Contacts of the strand formed by residues 317 - 322 (chain B) in PDB entry 4RO0
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 ILE 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLU* 3.7 38.8 - - + +
267B VAL 3.5 5.6 - - - +
268B PRO* 3.7 30.5 - - + -
296B VAL* 3.2 9.8 - - - +
297B GLY 2.9 30.2 + - - +
315B GLY 3.8 12.8 - - - +
316B ASP* 1.3 72.9 - - - +
318B ILE* 1.3 66.1 + - - +
319B LEU* 3.8 1.7 + - + +
245b ASP* 4.3 14.4 - - - +
247b TYR* 3.6 37.9 - - + +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B VAL* 3.1 13.4 - - + +
266B GLU* 3.4 1.6 - - - -
267B VAL* 2.7 35.3 + - + +
269B ILE* 3.7 29.8 - - + -
275B LEU* 4.8 6.3 - - + -
285B ILE* 5.2 6.5 - - + -
291B VAL* 6.0 1.1 - - + -
293B ILE* 3.8 26.9 - - + -
295B GLY 3.9 2.5 - - - -
296B VAL* 4.9 1.3 - - + +
312B PHE* 3.9 22.7 - - + -
317B ILE* 1.3 74.8 - - - +
319B LEU* 1.3 63.2 + - - +
320B GLY* 4.0 2.0 + - - +
330B LEU* 4.3 35.2 - - + -
334B ILE* 4.4 9.6 - - + -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B MET* 4.0 15.9 - - + -
265B VAL 3.2 17.9 - - - +
266B GLU* 4.0 9.0 - - + -
293B ILE* 3.8 2.1 - - - -
294B ILE* 2.8 43.5 + - + +
295B GLY 2.9 23.1 + - - +
302B LEU* 3.8 21.8 - - + -
317B ILE* 3.8 2.2 + - + +
318B ILE* 1.3 75.2 - - - +
320B GLY* 1.3 52.4 + - - +
247b TYR* 4.1 6.1 - - + +
248b GLU* 3.7 30.5 - - + +
251b PHE* 3.7 36.1 - - + -
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Residues in contact with GLY 320 (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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264B MET* 3.3 6.9 - - - +
265B VAL* 2.8 38.4 + - - +
291B VAL* 4.2 10.5 - - - -
292B ILE 3.0 15.9 - - - -
293B ILE* 4.5 0.7 - - - -
294B ILE* 3.9 5.6 - - - -
318B ILE* 4.0 2.7 + - - +
319B LEU* 1.3 76.1 - - - +
321B ILE* 1.3 63.3 + - - -
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Residues in contact with ILE 321 (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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251B PHE* 4.2 18.6 - - + -
255B VAL* 3.9 18.2 - - + -
262B ARG* 4.0 20.2 - - + +
263B ARG 3.4 9.9 - - - +
264B MET* 3.7 18.6 - - + -
290B GLY 4.6 0.9 - - - +
291B VAL* 3.3 7.2 - - - +
292B ILE* 3.1 43.9 + - + +
294B ILE* 3.4 28.9 - - + -
320B GLY* 1.3 72.5 - - - -
322B GLY* 1.3 61.2 + - - +
294b ILE* 4.6 19.3 - - + -
304b ILE* 4.7 7.6 - - + -
321b ILE* 6.0 0.2 - - + -
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Residues in contact with GLY 322 (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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262B ARG* 3.6 8.5 - - - -
263B ARG* 3.0 30.0 + - - +
265B VAL* 5.5 0.8 - - - +
291B VAL* 4.5 11.0 - - - +
320B GLY 4.2 0.6 + - - -
321B ILE* 1.3 77.5 - - - +
323B LYS* 1.3 66.1 + - - -
326B GLU* 3.4 11.2 - - - -
327B ILE* 3.6 12.4 - - - +
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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