Contacts of the helix formed by residues 37 - 46 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318 CYS* 5.2 1.1 - - - -
358 GLY 3.2 9.8 + - - +
368 GLN* 1.3 75.1 + - - +
388 GLU* 1.3 76.1 + - - +
398 GLU* 3.0 18.1 + - + +
408 GLY* 3.0 6.0 + - - +
418 MET* 2.9 21.7 + - - +
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Residues in contact with GLU 38 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38 ALA* 2.6 40.3 - - + +
78 GLN* 3.6 34.4 - - + +
88 LEU* 3.7 42.0 - - + +
118 GLU* 4.2 4.3 - - + +
318 CYS* 4.5 3.2 - - - +
378 ASN* 1.3 79.1 - - - +
398 GLU* 1.3 72.4 + - + +
418 MET* 4.1 0.9 - - - -
428 VAL* 3.1 31.5 + - - +
548H ARG* 6.0 0.2 - - - +
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Residues in contact with GLU 39 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78 GLN* 5.8 0.9 - - - +
118 GLU* 5.1 14.5 - - - +
378 ASN* 3.0 11.8 + - + +
388 GLU* 1.3 99.2 - - + +
408 GLY* 1.3 61.7 + - - +
428 VAL* 4.4 1.6 - - - +
438 GLY* 3.6 14.7 + - - -
548H ARG* 4.9 19.7 + - - +
551H ASP* 5.6 6.8 - - - +
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Residues in contact with GLY 40 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368 GLN* 4.3 13.5 - - - -
378 ASN* 3.0 10.1 + - - +
398 GLU* 1.3 78.1 - - - +
418 MET* 1.3 64.0 + - - +
438 GLY* 3.5 1.8 + - - -
448 GLU* 3.1 34.4 + - - +
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Residues in contact with MET 41 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88 LEU* 4.5 6.7 - - + -
278 LEU* 4.6 8.3 - - + +
308 LEU* 3.4 45.8 - - + +
318 CYS* 3.9 17.0 - - - -
348 TYR* 5.7 0.2 - - + -
368 GLN* 3.6 43.4 - - + +
378 ASN 2.9 13.1 + - - +
388 GLU 4.3 4.0 - - - +
408 GLY* 1.3 75.2 - - - +
428 VAL* 1.3 60.5 + - + +
448 GLU* 3.1 7.7 + - + +
458 LEU* 2.8 32.3 + - - +
658 PHE* 3.7 22.7 - - + -
708 LEU* 4.2 9.4 - - + -
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Residues in contact with VAL 42 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88 LEU* 3.9 26.7 - - + +
118 GLU* 3.5 40.2 - - + +
128 LEU* 4.7 3.4 - - + -
158 PHE* 4.0 10.1 - - + -
178 LEU* 4.4 7.0 - - + -
278 LEU* 6.5 0.4 - - - -
388 GLU 3.1 20.3 + - - +
398 GLU 4.7 2.0 - - - +
408 GLY 3.5 0.2 - - - -
418 MET* 1.3 74.2 - - - +
438 GLY* 1.3 59.4 + - - +
458 LEU* 4.2 6.5 - - + -
468 ILE* 3.0 51.2 + - + +
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Residues in contact with GLY 43 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398 GLU 3.6 11.4 + - - -
408 GLY* 3.5 6.6 + - - -
418 MET 3.1 0.8 - - - -
428 VAL* 1.3 82.5 - - - +
448 GLU* 1.3 64.8 + - - +
468 ILE* 4.2 4.3 + - - +
478 ALA* 4.0 14.7 + - - +
552H TYR* 6.4 3.8 - - - -
620H ALA 4.8 10.9 - - - +
621H MET* 5.8 0.3 - - - +
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Residues in contact with GLU 44 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368 GLN* 4.8 8.7 - - - +
408 GLY* 3.1 20.9 + - - +
418 MET* 3.9 7.0 - - + +
438 GLY* 1.3 80.6 - - - +
458 LEU* 1.3 65.4 + - - +
478 ALA* 3.3 19.3 + - - +
488 PHE 3.6 1.4 + - - -
658 PHE* 3.3 29.2 - - + -
698 PHE* 3.1 34.3 - - + -
708 LEU* 5.2 1.1 - - + -
738 ARG* 5.0 1.3 + - - -
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Residues in contact with LEU 45 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128 LEU* 6.3 2.0 - - + -
178 LEU* 5.7 2.2 - - + -
278 LEU* 4.1 12.3 - - + -
308 LEU* 5.0 0.2 - - + -
418 MET 2.8 17.8 + - - +
428 VAL* 3.9 9.2 - - + +
438 GLY 3.4 0.2 - - - -
448 GLU* 1.3 77.4 - - - +
468 ILE* 1.3 64.2 + - + +
478 ALA 3.1 0.2 - - - -
488 PHE* 3.0 28.7 + - + +
498 CYS* 3.6 8.8 + - - -
578 LEU* 4.2 22.9 - - + -
618 ILE* 5.1 0.4 - - + +
628 LEU* 3.5 36.8 - - + -
658 PHE* 3.6 40.4 - - + -
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Residues in contact with ILE 46 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158 PHE* 3.5 39.0 - - + -
178 LEU* 3.9 22.4 - - + -
428 VAL* 3.0 25.2 + - + +
438 GLY* 4.2 4.0 + - - +
448 GLU 3.5 0.2 - - - -
458 LEU* 1.3 76.3 - - + +
478 ALA* 1.3 57.7 + - - +
488 PHE 3.1 5.4 - - - -
498 CYS* 3.3 21.3 + - + +
508 THR* 3.2 17.2 + - - -
617H PHE* 4.9 6.3 - - + -
620H ALA* 3.9 17.7 - - + +
621H MET* 3.5 22.4 - - + +
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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