Contacts of the strand formed by residues 326 - 333 (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 PHE 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B LYS* 3.7 31.6 - - + -
283B PHE* 3.3 21.5 - - - +
284B ARG* 4.0 28.5 - - - -
285B LYS* 3.8 2.8 - - - +
322B ALA* 3.6 1.0 - - - -
323B SER* 2.8 36.1 + - - +
324B GLU 3.8 0.2 - - - -
325B GLU* 1.3 118.2 - - + +
327B CYS* 1.3 66.0 + - - +
328B TYR* 3.9 25.5 - - + -
411B TYR* 4.9 8.7 - + - -
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Residues in contact with CYS 327 (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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281B VAL 3.8 0.3 - - - +
282B LYS* 3.4 6.4 - - - +
283B PHE* 2.9 57.5 + - + +
285B LYS* 3.6 34.1 - - - -
286B PRO* 4.1 4.5 - - - -
293B LEU* 4.4 3.1 - - - -
297B LEU* 3.9 22.4 - - + -
321B LYS 3.4 7.6 - - - +
322B ALA* 4.1 10.5 - - - -
326B PHE* 1.3 73.8 - - - +
328B TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 4.8 9.9 - - + -
281B VAL 3.5 3.4 - - - -
282B LYS* 3.5 29.1 + - + -
297B LEU* 5.5 0.2 - - - +
320B PHE* 3.2 8.8 - - - +
321B LYS* 3.0 38.5 + - + +
323B SER* 4.1 5.7 + - - -
326B PHE* 3.9 33.3 - - + -
327B CYS* 1.3 79.7 - - - +
329B LEU* 1.3 64.5 + - - +
330B LEU* 4.0 8.3 - - + -
415B ILE* 5.6 1.6 - - + -
420B LEU* 5.6 1.3 - - + -
423B GLU* 2.8 38.6 + - + -
424B PRO* 3.5 29.9 - - + +
425B VAL* 3.7 28.0 - - + -
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA* 3.0 4.9 - - - -
281B VAL* 2.9 39.4 + - + +
283B PHE* 3.8 21.8 - - + -
297B LEU* 4.1 31.4 - - + +
300B ALA* 3.8 20.4 - - + -
301B SER* 4.4 6.1 - - - +
304B ILE* 3.7 26.7 - - + -
319B ALA 3.9 1.8 - - - -
320B PHE* 3.8 16.2 - - + -
328B TYR* 1.3 80.8 - - - +
330B LEU* 1.3 61.1 + - - +
331B PHE* 3.5 21.4 - - + -
408B ILE* 4.8 2.9 - - + -
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Residues in contact with LEU 330 (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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279B PHE 3.8 2.7 - - - +
280B ALA* 3.4 26.0 - - + -
318B SER* 3.3 6.8 - - - -
319B ALA* 3.0 43.0 + - + +
320B PHE* 4.4 7.9 - - - +
328B TYR* 4.2 5.2 - - + -
329B LEU* 1.3 74.8 - - - +
331B PHE* 1.3 67.2 + - - +
420B LEU* 4.5 3.4 - - + -
425B VAL* 4.1 37.7 - - + -
428B GLU* 3.9 28.5 - - + -
429B LEU* 4.6 15.3 - - + +
432B MET* 4.2 15.9 - - + -
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Residues in contact with PHE 331 (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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277B ALA 3.7 1.5 - - - +
278B VAL* 3.3 6.4 - - - +
279B PHE* 3.0 61.3 + + + -
281B VAL* 3.9 11.9 - - + -
301B SER* 3.5 25.6 - - - -
304B ILE* 3.6 28.7 - - + -
305B PHE* 4.0 13.2 - + - -
308B LEU* 4.0 17.0 - - + -
315B PRO* 5.7 1.1 - - + -
317B ARG 3.8 6.7 - - - +
318B SER* 3.9 18.4 - - - -
329B LEU* 3.5 33.2 - - + -
330B LEU* 1.3 79.2 - - - +
332B GLU* 1.3 63.0 + - - +
333B CYS* 5.2 0.7 - - - -
429B LEU* 5.8 0.4 - - - +
432B MET* 4.0 5.9 - - - +
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Residues in contact with GLU 332 (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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377A PHE* 4.9 1.4 - - - -
274B ARG* 2.6 41.7 + - - -
276B THR* 2.5 35.6 + - - +
277B ALA 3.5 2.2 - - - +
278B VAL* 3.4 16.9 - - + +
315B PRO* 3.3 3.1 - - - +
316B LEU* 2.4 54.8 + - + +
317B ARG* 3.5 9.7 + - - +
331B PHE* 1.3 76.6 - - - +
333B CYS* 1.3 57.5 + - - +
432B MET* 3.8 17.7 - - + +
433B MET* 3.7 10.0 - - - +
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Residues in contact with CYS 333 (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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276B THR* 3.0 23.4 - - - -
277B ALA* 3.0 19.8 + - + +
279B PHE* 4.4 7.6 - - - -
308B LEU* 3.9 32.8 - - - -
313B PHE* 3.5 18.4 - - + +
314B MET 3.8 3.8 - - - -
315B PRO* 3.9 15.3 - - - -
316B LEU* 5.0 0.4 - - - -
331B PHE* 5.2 0.2 - - - -
332B GLU* 1.3 80.5 - - - +
334B GLN* 1.3 63.1 + - - +
335B ILE 3.5 13.4 + - - +
385B PRO* 4.1 9.9 - - + -
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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