Contacts of the helix formed by residues 376 - 386 (chain E) in PDB entry 1R4N
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 SER 376 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373E GLU* 4.7 6.5 + - - -
374E SER 4.2 1.2 + - - -
375E ILE* 1.3 79.5 - - - +
377E GLU* 1.3 64.8 + - - +
378E LYS* 4.0 14.2 + - - +
379E GLU* 2.9 41.8 + - - +
380E LEU* 3.1 18.2 + - - +
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Residues in contact with GLU 377 (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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373E GLU* 5.1 2.8 + - - -
375E ILE 3.9 0.8 + - - -
376E SER* 1.3 73.5 - - - +
378E LYS* 1.3 59.2 + - + +
380E LEU* 3.1 11.9 + - + +
381E LYS* 2.8 63.3 + - + +
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Residues in contact with LYS 378 (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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376E SER* 4.1 11.0 - - - +
377E GLU* 1.3 80.4 - - + +
379E GLU* 1.3 63.7 + - - +
381E LYS* 3.4 5.0 + - - +
382E LEU* 3.1 25.4 + - - +
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Residues in contact with GLU 379 (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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172E ILE* 4.9 6.5 - - + +
303E SER* 3.5 22.3 + - - -
307E LEU* 4.6 11.6 - - + +
374E SER 4.8 3.1 - - - +
375E ILE* 4.2 13.6 - - + -
376E SER* 2.9 36.4 + - - +
378E LYS* 1.3 78.3 - - + +
380E LEU* 1.3 56.9 - - - +
382E LEU* 3.4 7.7 + - - +
383E LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 380 (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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307E LEU* 4.6 3.8 - - + -
354E ALA* 3.8 14.1 - - + +
355E ALA* 5.0 2.2 - - - -
357E VAL* 4.2 9.9 - - + -
358E GLY* 3.3 36.6 - - - +
361E VAL* 4.2 12.3 - - + -
375E ILE* 4.8 4.7 - - + +
376E SER 3.1 9.0 + - - +
377E GLU* 3.1 16.1 + - + +
378E LYS 3.1 0.4 - - - -
379E GLU* 1.3 75.9 - - - +
381E LYS* 1.3 64.2 + - + +
382E LEU 2.9 10.2 + - - -
383E LEU* 3.1 13.0 + - + +
384E CYS* 3.0 38.5 + - - -
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Residues in contact with LYS 381 (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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351E LYS* 4.3 32.4 - - - +
354E ALA* 4.9 17.0 - - + -
377E GLU* 2.8 48.7 + - + +
378E LYS* 4.2 4.5 - - - +
380E LEU* 1.3 76.8 - - + +
382E LEU* 1.3 57.3 + - - +
384E CYS* 4.2 7.2 - - - +
385E SER* 3.3 23.2 + - - -
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Residues in contact with LEU 382 (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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23E HIS* 5.7 5.2 - - + +
172E ILE* 4.3 13.9 - - + -
173E GLU* 4.3 27.6 - - + +
378E LYS 3.1 17.1 + - - +
379E GLU* 3.5 6.7 - - - +
380E LEU 2.9 0.8 - - - -
381E LYS* 1.3 75.6 - - - +
383E LEU* 1.3 67.7 + - - +
384E CYS 3.0 1.6 - - - -
385E SER* 3.0 7.4 + - - -
386E ASN* 3.0 50.6 + - - +
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Residues in contact with LEU 383 (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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172E ILE* 3.6 24.6 - - + +
304E PHE* 5.7 1.6 - - + -
307E LEU* 3.0 56.5 - - + +
308E ALA 5.3 0.2 - - - +
311E LEU* 3.7 27.4 - - + -
357E VAL* 4.9 1.8 - - + -
379E GLU 2.9 17.9 + - - +
380E LEU* 3.5 14.4 - - + +
382E LEU* 1.3 75.6 - - - +
384E CYS* 1.3 60.1 + - - +
386E ASN 3.5 1.9 - - - -
387E SER* 2.9 23.0 + - - -
390E LEU* 4.1 22.0 - - + -
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Residues in contact with CYS 384 (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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311E LEU* 4.8 2.7 - - - -
324E PRO* 4.6 15.1 - - + +
325E VAL 5.8 2.7 - - - +
326E ARG* 5.5 2.1 - - - -
350E ALA 5.8 1.3 - - - +
354E ALA* 4.2 18.8 - - + -
357E VAL* 4.0 36.1 - - - -
380E LEU* 3.0 29.2 + - - +
381E LYS* 4.3 6.1 - - - +
383E LEU* 1.3 76.9 - - - +
385E SER* 1.3 59.3 + - - +
387E SER* 2.6 38.6 + - - -
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Residues in contact with SER 385 (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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325E VAL 5.9 0.2 - - - -
326E ARG* 3.8 47.2 + - - +
328E THR* 5.9 3.1 - - - +
381E LYS 3.3 14.3 + - - -
382E LEU* 3.0 13.0 + - - -
384E CYS* 1.3 79.2 - - - +
386E ASN* 1.3 65.1 + - - +
387E SER* 3.5 2.4 + - - -
388E ALA 4.9 0.3 + - - -
389E PHE* 4.4 3.6 - - - -
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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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172E ILE* 3.4 26.0 - - + +
173E GLU* 3.9 19.8 - - - +
174E SER 4.3 3.1 + - - -
175E HIS 5.1 2.4 + - - -
176E PRO* 5.4 0.7 - - - +
382E LEU* 3.0 50.0 + - - +
383E LEU 3.5 3.1 - - - -
385E SER* 1.3 78.2 - - - +
387E SER* 1.3 66.1 + - - +
388E ALA 3.2 3.1 - - - -
389E PHE* 2.8 34.8 + - + -
390E LEU* 3.3 11.2 + - - +
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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