Contacts of the helix formed by residues 37 - 42 (chain v) in PDB entry 4IL6
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 CYS 37 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32v LEU 4.4 0.7 - - - -
33v PHE* 2.7 48.6 + - + +
34v GLN 4.2 0.2 + - - -
35v TYR 3.8 0.2 - - - -
36v ALA* 1.3 78.7 - - - +
38v ALA* 1.3 58.8 + - - +
39v SER* 3.2 4.1 + - - -
40v CYS* 3.0 9.9 + - - +
41v HIS* 3.0 25.9 + - + +
115v ILE* 4.2 9.0 - - - -
201v HEM 2.2 64.2 - - + +
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Residues in contact with ALA 38 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416c SER* 4.5 10.5 - - - +
417c VAL* 3.6 18.6 - - + +
33v PHE* 2.9 19.3 + - + +
34v GLN* 3.7 28.3 + - + +
37v CYS* 1.3 70.7 - - - +
39v SER* 1.3 62.1 + - - +
40v CYS 2.9 6.8 + - - -
41v HIS 3.7 0.2 - - - -
42v VAL* 3.0 38.4 + - - +
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Residues in contact with SER 39 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83c GLU* 5.3 1.8 - - - -
397c THR* 3.6 27.2 + - - +
398c HIS* 4.2 27.9 - - - -
417c VAL* 4.1 19.1 - - - +
34v GLN 4.9 2.4 + - - -
36v ALA 5.0 2.0 + - - -
37v CYS 3.2 1.7 + - - +
38v ALA* 1.3 76.7 - - - +
40v CYS* 1.3 62.2 + - - +
47v LYS* 3.8 13.3 + - - +
103v LYS* 5.0 8.1 + - - -
201v HEM 3.9 18.2 - - - +
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Residues in contact with CYS 40 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397c THR* 3.9 18.6 - - - -
37v CYS 3.0 2.8 + - - +
39v SER* 1.3 87.7 + - - +
41v HIS* 1.3 60.9 + - + +
42v VAL 3.6 2.0 - - - -
45v ILE* 3.4 1.7 - - - +
46v THR* 3.3 3.5 - - - -
47v LYS* 2.8 41.4 + - - +
48v THR* 4.2 3.4 - - - +
201v HEM 2.2 72.2 - - + +
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Residues in contact with HIS 41 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33v PHE* 3.5 18.3 - - + -
37v CYS* 3.0 10.7 + - + +
38v ALA* 4.0 0.7 - - - -
40v CYS* 1.3 77.2 - - - +
42v VAL* 1.3 67.9 + - - +
43v GLY 3.2 0.5 + - - -
44v GLY 2.8 15.2 + - - -
45v ILE 2.8 24.6 + - - +
46v THR* 2.9 25.4 + - + -
54v LEU* 3.7 25.3 - - + +
201v HEM 2.1 90.5 + + + -
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Residues in contact with VAL 42 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413c GLU* 4.2 6.5 - - - +
414c ILE* 3.8 25.6 - - + +
416c SER* 3.5 30.5 - - - +
417c VAL* 4.6 4.9 - - + -
33v PHE* 4.7 2.5 - - - -
38v ALA* 3.0 25.4 + - - +
41v HIS* 1.3 77.9 - - - +
43v GLY* 1.3 61.8 + - - +
44v GLY 3.0 3.6 + - - -
45v ILE* 3.2 20.8 - - + +
47v LYS* 3.7 36.8 - - + +
137v TYR* 5.4 7.2 + - - +
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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