Contacts of the strand formed by residues 315 - 322 (chain B) in PDB entry 3OUY
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 PRO 315 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A ARG* 5.1 2.3 - - - -
305B PHE* 3.3 47.1 - - + +
308B LEU* 3.9 15.9 - - + +
309B GLU* 3.6 35.7 - - + +
313B PHE 3.6 1.0 - - - -
314B MET* 1.3 89.0 - - - +
316B LEU* 1.3 66.4 + - - +
317B ARG 5.3 0.7 - - - +
331B PHE* 5.7 1.3 - - + -
332B GLU 3.4 8.7 - - - +
333B CYS* 3.9 9.6 - - - -
334B GLN* 5.1 0.2 - - - +
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Residues in contact with LEU 316 (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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341A VAL* 3.6 32.1 - - + +
343A ARG* 2.9 56.2 + - + +
377A PHE* 4.0 19.1 - - + -
276B THR* 4.3 4.7 - - + -
305B PHE* 4.1 3.7 - - - -
314B MET 3.4 1.0 + - - -
315B PRO* 1.3 77.7 - - - +
317B ARG* 1.3 58.5 + - + +
332B GLU* 2.4 48.7 + - + +
334B GLN* 3.1 42.6 - - + +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 3.8 12.6 - - - +
368A PHE* 3.3 61.9 - - + +
369A ILE 4.6 1.4 + - - -
370A GLU* 4.3 6.1 + - - +
377A PHE* 3.8 8.4 - - + -
237B ARG* 4.6 12.3 - - - +
305B PHE* 3.8 13.8 - - - -
315B PRO* 3.9 0.5 - - - +
316B LEU* 1.3 87.5 - - + +
318B SER* 1.3 68.7 + - - +
331B PHE* 3.8 4.0 - - - -
332B GLU* 3.5 23.9 + - - +
431B GLU* 3.2 26.6 + - - +
432B MET* 2.9 46.6 + - + +
434B GLY* 4.8 1.4 - - - +
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Residues in contact with SER 318 (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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301B SER* 3.3 23.7 + - - -
302B ARG* 5.5 0.5 - - - -
305B PHE* 3.2 29.1 - - - +
317B ARG* 1.3 78.7 + - - +
319B ALA* 1.3 64.3 + - - +
330B LEU 3.3 9.6 - - - -
331B PHE* 3.9 7.0 - - - -
432B MET* 3.8 8.7 - - - +
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Residues in contact with ALA 319 (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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301B SER* 4.0 5.9 + - - -
318B SER* 1.3 78.2 - - - +
320B PHE* 1.3 75.9 + - - +
329B LEU* 3.9 1.4 - - - -
330B LEU* 3.0 41.1 + - + +
428B GLU* 4.5 15.0 - - + +
432B MET* 3.8 19.1 - - + -
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Residues in contact with PHE 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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294B TYR* 3.7 29.9 - + + -
297B LEU* 4.1 24.5 - - + -
298B GLU* 3.6 38.1 - - + -
301B SER* 4.0 17.7 - - - -
318B SER* 5.9 0.4 - - - -
319B ALA* 1.3 86.8 - - - +
321B LYS* 1.3 62.8 + - - +
328B TYR 3.2 14.4 - - - +
329B LEU* 3.8 12.3 - - + -
330B LEU* 4.4 5.1 - - - +
428B GLU* 4.4 8.8 - - - +
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Residues in contact with LYS 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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294B TYR* 5.6 1.3 - - - -
297B LEU* 4.8 5.0 - - - +
320B PHE* 1.3 74.3 - - - +
322B ALA* 1.3 86.1 + - - +
323B SER* 4.4 14.8 - - - +
327B CYS* 3.4 4.3 - - - +
328B TYR* 3.0 35.7 + - + +
330B LEU* 5.0 1.1 - - + +
424B PRO* 3.3 28.3 - - + +
425B VAL* 4.2 17.3 - - + -
428B GLU* 3.4 33.7 - - + +
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Residues in contact with ALA 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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285B LYS* 4.0 13.1 + - - -
293B LEU* 3.9 28.3 - - + -
294B TYR* 4.4 20.3 + - - +
297B LEU* 4.4 4.9 - - + -
321B LYS* 1.3 90.3 + - - +
323B SER* 1.3 59.4 + - - +
326B PHE 3.6 4.3 - - - -
327B CYS* 4.1 9.0 - - - -
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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