Contacts of the strand formed by residues 300 - 310 (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 MET 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ASN* 3.4 40.2 + - + +
243A ILE 3.5 5.8 - - - +
244A GLY 4.1 1.8 - - - +
253A ILE* 3.6 29.4 - - + +
254A LEU 3.8 3.4 - - - -
255A GLU* 3.5 26.7 - - + +
265A PHE* 3.8 23.3 - - + -
294A TRP 3.1 27.1 - - - +
295A THR* 3.8 9.9 - - - +
296A SER 2.9 10.2 + - - +
297A LYS* 2.9 21.7 - - - +
299A LYS* 1.3 79.2 - - - +
301A ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 301 (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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242A ASN* 3.9 1.6 - - - -
243A ILE* 2.9 34.5 + - - +
297A LYS* 4.5 6.1 - - - +
298A ASP 5.7 2.9 - - - +
299A LYS 4.0 1.8 - - - -
300A MET* 1.3 74.7 - - - +
302A GLU* 1.3 70.0 + - - +
303A ASP* 3.5 2.0 + - + +
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Residues in contact with GLU 302 (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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240A LYS* 3.3 45.6 - - + +
241A LEU* 3.4 8.9 - - - +
242A ASN* 3.4 20.7 + - - +
301A ALA* 1.3 78.4 - - - +
303A ASP* 1.3 68.7 + - - +
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Residues in contact with ASP 303 (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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240A LYS* 3.1 5.2 - - - -
241A LEU 2.8 31.2 + - - +
243A ILE* 4.2 20.6 - - + +
301A ALA* 4.2 0.9 - - + +
302A GLU* 1.3 80.6 - - - +
304A GLU* 1.3 82.2 + - - +
305A VAL* 3.3 3.5 + - - +
386A PRO* 3.7 24.3 - - + +
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Residues in contact with GLU 304 (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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238A ARG* 2.9 42.3 + - + -
239A GLU* 3.6 11.9 - - - +
240A LYS* 4.1 24.5 + - + +
303A ASP* 1.3 78.7 + - - +
305A VAL* 1.3 58.6 + - - +
306A GLU* 5.8 0.5 - - - +
385A GLY* 4.3 4.5 - - - -
386A PRO* 3.2 22.9 - - - +
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Residues in contact with VAL 305 (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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237A LEU 3.7 1.2 - - - +
238A ARG* 3.4 2.9 - - - +
239A GLU 2.9 27.8 + - - +
241A LEU* 3.9 23.6 - - + +
243A ILE* 3.8 35.2 - - + -
254A LEU* 4.4 2.5 - - + -
303A ASP 3.5 17.0 - - - +
304A GLU* 1.3 75.8 - - - +
306A GLU* 1.3 78.2 - - - +
307A VAL* 3.9 15.1 + - + +
386A PRO* 3.3 20.4 - - + +
388A PHE* 4.1 7.0 - - + +
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Residues in contact with GLU 306 (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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236A TYR* 2.3 42.4 + - + +
237A LEU 3.5 4.3 - - - -
238A ARG* 3.4 42.3 + - + +
304A GLU 5.8 0.4 - - - +
305A VAL* 1.3 74.7 - - - +
307A VAL* 1.3 59.8 + - - +
308A TYR* 4.5 11.1 + - + -
385A GLY* 5.6 2.7 + - - -
386A PRO 2.9 12.1 + - - +
387A GLN* 3.5 29.9 + - - +
388A PHE 3.0 25.3 + - - +
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Residues in contact with VAL 307 (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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212A PHE* 3.9 20.5 - - + -
235A MET 3.6 0.5 - - - +
236A TYR* 3.3 8.4 - - - -
237A LEU* 2.6 38.2 + - + +
241A LEU* 3.7 29.8 - - + -
254A LEU* 3.9 24.2 - - + -
256A LEU* 4.6 0.9 - - + -
305A VAL* 4.0 11.2 - - + +
306A GLU* 1.3 79.4 - - - +
308A TYR* 1.3 65.7 - - - +
309A ILE* 3.7 24.7 - - + -
388A PHE* 3.6 6.3 - - + +
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Residues in contact with TYR 308 (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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215A LYS* 3.7 14.3 + - + -
220A TYR* 3.6 35.4 - + + -
234A MET* 4.1 13.9 - - + -
235A MET 3.4 7.4 - - - +
236A TYR* 3.4 42.5 - + + -
306A GLU* 4.5 13.7 + - + -
307A VAL* 1.3 78.9 - - - +
309A ILE* 1.3 61.6 + - - +
387A GLN* 4.9 9.9 - - + -
388A PHE 2.8 16.4 + - - +
389A VAL* 4.2 21.8 - - + -
390A ALA 2.6 31.5 + - - -
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Residues in contact with ILE 309 (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* 4.6 2.9 - - + -
212A PHE* 3.7 27.6 - - + -
234A MET* 3.4 4.9 - - - -
235A MET* 2.9 53.3 + - + +
256A LEU* 4.2 11.9 - - + -
264A MET* 5.7 1.3 - - - -
266A LEU* 4.1 22.2 - - + -
307A VAL* 3.7 16.8 - - + -
308A TYR* 1.3 79.1 - - - +
310A PRO* 1.3 76.5 - - + +
312A PHE* 5.3 3.1 - - + -
362A VAL* 4.4 11.2 - - + -
388A PHE* 4.4 5.2 - - + -
390A ALA* 4.0 11.4 - - + -
394A PHE* 5.6 0.4 - - + -
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Residues in contact with PRO 310 (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 PHE* 4.0 7.2 - - + -
232A VAL* 4.0 24.2 - - + -
233A GLN 3.6 7.0 - - - +
234A MET* 3.5 4.6 - - + -
235A MET* 3.4 10.7 - - - +
309A ILE* 1.3 95.5 - - + +
311A GLN* 1.3 67.4 + - - +
312A PHE* 3.4 17.2 - - + -
362A VAL* 4.2 0.7 - - - +
390A ALA* 3.4 26.7 - - + +
394A PHE* 4.1 10.3 - - + -
412A PHE* 3.9 26.0 - - + -
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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