Contacts of the helix formed by residues 37 - 46 (chain 3) in PDB entry 4E2I
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 37 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313 CYS* 5.2 0.9 - - - -
353 GLY 3.2 9.4 + - - +
363 GLN* 1.3 75.5 + - - +
383 GLU* 1.3 75.0 + - - +
393 GLU* 3.0 17.5 + - + +
403 GLY* 3.0 7.4 + - - +
413 MET* 2.9 21.8 + - - +
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Residues in contact with GLU 38 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33 ALA* 2.6 39.4 - - + +
73 GLN* 3.6 34.9 - - + +
83 LEU* 3.7 41.5 - - + +
113 GLU* 4.2 4.1 - - + +
313 CYS* 4.6 2.9 - - - +
363 GLN 3.8 0.2 + - - -
373 ASN* 1.3 79.6 - - - +
393 GLU* 1.3 73.2 + - + +
413 MET* 4.1 0.9 - - - -
423 VAL* 3.1 31.7 + - - +
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Residues in contact with GLU 39 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73 GLN* 5.4 1.6 - - - +
113 GLU* 5.1 17.0 - - + +
373 ASN* 3.0 12.0 + - + +
383 GLU* 1.3 98.9 - - - +
403 GLY* 1.3 61.3 + - - +
423 VAL* 4.7 1.4 - - - +
433 GLY* 3.6 14.9 + - - -
550C LYS* 6.0 5.8 - - + -
551C ASP* 4.2 28.7 - - + +
552C TYR* 5.3 15.2 - - + +
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Residues in contact with GLY 40 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363 GLN* 4.3 14.4 - - - -
373 ASN* 3.0 10.1 + - - +
393 GLU* 1.3 77.9 - - - +
413 MET* 1.3 63.7 + - - +
433 GLY* 3.5 2.0 + - - -
443 GLU* 3.1 34.2 + - - +
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Residues in contact with MET 41 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LEU* 4.5 7.2 - - + -
273 LEU* 4.6 7.6 - - + +
303 LEU* 3.4 44.4 - - + +
313 CYS* 3.9 16.8 - - - -
363 GLN* 3.6 43.7 - - + +
373 ASN 2.9 11.9 + - - +
383 GLU 4.3 3.8 - - - +
403 GLY* 1.3 75.8 - - - +
423 VAL* 1.3 61.1 + - - +
443 GLU* 3.2 7.8 + - + +
453 LEU* 2.8 32.0 + - - +
653 PHE* 3.7 23.8 - - + -
703 LEU* 4.3 9.4 - - + -
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Residues in contact with VAL 42 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83 LEU* 3.9 26.5 - - + -
113 GLU* 3.5 39.7 - - + +
123 LEU* 4.7 3.6 - - + -
153 PHE* 4.0 9.9 - - + -
173 LEU* 4.5 7.6 - - + -
273 LEU* 6.5 0.4 - - - -
383 GLU 3.1 20.5 + - - +
393 GLU 4.7 2.5 - - - +
403 GLY 3.5 0.2 - - - -
413 MET* 1.3 75.4 - - - +
433 GLY* 1.3 59.6 + - - +
453 LEU* 4.2 6.3 - - + -
463 ILE* 3.0 51.7 + - + +
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Residues in contact with GLY 43 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393 GLU 3.6 11.6 + - - -
403 GLY 3.5 5.6 + - - -
413 MET 3.1 1.0 - - - -
423 VAL* 1.3 81.9 - - - +
443 GLU* 1.3 65.0 + - - +
473 ALA* 4.1 0.5 - - - +
552C TYR* 6.2 0.2 - - - -
620C ALA* 3.5 23.0 - - - +
621C MET* 3.3 34.0 - - - +
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Residues in contact with GLU 44 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363 GLN* 4.8 9.0 - - - +
403 GLY* 3.1 20.0 + - - +
413 MET* 3.9 7.0 - - + +
433 GLY* 1.3 79.2 - - - +
453 LEU* 1.3 65.1 + - - +
473 ALA* 3.3 19.8 + - - +
483 PHE 3.6 1.4 + - - -
653 PHE* 3.3 29.0 - - + -
693 PHE* 3.1 33.7 - - + -
703 LEU* 5.2 1.1 - - + -
733 ARG* 5.0 1.1 + - - -
621C MET 5.1 5.4 - - - +
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Residues in contact with LEU 45 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 LEU* 6.3 1.8 - - + -
173 LEU* 5.7 2.2 - - + -
273 LEU* 4.1 12.1 - - + -
413 MET* 2.8 18.3 + - - +
423 VAL* 3.9 9.0 - - + +
433 GLY 3.4 0.2 - - - -
443 GLU* 1.3 77.7 - - - +
463 ILE* 1.3 64.9 + - + +
473 ALA 3.1 0.2 - - - -
483 PHE* 3.0 28.0 + - + +
493 CYS* 3.6 9.0 + - - -
573 LEU* 4.2 23.6 - - + -
613 ILE* 5.1 0.7 - - + +
623 LEU* 3.5 36.1 - - + -
653 PHE* 3.6 41.0 - - + -
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Residues in contact with ILE 46 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153 PHE* 3.5 40.4 - - + -
173 LEU* 3.9 22.7 - - + -
423 VAL* 3.0 24.1 + - + +
443 GLU 3.5 0.2 - - - -
453 LEU* 1.3 75.1 - - + +
473 ALA* 1.3 58.7 + - - +
483 PHE 3.1 5.2 - - - -
493 CYS* 3.3 21.1 + - + +
503 THR* 3.3 7.1 + - - -
617C PHE* 3.2 30.4 - - + -
620C ALA* 3.8 12.8 - - + -
621C MET* 3.8 8.3 - - + -
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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