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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222A LEU* 3.6 23.6 - - + +
225A GLY 5.5 1.6 - - - +
226A SER* 6.2 0.2 - - - -
317A ILE* 3.7 30.3 - - + -
318A LEU* 1.3 80.4 - - - +
320A GLY* 1.3 61.8 + - - +
402A ALA* 4.1 16.4 - - + +
405A PHE* 4.5 7.9 - - + -
406A THR* 3.4 29.2 - - + +
417A PHE 2.8 8.7 + - - +
418A PHE* 3.1 23.9 - - + -
419A TYR* 2.9 27.6 + - - -
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Residues in contact with GLY 320 (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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222A LEU 3.3 6.2 + - - +
224A SER* 2.9 25.3 + - - -
319A VAL* 1.3 81.3 - - - +
321A VAL* 1.3 69.7 - - - +
402A ALA* 4.9 0.3 - - - +
418A PHE* 4.0 5.6 - - - -
419A TYR* 3.2 33.0 - - - -
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Residues in contact with VAL 321 (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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224A SER* 4.0 9.4 - - - -
320A GLY* 1.3 80.8 - - - +
322A ASN* 1.3 67.5 + - - +
325A GLU* 3.4 12.3 - - - +
398A PHE 4.3 2.9 - - - +
399A ILE* 3.9 34.5 - - + +
402A ALA* 3.8 25.8 - - + -
418A PHE* 4.2 6.3 - - + -
419A TYR* 3.4 4.3 + - - -
420A TYR* 3.5 23.4 - - + -
421A PHE* 2.9 25.1 + - - +
514A LEU* 4.1 12.6 - - + -
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Residues in contact with ASN 322 (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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224A SER* 4.2 1.9 + - - -
321A VAL* 1.3 76.2 - - - +
323A LYS* 1.3 65.6 + - - +
324A ASP 3.3 0.4 - - - -
325A GLU* 2.7 37.7 + - + +
399A ILE* 4.0 8.5 - - - +
419A TYR* 4.5 1.6 - - - -
420A TYR* 4.4 2.5 - - - -
421A PHE* 3.2 33.9 - - - +
436A VAL* 3.7 15.7 - - + +
437A MET 3.0 21.9 + - - +
438A HIS* 4.0 1.2 - - - +
439A GLY 3.6 6.7 - - - +
440A TYR 3.9 1.4 - - - +
441A GLU* 2.8 35.8 + - - +
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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