Contacts of the strand formed by residues 251 - 258 (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 ALA 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A TYR* 3.4 12.8 - - - -
246A ILE* 2.9 37.9 + - + +
249A LEU 4.0 8.5 - - - +
250A LYS* 1.3 76.8 - - - +
252A GLN* 1.3 62.8 + - - +
267A LEU* 5.8 0.2 - - + -
268A LEU 3.4 15.5 - - - +
269A PRO* 3.8 9.2 - - + -
270A ASP* 3.7 2.9 - - - +
282A LEU* 4.2 24.2 - - + -
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Residues in contact with GLN 252 (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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243A ILE* 3.7 21.5 - - + +
244A GLY 3.4 9.2 - - - +
245A TYR* 3.8 22.2 - - + -
246A ILE* 5.1 1.3 - - - +
251A ALA* 1.3 77.3 - - - +
253A ILE* 1.3 59.5 + - - +
266A LEU 3.8 0.2 - - - +
267A LEU* 3.5 3.1 - - - +
268A LEU* 2.9 44.3 + - - +
270A ASP* 4.8 7.4 - - + +
386A PRO* 5.1 2.2 - - - +
387A GLN 2.8 34.0 + - - +
388A PHE* 3.8 25.0 - - + -
389A VAL* 4.7 1.0 + - - +
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Residues in contact with ILE 253 (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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243A ILE* 3.3 5.0 - - - +
244A GLY* 2.8 50.9 + - - +
245A TYR 4.5 0.2 - - - +
246A ILE* 4.4 15.7 - - + -
252A GLN* 1.3 75.0 - - - +
254A LEU* 1.3 62.6 + - - +
265A PHE* 4.4 7.6 - - + -
266A LEU 3.2 10.8 - - - +
267A LEU* 4.0 23.8 - - + -
291A LEU* 4.9 0.9 - - + -
294A TRP* 3.9 29.6 - - + +
295A THR* 3.8 28.7 - - + -
299A LYS 5.4 0.2 - - - +
300A MET* 3.6 13.1 - - + +
388A PHE* 4.4 0.9 - - - -
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Residues in contact with LEU 254 (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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241A LEU* 4.0 17.7 - - + -
242A ASN 3.4 17.5 - - - +
243A ILE* 4.1 16.8 - - + -
253A ILE* 1.3 74.8 - - - +
255A GLU* 1.3 70.4 + - - +
256A LEU* 3.7 28.3 - - + -
264A MET 3.6 1.0 - - - +
265A PHE* 3.3 4.7 - - - -
266A LEU* 2.9 33.4 + - + +
300A MET* 3.8 4.3 - - - -
305A VAL* 4.4 4.0 - - + -
307A VAL* 3.9 16.2 - - + -
388A PHE* 3.8 44.4 - - + -
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Residues in contact with GLU 255 (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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241A LEU* 3.6 17.0 - - - +
242A ASN* 3.1 40.3 + - + +
254A LEU* 1.3 79.9 - - - +
256A LEU* 1.3 61.3 + - - +
257A PRO* 3.5 15.6 - - + +
263A SER* 2.6 34.1 + - - +
264A MET 3.4 3.8 - - - +
265A PHE* 3.8 25.8 - - + -
300A MET* 3.5 6.1 - - + +
401A LYS* 3.2 31.9 + - - -
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Residues in contact with LEU 256 (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* 3.3 31.3 - - + -
212A PHE* 3.7 32.5 - - + -
237A LEU* 4.5 5.6 - - + -
241A LEU* 3.7 26.0 - - + -
254A LEU* 3.7 30.0 - - + -
255A GLU* 1.3 67.6 - - - +
257A PRO* 1.4 70.5 - - + +
263A SER* 3.5 1.5 - - - -
264A MET 2.9 35.3 + - - +
266A LEU* 3.9 18.8 - - + -
307A VAL* 4.6 2.2 - - + -
309A ILE* 4.2 14.8 - - + -
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Residues in contact with PRO 257 (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* 3.5 9.3 - - - -
209A LYS* 3.0 46.1 + - + +
241A LEU* 3.7 18.8 - - + -
255A GLU* 3.5 18.4 - - + +
256A LEU* 1.4 86.0 - - + +
258A TYR* 1.3 64.3 + - - +
263A SER* 3.3 19.1 - - - +
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Residues in contact with TYR 258 (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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204A PHE* 3.5 24.2 - + + -
206A GLY* 3.6 40.5 + - - -
207A LYS 3.4 12.8 - - - +
208A TRP* 3.5 41.7 - + - -
209A LYS* 3.4 11.4 + - - -
256A LEU 3.6 0.4 + - - -
257A PRO* 1.3 79.3 - - - +
259A ALA* 1.3 69.4 + - - +
260A GLY 3.9 0.9 - - - +
261A ASP* 3.8 2.3 + - - -
262A VAL* 2.8 44.0 + - + +
263A SER 4.4 1.3 - - - -
264A MET* 3.3 41.8 - - + +
360A VAL* 5.1 0.5 - - - +
361A ASP 5.6 1.0 + - - -
362A VAL* 4.4 6.4 - - - +
398A ILE* 4.2 6.3 - - + +
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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