Contacts of the helix formed by residues 373 - 381 (chain K) in PDB entry 3E20
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 LEU 373 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K VAL* 4.8 4.7 - - + -
306K MET* 4.1 18.4 - - + -
323K LEU* 5.1 2.2 - - + -
325K MET* 2.7 43.9 + - + +
326K ILE* 4.1 0.4 - - - +
327K ARG* 4.3 11.7 - - + -
341K TYR* 3.6 37.2 - - + -
371K MET 3.6 3.4 + - - -
372K LEU* 1.3 71.1 - - - +
374K SER* 1.3 63.6 + - - +
375K GLU 3.1 0.9 + - - -
376K TRP* 3.9 6.5 - - + +
377K LEU* 3.2 51.3 + - + +
408K ILE* 4.5 13.2 - - + -
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Residues in contact with SER 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K TRP* 3.3 25.3 - - - -
16K ARG* 6.5 0.4 - - - -
319K CYS* 4.5 13.4 - - - -
321K ALA 3.4 15.7 + - - -
323K LEU* 4.2 23.5 - - - +
325K MET 4.1 1.4 + - - -
372K LEU* 4.6 9.9 - - - -
373K LEU* 1.3 79.8 - - - +
375K GLU* 1.3 58.6 + - - +
377K LEU* 4.0 2.1 + - - +
378K ALA* 3.8 6.6 + - - +
390K PHE* 3.6 26.5 - - - -
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Residues in contact with GLU 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K TRP* 5.4 5.2 - - + +
16K ARG* 2.7 37.8 + - - +
371K MET* 4.2 23.2 - - + +
372K LEU* 2.7 25.2 + - + +
374K SER* 1.3 72.7 - - - +
376K TRP* 1.3 62.8 + - - +
377K LEU 3.2 2.0 - - - -
378K ALA* 3.2 16.8 + - + +
379K GLU* 3.3 19.1 + - + +
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Residues in contact with TRP 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K MET* 4.9 10.5 - - - -
309K LEU* 5.0 3.8 - - + -
327K ARG* 2.9 63.1 - - - +
371K MET* 3.8 26.6 - - + -
372K LEU 3.0 10.1 + - - +
373K LEU* 3.9 7.2 - - + +
375K GLU* 1.3 77.3 - - - +
377K LEU* 1.3 81.8 + - + +
379K GLU* 3.1 3.2 + - - -
380K HIS* 2.9 78.5 + + + +
384K TYR* 3.5 30.7 - + - -
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Residues in contact with LEU 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K MET* 3.5 26.0 - - + -
309K LEU* 4.0 15.5 - - + -
317K LEU* 4.1 18.2 - - + -
319K CYS* 4.4 20.2 - - + -
373K LEU* 3.2 34.3 + - + +
374K SER 4.2 3.8 - - - +
375K GLU 3.2 0.2 - - - -
376K TRP* 1.3 92.0 - - + +
378K ALA* 1.3 56.2 + - - +
381K TYR* 2.7 39.4 + - + +
388K LEU* 4.0 11.7 - - + -
390K PHE* 5.4 0.4 - - + -
408K ILE* 4.1 17.9 - - + -
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Residues in contact with ALA 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ILE* 4.8 5.0 - - + +
12K TRP* 4.1 15.7 - - + +
13K LYS* 4.9 17.0 + - + +
374K SER 3.8 3.7 + - - +
375K GLU* 3.2 12.0 + - + +
377K LEU* 1.3 78.6 - - - +
379K GLU* 1.3 58.8 + - + +
380K HIS 3.5 0.2 - - - -
381K TYR* 3.3 26.0 - - - -
388K LEU* 3.9 5.7 - - - +
390K PHE* 4.0 22.9 - - + -
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Residues in contact with GLU 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LYS* 4.1 21.6 + - + +
371K MET* 5.6 4.9 - - - -
375K GLU* 3.3 21.4 + - + +
376K TRP* 3.1 6.8 + - - +
377K LEU 3.1 0.4 - - - -
378K ALA* 1.3 82.5 - - + +
380K HIS* 1.3 77.7 + - + +
381K TYR* 5.3 0.2 - - - -
383K ASP* 4.8 2.8 - - - +
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Residues in contact with HIS 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K MET* 5.9 3.8 - - + -
376K TRP* 2.9 70.7 + + + +
377K LEU* 5.1 0.2 - - - -
379K GLU* 1.3 100.3 + - + +
381K TYR* 1.3 68.2 + - - +
382K LYS 3.2 3.1 - - - -
383K ASP* 3.1 21.9 + - + +
384K TYR* 3.0 24.4 - + + -
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Residues in contact with TYR 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K GLU* 6.1 1.2 - - - +
9K ILE* 3.6 34.2 - - + +
309K LEU* 5.3 5.6 - - - -
317K LEU* 4.9 9.9 - - + -
377K LEU* 2.7 35.2 + - + +
378K ALA* 3.3 25.8 - - - -
380K HIS* 1.3 73.8 - - - +
382K LYS* 1.3 98.1 + - + +
383K ASP 3.1 1.0 + - - -
384K TYR* 3.3 18.5 + - - +
386K ALA* 3.0 15.7 + - + +
387K ASN* 3.6 21.1 - - - -
388K LEU* 3.3 34.5 - - + -
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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