Contacts of the helix formed by residues 37 - 46 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317 CYS* 5.1 0.9 - - - -
357 GLY 3.2 10.1 + - - +
367 GLN* 1.3 76.3 + - - +
387 GLU* 1.3 75.6 + - - +
397 GLU* 3.0 17.7 + - + +
407 GLY* 3.0 6.6 + - - +
417 MET* 2.9 21.7 + - - +
551G ASP* 5.2 5.7 + - - +
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Residues in contact with GLU 38 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37 ALA* 2.6 40.5 - - + +
77 GLN* 3.6 34.3 - - + +
87 LEU* 3.7 41.5 - - + +
117 GLU* 4.2 3.6 - - + +
317 CYS* 4.5 3.4 - - - +
367 GLN 3.8 0.2 + - - -
377 ASN* 1.3 78.9 - - - +
397 GLU* 1.3 73.3 + - + +
417 MET* 4.1 0.9 - - - -
427 VAL* 3.1 31.9 + - - +
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Residues in contact with GLU 39 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 GLN* 5.4 2.3 - - - +
117 GLU* 5.1 8.6 - - + +
377 ASN* 3.0 9.6 - - + +
387 GLU* 1.3 97.9 - - + +
407 GLY* 1.3 61.4 + - - +
427 VAL* 4.4 1.8 - - - +
437 GLY* 3.6 14.6 + - - -
549G PRO 4.7 7.1 - - - +
550G LYS* 4.7 11.9 - - + -
551G ASP* 3.1 44.5 - - + +
552G TYR* 4.5 26.4 + - + +
620G ALA 4.9 0.2 - - - +
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Residues in contact with GLY 40 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 GLN* 4.3 14.4 - - - -
377 ASN* 3.0 10.7 + - - +
397 GLU* 1.3 78.2 - - - +
417 MET* 1.3 61.8 + - - +
437 GLY* 3.8 1.6 - - - -
447 GLU* 3.1 34.6 + - - +
551G ASP* 5.2 2.3 + - - -
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Residues in contact with MET 41 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 LEU* 4.5 7.0 - - + -
277 LEU* 4.6 8.1 - - + +
307 LEU* 3.4 45.1 - - + +
317 CYS* 3.9 17.7 - - - -
367 GLN* 3.6 44.6 - - + +
377 ASN 2.9 12.5 + - - +
387 GLU 4.3 3.4 - - - +
397 GLU 3.4 0.2 - - - -
407 GLY* 1.3 74.9 - - - +
427 VAL* 1.3 61.7 + - + +
447 GLU* 3.2 7.7 + - + +
457 LEU* 2.8 31.7 + - - +
657 PHE* 3.7 23.1 - - + -
707 LEU* 4.3 9.2 - - + -
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Residues in contact with VAL 42 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 LEU* 3.9 26.9 - - + +
117 GLU* 3.5 39.0 - - + +
127 LEU* 4.7 4.0 - - + -
157 PHE* 4.0 9.4 - - + -
177 LEU* 4.4 7.0 - - + -
277 LEU* 6.5 0.2 - - - -
387 GLU 3.1 21.2 + - - +
397 GLU 4.7 2.0 - - - +
417 MET* 1.3 75.5 - - - +
437 GLY* 1.3 59.6 + - - +
457 LEU* 4.2 6.1 - - + -
467 ILE* 3.1 52.5 + - + +
620G ALA* 5.5 0.2 - - + -
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Residues in contact with GLY 43 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397 GLU 3.6 10.5 + - - -
407 GLY* 3.5 6.0 + - - -
417 MET 3.1 1.0 - - - -
427 VAL* 1.3 81.5 - - - +
447 GLU* 1.3 64.5 + - - +
477 ALA* 4.1 0.9 - - - +
620G ALA 3.0 26.5 - - - -
621G MET* 3.3 35.9 - - - +
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Residues in contact with GLU 44 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367 GLN* 4.8 9.0 - - - +
407 GLY* 3.1 20.5 + - - +
417 MET* 3.9 6.7 - - + +
437 GLY* 1.3 79.4 - - - +
457 LEU* 1.3 64.0 + - - +
467 ILE 3.5 0.2 - - - -
477 ALA* 3.3 19.8 + - - +
487 PHE 3.6 1.6 + - - -
657 PHE* 3.3 28.7 - - + -
697 PHE* 3.1 34.4 - - + -
707 LEU* 5.2 1.1 - - + -
737 ARG* 5.0 1.1 + - - -
621G MET 4.7 7.6 - - - +
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Residues in contact with LEU 45 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127 LEU* 6.3 1.8 - - + -
177 LEU* 5.7 2.5 - - + -
277 LEU* 4.1 13.5 - - + -
307 LEU* 5.0 0.2 - - + -
417 MET 2.8 18.7 + - - +
427 VAL* 3.9 9.2 - - - +
447 GLU* 1.3 78.7 - - - +
467 ILE* 1.3 63.5 + - + +
477 ALA 3.1 0.2 - - - -
487 PHE* 3.0 28.6 + - + +
497 CYS* 3.6 8.8 + - - -
577 LEU* 4.2 23.1 - - + -
617 ILE 5.1 0.2 - - - +
627 LEU* 3.5 36.8 - - + -
657 PHE* 3.6 40.1 - - + -
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Residues in contact with ILE 46 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157 PHE* 3.5 36.3 - - + -
177 LEU* 3.9 23.6 - - + -
427 VAL* 3.1 23.2 + - + +
457 LEU* 1.3 76.1 - - + +
477 ALA* 1.3 58.0 + - - +
487 PHE 3.1 5.2 - - - -
497 CYS* 3.3 22.3 + - + +
507 THR* 3.2 16.8 + - - -
617G PHE* 3.5 22.4 - - + -
620G ALA* 3.7 16.2 - - + -
621G MET* 3.4 9.6 - - + -
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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