Contacts of the strand formed by residues 394 - 400 (chain A) in PDB entry 1BY7
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 PHE 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A PHE* 4.5 0.2 - + - -
266A LEU* 3.9 28.7 - - + -
267A LEU 3.1 21.1 - - - +
268A LEU* 4.1 9.0 - - + -
279A LEU* 3.9 10.4 - - - +
309A ILE* 5.6 0.2 - - + -
310A PRO* 4.1 12.3 - - + -
312A PHE* 4.1 17.9 - + - -
388A PHE* 5.8 0.2 - + - -
390A ALA* 3.7 25.8 - - + -
392A HIS 3.5 14.6 - - - -
393A PRO* 1.3 75.5 - - - +
395A LEU* 1.3 72.4 + - - +
396A PHE* 3.9 19.5 - + + -
411A ARG* 3.7 1.0 - - - -
412A PHE* 3.1 62.8 + + + -
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Residues in contact with LEU 395 (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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16A PHE* 3.7 30.3 - - + -
266A LEU* 3.5 1.6 - - - -
267A LEU* 2.8 47.7 + - + +
279A LEU* 4.0 10.5 - - + +
282A LEU* 4.5 19.7 - - + -
283A GLU* 3.8 33.2 - - + +
286A ILE* 4.9 12.1 - - + -
394A PHE* 1.3 76.7 - - - +
396A PHE* 1.3 63.5 + - - +
409A PHE* 4.9 15.5 - - + -
410A GLY 3.4 6.3 - - - +
411A ARG* 3.8 19.1 - - + -
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Residues in contact with PHE 396 (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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29A PHE* 3.6 38.1 - + - -
264A MET* 3.8 36.1 - - + -
265A PHE 3.1 11.9 - - - +
266A LEU* 4.4 1.8 - - + -
267A LEU* 4.9 1.3 - - - -
312A PHE* 4.0 11.2 - + - -
314A LEU* 3.8 20.9 - - + -
360A VAL* 4.5 4.7 - - + -
394A PHE* 3.9 24.9 - + + -
395A LEU* 1.3 77.6 - - - +
397A LEU* 1.3 70.9 - - - +
398A ILE* 4.5 5.6 - - + -
408A PHE* 6.1 0.2 - - + -
409A PHE* 3.6 4.7 - - - -
410A GLY* 2.9 51.8 + - - +
411A ARG 4.1 1.1 - - - -
412A PHE* 4.1 12.8 - - + -
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Residues in contact with LEU 397 (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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264A MET* 3.1 6.3 - - - +
265A PHE* 2.8 66.7 + - + +
267A LEU* 4.8 6.5 - - + -
291A LEU* 3.7 39.3 - - + -
295A THR* 5.9 1.1 - - + -
396A PHE* 1.3 79.1 - - - +
398A ILE* 1.3 65.7 + - - +
399A MET* 4.0 22.2 - - + -
406A ILE* 4.4 8.3 - - + -
408A PHE 3.3 13.9 - - - +
409A PHE* 3.6 22.9 - - + +
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Residues in contact with ILE 398 (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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29A PHE* 4.8 0.2 - - + -
204A PHE* 3.6 35.2 - - + -
258A TYR* 4.2 9.2 - - + +
262A VAL* 3.5 28.0 - - + -
263A SER 3.4 3.8 - - - +
264A MET* 4.2 22.9 - - + -
360A VAL* 4.4 10.8 - - + -
396A PHE* 4.5 7.6 - - + -
397A LEU* 1.3 78.5 - - - +
399A MET* 1.3 52.6 + - - +
406A ILE* 3.6 2.9 - - - -
407A LEU* 2.7 36.0 + - + -
408A PHE* 3.1 38.4 + - + -
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Residues in contact with MET 399 (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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262A VAL* 3.2 9.2 - - - -
263A SER 2.8 41.6 + - - +
265A PHE* 4.0 24.2 - - + -
291A LEU* 5.7 2.5 - - + -
295A THR* 6.1 4.5 - - + +
397A LEU* 4.0 14.1 - - + -
398A ILE* 1.3 73.7 - - - +
400A HIS* 1.3 66.6 - - - +
401A LYS* 3.3 11.5 + - + +
404A ASN* 3.5 38.8 - - - +
405A CYS 3.5 17.7 - - - +
406A ILE* 3.6 24.0 - - + -
407A LEU* 4.8 0.7 - - - -
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Residues in contact with HIS 400 (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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113A ALA* 3.8 16.1 + - + -
114A ILE* 3.7 32.4 + - + -
123A LEU* 6.4 0.4 - - + -
260A GLY 5.2 4.6 + - - -
261A ASP 4.1 3.3 + - - -
262A VAL* 3.9 22.0 - - + -
399A MET* 1.3 69.3 - - - +
401A LYS* 1.3 59.3 + - - +
402A ILE* 3.8 26.6 - - + +
403A THR* 2.7 35.8 + - + +
404A ASN* 2.7 30.1 + - - -
405A CYS* 2.9 16.5 + - + +
407A LEU* 4.2 17.7 - - + +
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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