Contacts of the helix formed by residues 30 - 36 (chain I) in PDB entry 6GYS
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 30 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4I ARG* 3.5 13.8 - - - +
17I CYS* 3.5 2.0 - - - -
20I ARG* 2.6 15.7 - - - +
25I ASP* 3.2 24.2 - - + +
26I ARG* 4.9 1.1 - - - -
27I MET* 4.2 1.6 - - - -
28I ILE 3.7 0.6 - - - -
29I PRO* 1.3 84.3 - - - +
31I GLY* 1.3 61.0 + - - +
32I ASN 3.3 0.9 - - - +
33I CYS* 3.5 15.3 - - + +
34I ARG* 3.4 20.8 + - - +
42I CYS* 3.6 0.2 - - - -
701I ZN 2.4 37.9 - - - -
702I ZN 3.3 7.2 - - - -
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Residues in contact with GLY 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ARG* 3.4 10.2 - - - +
23I LYS* 6.2 0.2 - - - -
25I ASP* 2.8 16.6 + - - -
30I CYS* 1.3 73.8 - - - +
32I ASN* 1.3 59.2 + - - +
34I ARG* 4.1 2.3 - - - +
35I LYS* 3.3 23.6 + - - +
530I GLY 5.0 0.2 - - - -
531I ASP* 3.1 39.2 + - - +
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Residues in contact with ASN 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ARG* 3.4 25.7 - - - +
22I VAL* 3.3 33.9 - - - +
23I LYS* 5.2 9.9 + - - +
25I ASP* 4.5 7.2 + - + +
30I CYS* 3.3 1.0 - - - +
31I GLY* 1.3 79.8 - - - +
33I CYS* 1.3 59.9 + - - +
34I ARG 3.3 0.2 - - - -
35I LYS* 3.1 10.2 + - - +
36I ARG* 3.0 38.2 + - - +
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Residues in contact with CYS 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I VAL* 3.6 20.0 - - + -
17I CYS* 3.9 0.9 - - - -
20I ARG* 2.7 35.2 - - - +
29I PRO* 5.4 0.2 - - + -
30I CYS* 3.5 7.6 - - + +
32I ASN* 1.3 76.8 - - - +
34I ARG* 1.3 61.9 + - - +
36I ARG* 3.4 9.5 + - - +
38I GLN* 2.8 44.9 + - - +
39I ASP* 5.1 0.7 - - - -
42I CYS* 3.8 2.2 - - + -
701I ZN 3.4 1.6 - - - -
702I ZN 2.2 37.5 - - - -
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Residues in contact with ARG 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ARG* 3.4 25.3 - - - +
30I CYS 3.4 16.7 + - - +
31I GLY* 4.3 3.6 - - - +
32I ASN 3.3 0.4 - - - -
33I CYS* 1.3 74.4 - - - +
35I LYS* 1.3 64.0 + - - +
37I GLY* 3.1 13.3 + - - -
39I ASP* 3.3 37.8 + - + +
528I ASP* 2.4 27.9 + - - -
530I GLY* 2.2 52.0 + - - +
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Residues in contact with LYS 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLY 3.3 19.1 + - - +
32I ASN* 3.1 16.9 + - - +
34I ARG* 1.3 79.2 - - - +
36I ARG* 1.3 58.4 + - + +
37I GLY 3.2 2.7 + - - -
529I SER* 4.5 11.9 + - - +
530I GLY* 4.4 19.1 - - - -
531I ASP* 5.5 2.5 - - - +
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Residues in contact with ARG 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ARG* 3.2 40.3 - - - +
20I ARG* 4.0 26.1 + - - +
22I VAL* 5.7 3.0 - - - +
32I ASN* 3.0 29.1 + - - +
33I CYS* 3.8 6.7 - - - +
34I ARG 3.2 0.8 - - - -
35I LYS* 1.3 76.2 - - + +
37I GLY* 1.3 57.8 - - - +
38I GLN* 3.1 22.8 + - - +
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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