Contacts of the strand formed by residues 405 - 412 (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 CYS 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU 4.8 1.3 - - - -
5A CYS* 2.0 50.7 - - - +
8A ASN* 4.3 14.1 - - - -
33A TRP* 4.8 7.0 - - + -
110A LEU* 4.5 3.6 - - - -
114A ILE* 4.0 20.6 - - + -
399A MET* 3.5 2.7 - - - +
400A HIS* 2.9 34.3 + - + +
403A THR* 3.2 10.0 - - - +
404A ASN* 1.3 78.3 - - - +
406A ILE* 1.3 65.9 + - - +
407A LEU* 3.2 4.0 + - + +
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Residues in contact with ILE 406 (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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8A ASN* 3.0 27.4 + - - +
9A THR* 3.3 38.8 + - + +
12A ALA* 5.1 4.3 - - + -
13A LEU* 5.9 1.1 - - + -
32A PRO* 4.1 13.0 - - + +
33A TRP* 3.5 9.2 + - - +
291A LEU* 4.3 15.9 - - + -
397A LEU* 4.4 12.8 - - + -
398A ILE 3.7 5.6 - - - +
399A MET* 3.6 28.0 - - + -
404A ASN 3.9 0.6 + - - -
405A CYS* 1.3 71.6 - - - +
407A LEU* 1.3 62.8 + - - +
408A PHE 3.1 30.3 - - - +
409A PHE* 4.5 9.2 - - + -
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Residues in contact with LEU 407 (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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31A SER* 2.7 32.6 + - - -
32A PRO* 3.5 1.6 - - - +
33A TRP* 3.8 35.6 + - + -
114A ILE* 4.0 21.5 - - + -
123A LEU* 4.3 21.5 - - + -
204A PHE* 5.4 2.0 - - + -
262A VAL* 4.4 21.3 - - + -
398A ILE* 2.7 14.8 + - + +
400A HIS* 4.2 22.7 - - + +
405A CYS* 4.0 11.4 - - + +
406A ILE* 1.3 75.8 - - - +
408A PHE* 1.3 76.0 + - + +
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Residues in contact with PHE 408 (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* 3.4 39.0 - + + -
30A LEU 3.2 10.5 - - - +
31A SER* 3.6 25.4 - - - -
32A PRO* 3.7 1.3 - - - -
33A TRP* 5.5 0.4 - + - -
123A LEU* 3.6 26.2 - - + -
202A VAL* 3.8 24.0 - - + -
204A PHE* 3.5 31.0 - + + -
358A ALA* 4.7 2.5 - - + -
359A MET 4.9 0.4 - - - -
396A PHE* 6.2 0.2 - - - -
397A LEU* 3.3 1.2 - - - -
398A ILE* 3.1 47.2 + - + -
406A ILE* 3.1 13.2 - - - +
407A LEU* 1.3 90.6 - - + +
409A PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 409 (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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12A ALA* 5.3 6.1 - - + -
13A LEU* 4.0 28.5 - - + -
16A PHE* 3.6 50.7 - + + -
28A LEU* 4.4 0.7 - - - +
29A PHE* 3.7 5.2 - - - -
30A LEU* 2.9 38.3 + - + +
32A PRO* 3.8 17.7 - - + +
267A LEU* 6.4 1.1 - - + -
286A ILE* 4.2 15.0 - - + -
291A LEU* 4.9 1.3 - - + -
395A LEU* 4.9 12.6 - - + -
396A PHE 3.6 6.7 - - - -
397A LEU* 3.6 35.0 - - + -
406A ILE* 4.5 9.6 - - + -
408A PHE* 1.3 74.7 - - - +
410A GLY* 1.3 68.9 + - - +
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Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.9 0.4 - - - -
28A LEU* 3.0 18.2 - - - -
29A PHE* 4.1 4.0 - - - -
395A LEU* 3.4 8.4 - - - +
396A PHE* 2.9 47.3 + - - +
409A PHE* 1.3 83.6 - - - +
411A ARG* 1.3 61.2 + - - -
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Residues in contact with ARG 411 (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* 4.0 6.6 - - + -
20A ALA* 3.5 13.3 - - - +
23A SER* 2.7 33.3 + - - -
24A PRO 3.4 12.8 + - - -
25A THR* 3.5 18.7 - - - +
26A GLN 2.8 34.1 + - - -
27A ASN* 3.3 7.4 - - - +
28A LEU* 2.8 48.5 + - + +
277A THR* 4.7 2.6 - - - +
279A LEU* 3.6 28.7 - - + -
283A GLU* 2.8 37.2 + - - -
314A LEU* 4.3 2.8 - - - +
394A PHE 3.7 4.3 - - - -
395A LEU* 3.8 9.2 - - + -
396A PHE* 4.3 1.8 - - - -
410A GLY* 1.3 73.8 - - - -
412A PHE* 1.3 61.6 + - - +
413A SER* 4.2 3.8 - - - -
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Residues in contact with PHE 412 (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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27A ASN* 3.7 5.4 - - - -
222A PHE* 3.7 30.5 - + - -
232A VAL* 5.3 0.2 - - + -
310A PRO* 3.9 13.7 - - + -
311A GLN 5.2 0.4 - - - -
312A PHE* 3.5 42.6 - + + -
313A LYS 5.5 0.2 - - - -
314A LEU* 3.9 19.1 - - + -
393A PRO* 3.2 5.5 - - - +
394A PHE* 3.1 64.3 + + + -
396A PHE* 4.1 10.2 - - + -
411A ARG* 1.3 72.1 - - - +
413A SER* 1.3 60.3 + - - +
414A SER 4.5 1.1 - - - -
415A PRO* 3.8 36.3 - - + -
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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