Contacts of the strand formed by residues 355 - 362 (chain A) in PDB entry 1EFU
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 ASN 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ALA* 3.0 43.6 + - + +
88A VAL* 3.8 15.9 - - + +
89A LYS* 3.7 13.9 - - - +
92A ILE* 4.9 1.3 - - + -
307A GLU* 5.9 0.9 - - - +
308A VAL 3.3 6.3 - - - +
309A TYR* 2.8 32.6 - - - +
353A GLY 4.0 1.1 + - - -
354A ASP* 1.3 75.6 - - - +
356A ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLU* 4.8 3.4 + - - -
308A VAL* 2.7 52.7 + - + +
310A ILE* 5.0 1.8 - - + -
343A LEU* 3.4 27.6 - - + -
344A PRO* 3.9 7.9 - - + -
347A VAL* 3.6 22.2 - - + -
350A VAL* 3.5 31.2 - - + -
354A ASP* 5.3 0.4 - - + -
355A ASN* 1.3 76.3 - - - +
357A LYS* 1.3 71.8 + - - +
358A MET* 3.5 26.0 - - + -
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 3.7 26.7 + - - +
306A SER 3.0 9.9 - - - +
307A GLU* 3.3 36.3 - - - +
344A PRO* 3.1 36.7 - - + +
356A ILE* 1.3 78.3 - - - +
358A MET* 1.3 62.3 + - - +
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Residues in contact with MET 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A GLU* 3.6 1.4 - - - -
306A SER* 2.9 50.2 + - - +
308A VAL* 3.9 25.8 - - + -
310A ILE* 5.0 0.9 - - + -
322A PHE* 4.1 21.8 - - + -
326A TYR* 6.0 0.7 - - + -
330A PHE* 4.9 5.4 - - - -
341A ILE* 3.7 29.4 - - + -
342A GLU 3.3 15.5 - - - +
343A LEU* 4.2 13.7 - - + -
344A PRO* 5.0 0.4 - - - -
356A ILE* 3.5 28.3 - - + -
357A LYS* 1.3 75.9 - - - +
359A VAL* 1.3 65.6 + - - +
360A VAL* 3.6 8.2 + - + -
376A ILE* 5.0 3.1 - - + -
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LYS* 3.9 23.6 - - + -
304A PHE 3.2 14.8 - - - +
305A GLU* 4.3 18.6 - - + +
341A ILE* 3.7 1.0 - - - -
342A GLU* 2.7 59.7 + - + +
358A MET* 1.3 70.8 - - - +
360A VAL* 1.3 58.0 + - - +
392A LEU* 3.7 20.4 - - + -
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR 3.8 1.0 - - - +
303A LYS* 3.3 7.4 - - - +
304A PHE* 2.9 63.0 + - + -
306A SER* 3.7 21.3 - - - +
308A VAL* 5.7 0.2 - - + -
330A PHE* 3.5 47.6 - - + -
340A THR 3.5 7.6 - - - +
341A ILE* 4.7 1.6 - - + +
358A MET* 4.2 11.2 - - + +
359A VAL* 1.3 75.4 - - - +
361A THR* 1.3 65.6 + - - +
362A LEU* 4.0 7.2 - - + -
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Residues in contact with THR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR* 3.6 12.8 - - + -
303A LYS* 2.8 35.7 + - + +
339A GLY* 3.2 2.0 - - - -
340A THR* 3.0 46.2 + - - +
342A GLU* 2.9 13.8 + - - -
360A VAL* 1.3 73.6 + - - +
362A LEU* 1.3 69.1 + - - +
363A ILE* 5.0 1.2 - - - +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A HIS 3.7 7.0 - - - +
302A THR* 2.9 36.6 + - - +
304A PHE* 3.9 5.6 - - + -
330A PHE* 3.9 17.7 - - + -
332A PHE* 4.0 13.5 - - + -
337A VAL* 3.8 28.0 - - + +
338A THR 3.5 2.2 - - - +
339A GLY* 4.0 0.2 - - - -
360A VAL* 4.1 6.7 - - + -
361A THR* 1.3 78.2 - - - +
363A ILE* 1.3 60.7 + - - +
364A HIS 3.1 19.1 - - - +
366A ILE* 3.4 20.4 - - + -
368A MET* 3.4 31.9 - - + -
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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