Contacts of the helix formed by residues 37 - 46 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311 CYS* 5.1 1.1 - - - -
351 GLY 3.2 8.9 + - - +
361 GLN* 1.3 74.1 + - - +
381 GLU* 1.3 76.4 + - - +
391 GLU* 3.0 17.9 + - + +
401 GLY* 3.0 6.8 + - - +
411 MET* 2.9 21.7 + - - +
551A ASP* 5.7 2.8 + - - +
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Residues in contact with GLU 38 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31 ALA* 2.6 39.3 - - + +
71 GLN* 3.6 34.8 - - + +
81 LEU* 3.7 40.8 - - + +
111 GLU* 4.2 4.2 - - + +
311 CYS* 4.6 3.2 - - - +
361 GLN 3.8 0.2 + - - -
371 ASN* 1.3 78.9 - - - +
391 GLU* 1.3 71.6 - - - +
411 MET* 4.1 1.1 - - - -
421 VAL* 3.1 31.7 + - - +
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Residues in contact with GLU 39 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 GLN* 5.4 2.1 - - - +
111 GLU* 5.1 9.3 - - + +
371 ASN* 3.0 12.8 + - + +
381 GLU* 1.3 98.5 - - + +
401 GLY* 1.3 61.5 + - - +
411 MET 3.4 0.2 - - - -
421 VAL* 4.7 1.4 - - - +
431 GLY* 3.6 15.1 + - - -
548A ARG* 5.7 3.1 + - - -
549A PRO 5.1 4.7 - - - +
550A LYS* 4.9 12.8 - - + -
551A ASP* 3.7 29.3 - - + +
552A TYR* 4.4 35.4 - - + +
620A ALA 4.7 1.7 - - - +
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Residues in contact with GLY 40 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 GLN* 4.3 14.4 - - - -
371 ASN* 3.0 10.9 + - - +
391 GLU* 1.3 77.7 - - - +
411 MET* 1.3 62.7 + - - +
431 GLY* 3.5 2.3 + - - -
441 GLU* 3.1 34.3 + - - +
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Residues in contact with MET 41 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81 LEU* 4.5 7.4 - - + -
271 LEU* 4.6 7.0 - - + +
301 LEU* 3.4 44.4 - - + +
311 CYS* 3.9 17.9 - - - -
341 TYR* 5.7 0.2 - - + -
361 GLN* 3.6 43.7 - - + +
371 ASN 2.9 11.6 + - - +
381 GLU 4.3 3.8 - - - +
401 GLY* 1.3 75.5 - - - +
421 VAL* 1.3 59.9 + - - +
441 GLU* 3.1 8.2 + - + +
451 LEU* 2.8 32.7 + - - +
651 PHE* 3.7 24.0 - - + -
701 LEU* 4.3 9.4 - - + -
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Residues in contact with VAL 42 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 LEU* 3.9 27.4 - - + +
111 GLU* 3.5 38.6 - - + +
121 LEU* 4.7 3.8 - - + -
151 PHE* 4.0 9.6 - - + -
171 LEU* 4.5 7.6 - - + -
381 GLU 3.1 21.2 + - - +
391 GLU 4.7 2.2 - - - +
401 GLY 3.5 0.2 - - - -
411 MET* 1.3 76.0 - - - +
431 GLY* 1.3 58.4 + - - +
451 LEU* 4.2 6.5 - - + -
461 ILE* 3.0 51.3 + - + +
620A ALA* 5.0 0.9 - - + -
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Residues in contact with GLY 43 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 GLU 3.6 9.6 + - - -
401 GLY* 3.5 6.2 + - - -
411 MET 3.1 1.2 - - - -
421 VAL* 1.3 81.5 - - - +
441 GLU* 1.3 63.2 + - - +
471 ALA* 4.0 0.2 - - - +
620A ALA* 3.0 28.9 - - - -
621A MET* 2.9 36.2 - - - +
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Residues in contact with GLU 44 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 GLN* 4.8 8.7 - - - +
401 GLY* 3.1 19.6 + - - +
411 MET* 3.9 7.2 - - + +
431 GLY* 1.3 78.7 - - - +
451 LEU* 1.3 65.8 + - - +
471 ALA* 3.4 19.9 + - - +
481 PHE 3.6 1.6 + - - -
651 PHE* 3.2 28.7 - - + -
691 PHE* 3.1 34.5 - - + -
701 LEU* 5.2 0.9 - - + -
731 ARG* 5.0 1.4 + - - -
621A MET* 4.9 6.9 - - - +
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Residues in contact with LEU 45 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 LEU* 6.3 1.8 - - + -
171 LEU* 5.7 2.2 - - + -
271 LEU* 4.1 12.8 - - + -
301 LEU* 5.0 0.2 - - + -
411 MET 2.8 18.5 + - - +
421 VAL* 3.9 9.2 - - + +
441 GLU* 1.3 77.6 - - - +
461 ILE* 1.3 63.7 + - + +
471 ALA 3.1 0.2 - - - -
481 PHE* 3.0 29.0 + - + +
491 CYS* 3.6 9.2 + - - -
571 LEU* 4.2 22.9 - - + -
611 ILE* 5.1 0.7 - - + +
621 LEU* 3.5 37.2 - - + -
651 PHE* 3.6 39.6 - - + -
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Residues in contact with ILE 46 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151 PHE* 3.5 28.5 - - + -
171 LEU* 3.9 23.3 - - + -
421 VAL* 3.0 24.5 + - + +
451 LEU* 1.3 75.6 - - + +
471 ALA* 1.3 58.0 + - - +
481 PHE 3.1 5.2 - - - -
491 CYS* 3.3 23.0 + - + +
501 THR* 3.3 8.9 + - - +
617A PHE* 3.1 30.9 - - + -
620A ALA* 3.5 24.2 - - + -
621A MET* 3.6 8.1 - - + -
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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