Contacts of the strand formed by residues 295 - 300 (chain B) in PDB entry 1E8U
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 TRP 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ALA 3.3 1.0 - - - +
267B PRO* 3.5 12.5 - - - +
292B PHE* 2.9 39.6 + + + +
293B GLU 3.2 1.2 + - - -
294B ASP* 1.3 90.2 - - + +
296B VAL* 1.3 60.0 + - - +
297B ALA 3.3 22.2 - - - +
298B ASN* 3.8 21.1 - - + +
316B VAL* 5.2 1.8 - - + -
317B TYR* 4.0 3.6 - - - -
318B GLY 3.6 28.5 - - - -
319B GLY 3.3 11.0 - - - -
320B LEU* 3.4 20.0 - - + +
321B LYS* 2.8 26.1 + - - -
326B SER* 4.9 4.0 + - - -
370B GLN* 3.7 25.8 - - + -
372B ALA* 3.8 27.1 - - + -
388B LEU* 3.6 19.3 - - + +
390B VAL* 4.3 10.6 - - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ASP* 2.7 11.6 - - - +
262B TYR* 3.8 24.9 - - + +
264B SER 3.6 8.5 - - - +
265B ALA* 3.6 17.7 - - - +
266B VAL 3.0 2.9 - - - +
267B PRO* 4.3 0.9 - - - -
295B TRP* 1.3 73.3 - - - +
297B ALA* 1.3 54.2 + - + +
319B GLY* 2.8 26.6 + - - +
320B LEU 4.1 1.8 - - - +
321B LYS* 3.7 34.3 - - + -
322B PRO* 4.7 2.2 - - + -
367B LYS* 4.3 22.9 - - + +
1003B CA 2.2 32.8 - - - -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ASP* 3.2 23.6 - - - +
262B TYR* 3.5 46.4 - - + +
268B THR* 3.4 2.9 - - - -
295B TRP* 3.3 9.7 - - - -
296B VAL* 1.3 79.3 - - - +
298B ASN* 1.3 62.9 + - - +
299B TYR* 4.4 2.0 - - + -
318B GLY* 3.1 3.4 - - - -
319B GLY 2.8 22.2 + - - -
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Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B SER* 3.0 13.7 + - - -
267B PRO* 3.6 9.4 - - - +
268B THR* 2.9 57.7 + - - -
270B MET* 3.6 18.7 - - - +
292B PHE* 3.6 40.3 - - + +
295B TRP* 3.8 9.9 - - + +
297B ALA* 1.3 79.2 - - - +
299B TYR* 1.3 64.8 + - - +
316B VAL* 5.8 0.9 - - + -
317B TYR 3.3 8.7 - - - +
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B LYS* 3.7 25.2 - - + +
237B SER* 3.8 10.3 - - - +
252B SER* 3.3 26.2 - - - -
254B VAL* 3.8 11.5 - - + +
256B GLU 5.2 0.2 + - - -
257B THR 4.9 0.9 + - - -
258B GLU* 4.3 12.3 + - + -
261B ASP* 2.8 33.8 + - - +
262B TYR* 4.4 17.0 - + - -
268B THR* 4.1 4.3 - - + -
270B MET* 3.9 5.6 - - - +
297B ALA* 4.4 9.2 - - + -
298B ASN* 1.3 82.2 - - - +
300B PRO* 1.3 79.5 - - + +
316B VAL* 3.3 3.9 - - - +
317B TYR* 2.8 46.7 + + + -
1573B SLB 3.6 23.6 - - + -
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Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B SER* 2.7 42.9 + - - +
239B SER* 3.8 13.0 - - - +
250B LEU* 3.2 37.2 - - + +
251B CYS* 3.8 3.1 - - - -
252B SER* 3.3 19.7 - - - +
270B MET* 3.5 18.4 - - + -
299B TYR* 1.3 88.5 - - + +
301B GLY* 1.3 59.3 + - - +
302B VAL 3.2 2.2 + - - -
315B SER 3.8 6.1 - - - +
316B VAL* 4.3 2.5 - - + -
317B TYR* 3.6 5.0 - - - -
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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