Contacts of the helix formed by residues 14 - 21 (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 14 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I HIS* 3.9 1.2 + - - -
13I PRO* 1.3 78.0 - - - +
15I SER* 1.3 61.9 + - - +
16I VAL* 3.3 21.8 - - - -
17I CYS* 3.5 8.0 + - - -
18I THR* 3.3 23.5 + - - +
41I GLU 4.6 4.0 - - - +
42I CYS* 3.6 26.6 - - - +
44I LYS 5.2 3.1 - - - +
45I SER* 4.6 18.2 - - - -
702I ZN 3.5 28.0 - - - -
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Residues in contact with SER 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I CYS* 1.3 74.3 - - - +
16I VAL* 1.3 70.6 + - - +
18I THR* 2.4 29.2 + - - -
19I ARG* 2.9 15.0 + - - +
41I GLU 5.2 1.0 + - - -
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Residues in contact with VAL 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I CYS* 3.3 9.6 - - - -
15I SER* 1.3 81.8 - - - +
17I CYS* 1.3 59.7 + - - +
19I ARG* 3.3 18.2 + - - +
20I ARG* 2.9 27.8 + - - +
33I CYS* 3.6 22.9 - - + -
38I GLN* 3.3 29.4 - - + +
41I GLU* 3.4 39.7 - - + +
702I ZN 4.2 1.6 - - - -
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Residues in contact with CYS 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I PRO* 4.1 13.9 - - + -
14I CYS* 3.5 18.7 - - - +
15I SER 3.3 0.4 - - - -
16I VAL* 1.3 75.0 - - - +
18I THR* 1.3 60.5 + - - +
20I ARG* 3.0 23.5 + - - +
21I LYS* 3.1 11.3 + - - -
22I VAL 4.6 4.0 + - - +
24I CYS* 4.7 9.9 - - + -
30I CYS* 3.5 2.5 - - - -
42I CYS* 3.8 1.8 - - - -
701I ZN 1.8 48.5 - - - -
702I ZN 3.1 21.1 - - - -
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Residues in contact with THR 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I PRO* 5.0 8.7 - - + +
14I CYS 3.3 15.0 + - - +
15I SER* 2.4 32.4 + - - -
17I CYS* 1.3 73.4 - - - +
19I ARG* 1.3 57.9 + - - +
21I LYS* 2.2 43.1 + - - +
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Residues in contact with ARG 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I SER 2.9 13.1 + - - +
16I VAL* 3.4 26.9 + - - +
18I THR* 1.3 76.5 + - - +
20I ARG* 1.3 70.5 + - - +
21I LYS* 3.5 13.3 + - - +
33I CYS* 5.7 0.2 - - - +
36I ARG* 3.2 48.8 - - - +
38I GLN* 2.4 39.7 + - - +
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Residues in contact with ARG 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I VAL 2.9 14.7 + - - +
17I CYS* 3.0 10.9 + - - +
19I ARG* 1.3 84.6 - - - +
21I LYS* 1.3 67.0 + - - +
22I VAL* 3.2 33.2 + - + +
23I LYS 3.1 22.0 + - - -
24I CYS* 3.4 5.3 - - - +
25I ASP 3.3 14.1 - - - +
30I CYS* 2.6 20.8 - - - +
32I ASN* 3.4 27.6 - - - +
33I CYS* 2.7 30.5 - - - +
36I ARG* 4.0 23.7 + - - +
701I ZN 1.9 39.5 - - - -
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Residues in contact with LYS 21 (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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17I CYS 3.1 9.9 + - - -
18I THR* 2.2 38.6 + - - +
19I ARG* 3.5 12.6 - - - +
20I ARG* 1.3 76.4 - - - +
22I VAL* 1.3 62.6 + - - +
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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