Contacts of the strand formed by residues 305 - 311 (chain B) in PDB entry 5NER
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 LEU 305 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B LEU* 3.8 28.5 - - + -
244B HIS 2.6 14.6 + - - +
245B LEU* 3.6 11.4 - - + -
246B LEU* 2.8 29.5 + - - +
303B ASN* 4.9 9.9 - - - +
304B VAL* 1.3 80.6 - - - +
306B LEU* 1.3 60.2 + - - +
307B ILE* 3.8 2.1 + - + +
326B PRO 4.7 2.2 - - - +
327B GLY* 3.8 31.0 - - - +
351B LEU* 3.7 32.5 - - + -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ILE* 4.2 17.7 - - + -
246B LEU* 3.5 31.9 - - + +
248B PHE* 4.1 21.1 - - + -
295B LEU* 5.9 2.0 - - + -
299B LEU* 3.7 32.5 - - + -
304B VAL 3.9 1.4 + - - -
305B LEU* 1.3 71.4 - - - +
307B ILE* 1.3 61.8 + - - +
308B PHE* 3.5 33.0 - - + -
325B ILE* 4.2 9.2 - - + +
327B GLY 3.8 5.9 + - - +
328B ALA* 3.2 13.4 - - + +
329B THR 3.0 26.0 + - - +
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Residues in contact with ILE 307 (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 LEU* 4.6 23.1 - - + -
246B LEU 2.8 16.8 + - - +
247B VAL* 3.5 21.0 - - + +
248B PHE* 2.8 28.1 + - - -
305B LEU* 4.5 5.6 - - + +
306B LEU* 1.3 74.6 - - - +
308B PHE* 1.3 66.2 + - - +
309B ALA* 3.2 7.1 + - + +
329B THR* 3.5 15.3 - - - +
330B VAL 5.3 3.6 - - - -
331B GLY* 5.4 1.3 - - - +
343B LEU* 5.6 2.7 - - + +
344B ILE* 4.8 11.4 - - + +
347B ALA* 3.7 33.2 - - + -
351B LEU* 4.3 18.8 - - + -
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Residues in contact with PHE 308 (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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223B PHE* 4.9 6.7 - + - -
226B ILE* 4.4 6.3 - - + -
248B PHE* 3.8 25.8 - + + -
306B LEU* 3.5 36.3 - - + -
307B ILE* 1.3 69.2 - - - +
309B ALA* 1.3 56.5 + - - +
310B VAL* 3.2 8.6 + - + +
318B TYR* 3.6 59.0 - + + -
321B TYR* 4.3 6.1 - - + -
322B ALA* 4.2 17.0 - - + -
325B ILE* 4.4 10.1 - - + -
328B ALA* 4.7 2.2 - - + -
329B THR 2.8 20.7 + - - +
330B VAL* 3.3 11.8 - - + +
331B GLY 2.8 31.3 + - - -
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Residues in contact with ALA 309 (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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247B VAL* 4.1 12.1 - - + -
248B PHE 2.6 21.9 + - - +
249B VAL* 3.5 18.1 - - + -
250B SER 3.4 15.1 + - - +
307B ILE* 3.2 6.3 + - + +
308B PHE* 1.3 67.5 - - - +
310B VAL* 1.3 59.3 + - - +
331B GLY* 3.6 8.7 - - - +
333B LEU* 3.6 17.0 - - + +
340B ILE* 5.7 3.4 - - + -
343B LEU* 4.2 19.5 - - + -
344B ILE* 6.2 0.4 - - + -
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Residues in contact with VAL 310 (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 PHE* 4.6 9.4 - - + -
250B SER 3.3 14.4 - - - +
308B PHE* 3.2 16.6 + - + +
309B ALA* 1.3 77.9 - - - +
311B THR* 1.3 60.6 + - - +
314B GLN* 3.9 10.5 - - + +
315B VAL* 3.8 31.3 - - + +
318B TYR* 3.6 42.0 - - + -
330B VAL* 5.2 2.0 - - + -
331B GLY 2.9 9.6 + - - +
332B LEU* 3.5 2.8 - - - -
333B LEU* 2.7 28.5 + - - -
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Residues in contact with THR 311 (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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250B SER 3.7 2.0 + - - -
251B ASP* 3.6 38.0 + - + +
310B VAL* 1.3 78.7 - - - +
312B GLN* 1.3 76.5 + - - +
313B GLU* 4.8 3.4 + - - -
314B GLN* 3.2 6.6 + - - +
315B VAL* 3.2 18.9 + - - -
333B LEU* 3.2 31.0 - - + +
334B GLN 3.8 19.3 - - - +
335B LYS* 4.6 8.1 - - + +
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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