Contacts of the strand formed by residues 353 - 362 (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 GLU 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A SER 5.6 3.8 - - - +
196A MET 3.6 1.0 + - - -
197A VAL* 3.4 6.6 - - + +
198A LEU 3.1 23.7 + - - +
319A GLU* 3.6 24.5 - - + +
320A LEU 3.2 4.0 + - - -
321A ARG* 2.8 52.9 + - - +
333A PHE* 4.4 5.4 - - - -
351A LEU* 3.5 4.8 - - - +
352A SER* 1.3 86.9 - - - +
354A VAL* 1.3 80.7 + - - +
355A PHE* 3.5 39.3 - - + -
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Residues in contact with VAL 354 (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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35A ILE* 5.7 3.4 - - + -
38A THR* 5.9 0.7 - - - +
39A MET* 3.9 26.9 - - + -
198A LEU* 3.3 24.9 - - + +
200A ASN* 5.9 2.9 - - + -
318A TYR 3.6 0.5 - - - +
319A GLU* 3.3 3.5 - - - -
320A LEU* 2.9 49.7 + - + +
321A ARG 4.7 0.2 - - - +
324A LEU* 4.2 10.3 - - + -
333A PHE* 4.2 3.6 - - + -
351A LEU* 4.0 16.6 - - + -
353A GLU* 1.3 86.6 + - - +
355A PHE* 1.3 69.9 - - - +
356A HIS* 3.9 2.8 + - + +
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Residues in contact with PHE 355 (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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184A LEU* 3.9 29.1 - - + +
185A LEU* 3.7 31.6 - - + -
186A PRO* 4.3 5.2 - - + -
189A SER* 3.8 32.3 - - - -
190A VAL* 5.0 0.2 - - + -
197A VAL* 4.2 15.5 - - + -
198A LEU 2.8 16.8 + - - +
199A VAL* 3.5 5.8 - - + -
200A ASN* 2.9 29.1 + - - +
318A TYR 3.5 4.5 - - - +
319A GLU* 3.7 37.2 - - + -
353A GLU* 3.5 27.1 - - + -
354A VAL* 1.3 76.2 - - - +
356A HIS* 1.3 59.1 + - - +
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Residues in contact with HIS 356 (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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30A LEU* 3.7 22.2 - - + +
31A SER* 2.9 29.6 + - - -
34A SER* 3.5 10.1 - - - -
35A ILE* 3.6 20.6 - - + +
184A LEU* 5.2 1.6 - - - -
200A ASN* 2.9 36.6 + - + +
202A VAL* 4.4 1.6 - - + -
317A HIS* 3.4 2.8 - - - +
318A TYR* 2.9 48.2 + + + +
320A LEU* 4.0 21.8 - - + -
354A VAL* 3.9 3.3 + - + -
355A PHE* 1.3 72.2 - - - +
357A GLN* 1.3 74.4 + - - +
358A ALA* 4.0 3.4 - - + +
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Residues in contact with GLN 357 (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* 2.8 35.3 - - + +
184A LEU* 3.8 16.2 - - + +
200A ASN 2.8 12.1 + - - +
201A ALA* 3.1 9.0 - - + -
202A VAL 2.7 26.3 + - - -
315A GLU* 2.3 35.8 + - + -
316A GLU 3.5 10.5 - - - +
317A HIS* 2.6 39.1 + - + +
356A HIS* 1.3 81.2 - - - +
358A ALA* 1.4 64.6 + - - +
359A MET* 3.1 8.2 - - + -
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Residues in contact with ALA 358 (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 37.4 + - + +
30A LEU* 3.7 17.5 - - - -
31A SER* 4.1 1.3 - - - +
202A VAL* 3.5 5.4 - - + +
315A GLU* 3.5 2.1 - - - -
316A GLU 3.1 32.1 + - - -
356A HIS* 4.0 8.6 - - + +
357A GLN* 1.4 76.1 - - - +
359A MET* 1.3 65.5 + - - +
408A PHE* 4.6 6.1 - - + -
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Residues in contact with MET 359 (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 5.7 - - - -
180A LYS* 3.3 51.1 - - + +
181A ILE* 3.3 11.9 - - - -
202A VAL 3.0 16.0 + - - +
203A TYR* 3.4 20.8 - - + -
204A PHE* 3.0 24.3 + - - +
314A LEU 3.1 11.0 - - - +
315A GLU* 3.8 16.6 - - + +
357A GLN* 3.1 30.5 - - + +
358A ALA* 1.3 78.9 - - - +
360A VAL* 1.3 63.5 + - - +
361A ASP* 5.9 0.4 - - - +
408A PHE* 4.9 0.9 - - - -
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Residues in contact with VAL 360 (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 38.6 - - + -
204A PHE* 3.2 31.4 - - + +
258A TYR* 5.1 0.4 - - - +
312A PHE* 4.4 16.4 - - + -
313A LYS* 3.3 3.3 - - - +
314A LEU* 2.7 45.2 + - + +
359A MET* 1.3 75.7 - - - +
361A ASP* 1.3 72.3 + - - +
362A VAL* 4.0 16.6 - - + -
396A PHE* 4.5 2.5 - - + -
398A ILE* 4.4 6.5 - - + -
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Residues in contact with ASP 361 (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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203A TYR* 2.2 39.8 + - - +
204A PHE 3.2 4.0 + - - -
205A LYS* 3.5 38.0 + - + +
206A GLY 4.9 1.4 + - - +
258A TYR* 5.6 0.5 + - - -
312A PHE 3.8 2.9 - - - -
313A LYS* 2.9 42.1 - - + +
359A MET* 5.9 0.5 - - - +
360A VAL* 1.3 79.8 - - - +
362A VAL* 1.3 63.9 + - - +
363A ASN* 3.9 4.0 + - + +
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Residues in contact with VAL 362 (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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208A TRP* 4.1 21.8 - - + +
235A MET* 4.2 15.5 - - + -
258A TYR* 4.4 4.5 - - - +
264A MET* 3.9 19.7 - - + -
309A ILE* 4.4 3.8 - - + -
310A PRO 4.2 0.4 - - - +
311A GLN* 3.3 7.1 - - - +
312A PHE* 2.5 86.0 + - + +
313A LYS* 4.9 0.4 - - - +
360A VAL* 4.0 13.7 - - + -
361A ASP* 1.3 77.0 - - - +
363A ASN* 1.3 60.3 - - - +
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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