Contacts of the helix formed by residues 360 - 370 (chain A) in PDB entry 3U7U
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 ASP 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A SER* 5.4 0.8 - - - -
358A ALA 3.7 2.2 + - - -
359A ILE* 1.4 75.6 - - - +
361A PRO* 1.4 77.3 - - - +
362A GLU* 3.5 19.5 + - - +
363A LYS* 2.9 50.3 + - + +
364A LEU* 3.8 2.8 + - - +
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Residues in contact with PRO 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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359A ILE* 3.3 9.4 - - + +
360A ASP* 1.4 88.2 - - - +
362A GLU* 1.3 59.8 + - - +
364A LEU* 3.3 23.7 + - + +
365A ASN* 4.6 2.3 + - - -
383A PRO* 4.0 37.7 - - + -
385A ASN* 4.1 17.5 - - - +
386A MET* 4.1 13.2 - - + +
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Residues in contact with GLU 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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360A ASP* 3.0 19.1 + - - +
361A PRO* 1.3 76.4 - - - +
363A LYS* 1.4 62.3 + - + +
365A ASN* 2.7 42.9 + - - +
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Residues in contact with LYS 363 (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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325A SER* 4.3 12.4 + - - +
328A ILE* 3.7 31.6 - - + +
329A ASP* 3.1 39.0 + - - +
359A ILE* 5.1 0.4 - - + -
360A ASP* 2.9 41.7 + - + +
362A GLU* 1.4 71.8 - - + +
364A LEU* 1.3 54.9 + - - +
365A ASN 3.0 10.9 + - - -
366A VAL* 3.2 29.5 + - + +
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Residues in contact with LEU 364 (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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328A ILE* 4.0 11.9 - - + -
343A PHE* 3.8 31.4 - - + -
348A ILE* 4.4 4.5 - - + -
359A ILE* 4.5 11.4 - - + -
360A ASP 3.8 2.0 + - - +
361A PRO* 3.3 13.8 + - + +
362A GLU 3.1 1.6 + - - -
363A LYS* 1.3 75.3 - - - +
365A ASN* 1.4 58.1 + - - +
366A VAL 3.1 3.2 + - - -
367A PHE* 3.3 27.7 + - + -
382A TRP* 3.9 18.2 - - + -
383A PRO* 3.7 37.7 - - + -
386A MET* 3.9 9.2 - - + -
391A VAL* 3.4 26.3 - - + +
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Residues in contact with ASN 365 (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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361A PRO 4.6 1.6 + - - -
362A GLU* 2.7 45.6 + - - +
363A LYS 3.0 1.6 - - - -
364A LEU* 1.4 74.4 - - - +
366A VAL* 1.4 62.2 + - - +
367A PHE 3.1 2.9 - - - -
368A ARG* 2.8 58.6 + - - +
369A THR* 6.0 0.2 - - - +
391A VAL* 3.6 11.9 - - - +
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Residues in contact with VAL 366 (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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328A ILE* 3.7 31.2 - - + +
329A ASP* 4.7 4.3 - - - +
331A PHE* 3.9 24.7 - - + +
332A ILE* 3.5 34.1 - - + +
333A ASN 4.8 1.7 + - - -
363A LYS* 3.2 20.6 + - + +
365A ASN* 1.4 77.0 - - - +
367A PHE* 1.3 68.9 + - + +
368A ARG 3.2 1.0 + - - -
369A THR* 3.1 25.1 + - - +
370A VAL* 4.9 0.5 - - - +
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Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A VAL* 4.1 6.1 - - + -
328A ILE* 3.6 30.1 - - + -
331A PHE* 3.8 35.4 - + + -
341A LEU* 3.7 29.6 - - + -
343A PHE* 3.8 26.0 - + - -
364A LEU* 3.3 27.1 - - + +
365A ASN 3.1 0.4 - - - -
366A VAL* 1.3 76.7 - - + +
368A ARG* 1.3 55.9 + - - +
369A THR 3.1 6.3 - - - -
370A VAL* 3.0 39.9 + - + +
391A VAL* 3.1 14.4 - - + +
392A PHE* 3.7 28.0 - + + -
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Residues in contact with ARG 368 (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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365A ASN* 2.8 46.2 + - - +
367A PHE* 1.3 76.1 - - - +
369A THR* 1.3 60.2 + - + +
370A VAL 3.5 0.2 - - - -
390A SER* 3.5 42.0 + - - +
391A VAL* 3.1 24.8 + - - +
393A SER* 4.5 9.2 - - - +
394A ASN* 3.3 34.8 + - - +
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Residues in contact with THR 369 (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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333A ASN* 3.7 22.6 - - - +
334A CYS 2.7 32.9 + - - +
335A THR* 3.6 17.8 - - - +
366A VAL 3.1 17.3 + - - +
368A ARG* 1.3 79.4 - - + +
370A VAL* 1.4 63.6 + - - +
371A ARG* 3.4 10.0 + - - +
394A ASN* 4.8 4.1 + - - +
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Residues in contact with VAL 370 (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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331A PHE 5.5 0.4 - - - +
334A CYS* 3.5 18.8 - - + +
335A THR 3.8 2.0 - - - +
337A ILE* 3.9 30.1 - - + -
341A LEU* 5.2 1.3 - - + -
366A VAL 4.9 0.9 - - - +
367A PHE* 3.0 39.2 + - + +
369A THR* 1.4 74.8 - - - +
371A ARG* 1.4 60.6 + - - +
372A GLU 3.5 22.9 - - - +
373A ILE* 4.0 14.6 - - + -
392A PHE* 5.1 3.9 - - + -
394A ASN* 3.3 5.5 - - - +
395A LEU* 3.1 28.8 + - + +
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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