Contacts of the strand formed by residues 309 - 315 (chain B) in PDB entry 4EUT
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 MET 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B HIS 4.0 1.2 + - - -
308B ARG* 1.3 74.5 - - - +
310B VAL* 1.3 71.6 + - - +
311B ILE* 4.2 18.8 - - + -
324B ILE 3.4 1.7 - - - +
325B TYR* 3.7 2.4 - - - -
326B ILE* 2.8 45.6 + - + +
327B HIS* 4.9 0.2 - - - +
328B SER* 4.3 19.0 - - - +
367B ALA* 4.0 32.8 - - - +
368B GLN* 4.3 9.4 - - - -
370B PHE* 5.8 1.3 - - + +
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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
----------------------------------------------------------
113B LEU* 5.9 1.6 - - + -
308B ARG 5.4 0.9 - - - +
309B MET* 1.3 84.0 - - - +
311B ILE* 1.3 73.0 + - - +
312B HIS* 3.6 36.4 + - + +
323B LYS* 4.0 18.4 - - + -
324B ILE 3.5 2.0 - - - -
325B TYR* 3.6 45.1 - - + +
373B THR* 4.0 6.9 + - - +
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Residues in contact with ILE 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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309B MET* 4.2 12.8 - - + -
310B VAL* 1.3 78.3 - - - +
312B HIS* 1.3 67.2 + - - +
313B VAL 3.6 1.6 + - - -
324B ILE* 2.9 34.6 + - + +
326B ILE* 3.5 32.3 - - + -
335B PHE* 3.7 37.5 - - + -
367B ALA* 4.5 6.3 - - + -
370B PHE* 3.9 24.2 - - + -
373B THR* 3.5 23.1 - - + +
379B ILE* 4.1 12.3 - - + -
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Residues in contact with HIS 312 (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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310B VAL* 3.6 29.4 + - + +
311B ILE* 1.3 71.8 - - - +
313B VAL* 1.3 62.2 + - - +
322B HIS 3.5 6.5 + - - +
323B LYS* 4.1 21.4 - - - +
373B THR* 2.8 41.8 + - - +
374B THR* 3.7 19.5 - - - +
375B GLU* 3.6 35.0 - - + +
378B PRO* 3.3 5.4 - - + +
379B ILE* 2.8 26.2 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ILE* 3.6 1.8 + - + +
312B HIS* 1.3 79.0 - - - +
314B PHE* 1.3 65.5 + - - +
315B SER 4.6 0.4 - - - +
321B ALA* 3.6 2.6 - - - +
322B HIS* 2.8 48.3 + - + +
324B ILE* 3.7 26.5 - - + -
335B PHE* 3.7 24.7 - - + -
339B VAL* 4.6 9.4 - - + -
343B THR* 5.5 1.3 - - + -
352B LEU* 6.1 0.7 - - + -
378B PRO* 4.2 2.7 - - - -
379B ILE* 3.2 17.5 - - + +
381B VAL* 3.8 28.5 - - + -
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Residues in contact with PHE 314 (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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313B VAL* 1.3 77.9 - - - +
315B SER* 1.3 77.0 + - - +
316B LEU* 3.3 26.3 + - + -
319B MET* 3.7 37.5 - - + -
320B THR 3.6 14.6 - - - -
321B ALA* 3.9 17.3 - - + -
375B GLU 5.9 1.8 - - - -
378B PRO* 3.9 14.8 - - + +
379B ILE 3.1 6.5 + - - -
380B PHE* 3.3 23.6 - + + -
381B VAL 3.0 22.1 + - - -
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Residues in contact with SER 315 (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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314B PHE* 1.3 71.2 - - - +
316B LEU* 1.3 54.0 + - - +
317B GLN* 4.1 4.9 + - - +
318B GLN* 2.5 35.2 + - - +
319B MET* 2.7 31.5 + - - -
320B THR* 2.9 23.3 + - - -
322B HIS* 3.9 14.7 - - - -
343B THR* 4.8 2.5 - - - -
345B ILE* 4.4 3.6 - - - +
381B VAL* 3.6 22.0 + - - +
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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