Contacts of the strand formed by residues 312 - 319 (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 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A MET* 4.7 5.6 - - + -
266A LEU* 6.2 0.2 - - + -
309A ILE* 5.3 3.6 - - + -
310A PRO* 3.4 19.7 - - + -
311A GLN* 1.3 77.5 - - - +
313A LYS* 1.3 64.2 + - - +
314A LEU* 3.9 16.6 - - + -
360A VAL* 4.4 3.6 - - + -
361A ASP* 3.8 0.3 - - - -
362A VAL* 2.5 79.7 + - + +
394A PHE* 4.1 23.1 - + - -
396A PHE* 4.0 32.8 - + - -
412A PHE* 3.5 40.4 - + + -
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Residues in contact with LYS 313 (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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205A LYS* 6.1 1.1 - - - +
312A PHE* 1.3 80.3 - - - +
314A LEU* 1.3 70.6 + - - +
360A VAL 3.3 4.7 - - - -
361A ASP* 2.9 36.6 - - - +
362A VAL 4.9 0.2 - - - +
412A PHE* 5.5 0.2 - - - -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.5 37.9 - - + +
28A LEU 4.2 6.7 - - - +
29A PHE* 3.9 23.6 - - + -
312A PHE* 3.9 13.2 - - + -
313A LYS* 1.3 82.7 - - - +
315A GLU* 1.3 59.7 + - - +
316A GLU* 4.3 4.0 - - + +
358A ALA 4.4 0.2 - - - -
359A MET* 3.1 6.7 - - - +
360A VAL* 2.7 40.4 + - + +
396A PHE* 3.8 33.7 - - + -
411A ARG 4.3 6.1 - - - +
412A PHE* 3.9 14.1 - - + -
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Residues in contact with GLU 315 (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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180A LYS* 4.4 7.1 - - - +
181A ILE* 3.9 5.2 - - - +
314A LEU* 1.3 75.5 - - - +
316A GLU* 1.3 71.3 + - - +
317A HIS* 3.0 21.7 + - + -
357A GLN* 2.3 37.3 + - - +
358A ALA 3.5 4.3 - - - -
359A MET* 3.8 18.3 - - + +
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Residues in contact with GLU 316 (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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26A GLN* 3.3 26.3 + - - +
27A ASN* 3.6 30.3 + - + +
28A LEU* 4.3 0.4 - - - -
29A PHE* 3.7 20.4 - - + +
314A LEU* 4.3 3.6 - - + +
315A GLU* 1.3 82.8 + - - +
317A HIS* 1.3 68.5 + - - +
318A TYR* 3.3 37.4 + - + +
356A HIS 4.0 0.7 - - - +
357A GLN* 3.5 3.6 - - - +
358A ALA 3.1 31.3 + - - -
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Residues in contact with HIS 317 (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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181A ILE* 4.6 6.7 - - + +
183A ASN 5.5 1.9 + - - -
184A LEU* 4.6 20.4 - - + +
315A GLU* 3.0 29.0 + - + +
316A GLU* 1.3 82.5 + - - +
318A TYR* 1.3 70.0 + - - +
356A HIS 3.4 6.7 - - - +
357A GLN* 2.6 32.2 + - + +
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Residues in contact with TYR 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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19A LEU* 3.8 36.6 - - + -
23A SER* 5.9 4.3 - - - -
26A GLN* 6.2 1.3 - - - -
27A ASN 4.4 0.9 + - - -
28A LEU* 3.5 11.5 - - + +
29A PHE 3.2 44.7 + - - -
30A LEU* 4.4 5.6 - - + -
316A GLU* 3.3 29.8 + - + +
317A HIS* 1.3 81.1 - - - +
319A GLU* 1.3 66.4 + - - +
320A LEU* 3.5 24.9 - - + -
354A VAL 3.6 0.2 - - - +
355A PHE* 3.5 6.1 - - - +
356A HIS* 2.9 51.0 + + + +
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Residues in contact with GLU 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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186A PRO* 4.0 21.5 - - - +
189A SER* 5.3 3.4 - - - -
318A TYR* 1.3 74.4 - - - +
320A LEU* 1.3 58.9 + - - +
321A ARG 3.3 8.1 + - - -
322A SER* 4.6 5.0 + - - -
323A ILE* 4.8 4.9 - - - +
353A GLU* 3.4 19.9 - - - +
354A VAL 3.3 6.3 - - - -
355A PHE* 3.7 28.4 - - + -
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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