Contacts of the strand formed by residues 242 - 250 (chain B) in PDB entry 4EGA
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B VAL* 4.2 24.9 - - + -
240B LYS 3.5 3.4 + - - -
241B VAL* 1.3 68.3 - - - +
243B PHE* 1.3 57.4 + - - +
244B VAL* 4.1 15.7 - - + -
269B ILE* 3.8 15.5 - - + -
273B HIS* 3.1 57.7 - + + -
278B GLU* 4.5 1.8 - - + -
279B ARG 2.7 18.1 + - - +
280B VAL* 3.2 12.4 - - + +
281B PHE 2.7 32.6 + - - +
511B ASP* 3.5 34.5 - - + -
512B VAL* 4.0 16.2 - - + -
657B LEU* 6.1 0.7 - - + -
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Residues in contact with PHE 243 (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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240B LYS* 3.9 0.7 - - - +
241B VAL 3.9 2.2 - - - +
242B PHE* 1.3 74.1 - - - +
244B VAL* 1.3 59.5 + - - +
245B THR* 3.6 25.1 - - + -
281B PHE* 3.1 40.8 - + + +
283B LEU* 3.9 15.9 - - + -
481B TYR* 3.4 28.3 - - + -
485B SER* 4.0 14.8 - - - -
507B ARG* 3.3 37.9 - - + +
508B PHE* 4.4 4.5 - + - -
510B ALA* 3.5 27.4 - - + -
511B ASP* 2.8 39.1 + - - +
512B VAL 3.3 4.7 + - - -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.1 18.2 - - + -
243B PHE* 1.3 74.4 - - - +
245B THR* 1.3 70.9 + - - +
266B THR* 3.9 19.9 - - + +
269B ILE* 3.9 19.5 - - + -
270B GLY* 4.0 21.5 - - - +
280B VAL* 4.7 1.8 - - + -
281B PHE 3.1 6.6 + - - +
282B ALA* 3.2 23.1 - - + +
283B LEU 3.1 22.3 + - - -
512B VAL* 3.2 16.4 - - + +
514B VAL* 4.3 3.6 - - + -
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Residues in contact with THR 245 (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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243B PHE* 3.6 36.6 - - + -
244B VAL* 1.3 79.0 - - - +
246B SER* 1.3 60.7 + - - +
266B THR* 2.8 15.3 + - - -
283B LEU* 3.5 11.0 - - + -
481B TYR* 3.2 29.6 + - + -
510B ALA* 4.3 2.2 - - + -
512B VAL 3.0 6.9 + - - -
513B HIS* 2.7 33.4 + - + +
514B VAL* 3.0 23.7 + - - +
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Residues in contact with SER 246 (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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245B THR* 1.3 75.8 - - - +
247B PRO* 1.3 78.0 + - - +
248B ILE* 3.7 1.4 + - - +
249B TYR* 3.2 15.1 + - - -
262B SER 4.6 0.2 - - - -
263B THR* 4.0 8.3 - - - -
266B THR* 3.3 17.4 + - - -
283B LEU* 2.9 12.2 + - - +
284B THR* 2.7 34.0 + - - -
480B ASN* 5.0 0.2 - - - +
481B TYR* 3.5 17.5 - - - -
514B VAL 3.8 3.1 - - - -
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Residues in contact with PRO 247 (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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246B SER* 1.3 103.2 + - - +
248B ILE* 1.3 64.0 + - - +
249B TYR* 3.0 35.6 - - + +
262B SER* 4.0 12.8 - - - +
284B THR* 4.1 0.5 + - - -
481B TYR* 3.6 12.1 - - - +
514B VAL 3.1 17.9 - - - +
515B ILE* 3.9 14.6 - - + -
516B GLY 4.7 1.8 - - - +
519B ILE* 3.9 22.7 - - + -
813B 0P8 4.0 6.1 - - + -
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Residues in contact with ILE 248 (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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246B SER 3.7 1.7 + - - +
247B PRO* 1.3 75.8 - - - +
249B TYR* 1.3 61.3 + - - +
250B TYR 4.3 0.5 + - - -
284B THR* 4.3 1.6 - - - -
285B GLY* 3.0 28.5 - - - +
286B THR 3.8 2.9 - - - +
287B ASP* 3.5 26.7 - - + +
330B ILE* 3.8 15.7 - - + -
332B THR* 3.5 25.4 - - + -
477B ALA* 3.7 23.3 - - + +
480B ASN* 3.5 32.8 - - + +
481B TYR* 4.7 0.4 + - - -
812B SO4 4.5 2.6 + - - -
813B 0P8 3.8 26.5 - - + +
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Residues in contact with TYR 249 (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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246B SER* 3.2 14.7 + - - -
247B PRO* 3.0 33.2 - - + +
248B ILE* 1.3 73.5 - - - +
250B TYR* 1.3 61.7 + - - +
251B VAL 3.6 1.4 + - - -
259B HIS* 3.4 28.9 - + + -
262B SER* 3.4 17.1 - - - -
263B THR* 2.8 23.1 + - - -
284B THR* 3.4 17.3 - - - -
285B GLY 2.8 24.7 + - - +
286B THR* 3.3 9.6 - - + +
287B ASP* 2.8 20.0 + - - -
315B PHE* 3.6 33.0 - + + -
319B PHE* 3.8 7.9 - + - -
812B SO4 3.1 20.0 - - - +
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Residues in contact with TYR 250 (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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248B ILE 4.3 0.2 + - - -
249B TYR* 1.3 70.8 - - - +
251B VAL* 1.3 58.1 + - - +
252B ASN* 3.2 42.3 + - + +
253B ALA* 3.8 13.2 + - - +
259B HIS* 5.1 1.0 + - - -
287B ASP* 3.0 21.7 - - - +
289B HIS 2.6 29.7 + - - -
290B GLY* 3.6 8.8 - - - -
292B LYS* 4.1 17.9 + - + +
293B VAL* 3.4 25.8 + - + +
315B PHE* 4.3 6.6 - - - -
812B SO4 3.1 29.8 + - - +
813B 0P8 3.1 56.7 + + + -
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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