Contacts of the helix formed by residues 385 - 396 (chain E) in PDB entry 2P1N
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 THR 385 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361E GLU* 3.9 8.4 + - - +
384E MET* 1.3 82.0 - - - +
386E ASN* 1.3 65.5 + - - +
387E ALA* 3.6 9.4 + - - +
388E ALA* 2.9 26.7 + - - +
389E LEU* 3.0 23.9 + - - +
413E ASP* 3.6 23.3 - - - +
414E TYR* 3.5 24.2 - - + -
415E LEU* 4.1 17.0 - - + -
420E LEU* 4.0 6.1 - - - -
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Residues in contact with ASN 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E THR* 1.3 69.6 - - - +
387E ALA* 1.3 61.7 + - - +
389E LEU* 3.2 2.3 + - - +
390E ILE* 2.7 32.0 + - + +
413E ASP* 3.1 20.8 + - - +
416E THR* 4.6 1.4 - - - +
418E GLU* 4.5 8.7 + - - +
419E PRO 3.1 21.4 + - - -
420E LEU* 3.0 29.5 - - - +
422E ILE* 3.3 38.3 - - + +
423E GLY* 3.1 17.8 + - - +
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Residues in contact with ALA 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E THR* 3.2 9.5 + - - +
386E ASN* 1.3 78.2 - - - +
388E ALA* 1.3 60.2 + - - +
390E ILE* 3.6 7.8 + - - +
391E THR* 3.2 26.9 + - - -
413E ASP* 4.6 0.8 + - - -
415E LEU* 6.3 2.2 - - + -
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Residues in contact with ALA 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361E GLU* 3.5 29.6 - - + -
365E VAL* 3.5 19.0 - - + +
384E MET* 4.2 5.2 - - - -
385E THR* 2.9 25.7 + - - +
387E ALA* 1.3 69.0 - - - +
389E LEU* 1.3 61.1 + - - +
391E THR* 3.4 3.5 + - - -
392E ILE* 2.9 38.5 + - + +
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Residues in contact with LEU 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E MET* 4.0 26.2 - - + -
385E THR 3.0 19.0 + - - +
386E ASN 3.7 0.2 - - - +
388E ALA* 1.3 78.5 - - - +
390E ILE* 1.3 56.5 + - - +
392E ILE* 3.4 7.0 + - + +
393E ALA* 3.0 26.7 + - - +
402E PHE* 4.0 18.4 - - + -
404E LEU* 4.5 2.2 - - + -
420E LEU* 4.2 10.3 - - + -
423E GLY* 3.2 38.6 - - - +
424E PHE* 4.0 27.8 - - + -
427E ILE* 3.3 27.6 - - + +
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Residues in contact with ILE 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E ASN* 2.7 23.1 + - + +
387E ALA* 4.2 7.0 - - - +
389E LEU* 1.3 74.3 - - - +
391E THR* 1.3 60.5 + - - +
393E ALA* 3.8 0.8 - - - +
394E ARG* 3.0 51.6 + - - +
422E ILE* 4.3 31.4 - - + +
423E GLY* 4.5 1.6 - - - -
426E ALA* 3.7 22.9 - - + -
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Residues in contact with THR 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E VAL* 4.1 14.1 - - + -
369E MET* 4.1 14.6 - - + -
387E ALA* 3.2 19.9 + - - +
388E ALA* 3.8 5.8 - - - -
389E LEU 3.3 0.2 - - - -
390E ILE* 1.3 75.9 - - - +
392E ILE* 1.3 66.0 + - - +
394E ARG* 3.5 5.2 + - - +
395E ASN* 3.1 42.1 + - - +
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Residues in contact with ILE 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361E GLU 5.1 0.4 - - - +
364E LEU* 3.4 36.1 - - + -
365E VAL* 4.0 20.4 - - + +
368E SER* 3.2 26.3 + - - +
384E MET* 5.4 3.4 - - - -
388E ALA* 2.9 30.9 + - + +
389E LEU* 3.6 10.3 - - + +
391E THR* 1.3 73.1 - - - +
393E ALA* 1.3 62.3 + - - +
395E ASN 3.6 0.2 + - - -
396E ARG* 3.1 25.5 + - - +
399E MET* 4.5 11.4 - - + +
402E PHE* 4.0 27.1 - - + -
427E ILE* 5.1 3.8 - - + -
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Residues in contact with ALA 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E LEU 3.0 16.8 + - - +
390E ILE 3.8 4.3 - - - +
391E THR 3.2 0.2 - - - -
392E ILE* 1.3 77.2 - - - +
394E ARG* 1.3 64.0 + - - +
396E ARG 3.5 9.0 + - - +
397E PRO* 3.7 9.9 - - - +
426E ALA* 3.5 35.4 - - + +
427E ILE* 3.8 13.0 - - + -
430E HIS* 3.6 20.5 - - + +
431E CYS* 4.5 6.7 - - - -
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Residues in contact with ARG 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390E ILE* 3.0 38.4 + - + +
391E THR* 4.1 4.9 - - - +
393E ALA* 1.3 78.6 - - - +
395E ASN* 1.3 62.9 + - - +
396E ARG 3.5 0.3 + - - -
397E PRO* 3.6 10.9 - - - +
426E ALA* 6.2 0.4 - - - +
430E HIS* 3.5 41.1 + - + +
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Residues in contact with ASN 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E SER* 3.6 20.5 - - - +
369E MET* 3.1 57.7 - - - +
391E THR* 3.1 23.5 + - - +
392E ILE 3.9 3.1 - - - +
394E ARG* 1.3 77.1 - - - +
396E ARG* 1.3 86.6 + - + +
397E PRO* 3.3 4.9 - - - +
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Residues in contact with ARG 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E SER* 3.0 50.2 + - - +
369E MET* 4.6 7.1 + - - +
371E CYS 3.4 22.3 + - - +
372E PRO* 3.4 30.0 + - - +
374E LEU* 3.4 26.2 - - + +
392E ILE 3.1 14.7 + - - +
393E ALA 3.8 2.9 - - - -
394E ARG 3.4 0.8 - - - -
395E ASN* 1.3 93.9 + - - +
397E PRO* 1.3 62.8 - - - +
398E ASN* 2.7 28.0 + - - +
399E MET* 2.8 44.9 + - + +
431E CYS* 3.6 5.7 - - - -
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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