Contacts of the helix formed by residues 16 - 22 (chain G) in PDB entry 6V3O
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 ILE 16 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G SER* 1.3 77.0 + - - +
17G ASP* 1.3 64.2 + - - +
18G ALA 3.2 1.5 + - - -
19G GLN* 3.2 17.2 + - - +
20G LEU* 3.5 20.2 + - + +
38G ASP 5.5 0.2 - - - +
39G ALA* 4.7 8.1 - - - -
42G VAL* 4.3 13.7 - - + -
43G ASP* 3.1 17.8 + - - +
46G LEU* 4.1 16.8 - - + -
62G GLN* 3.9 28.3 - - + +
65G TYR* 3.3 50.6 + - + +
66G GLU* 5.2 0.7 - - - +
105G MET* 5.6 0.4 - - + -
897G TYR* 4.7 6.3 - - - +
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Residues in contact with ASP 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G SER* 3.2 26.9 + - - +
16G ILE* 1.3 76.9 - - - +
18G ALA* 1.3 86.9 + - - +
20G LEU* 3.1 17.1 + - - +
21G ARG* 3.2 36.4 + - - +
35G ILE* 4.6 3.2 - - + +
39G ALA* 4.1 19.8 - - + +
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G HIS* 6.4 0.4 - - + -
15G SER 4.9 2.0 - - - +
16G ILE 3.2 0.8 + - - -
17G ASP* 1.3 92.5 + - - +
19G GLN* 1.3 69.1 + - + +
21G ARG* 2.9 30.5 + - - +
22G GLN* 3.6 7.3 + - - +
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Residues in contact with GLN 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G HIS* 3.9 13.6 + - - -
15G SER 3.6 13.2 - - - +
16G ILE* 3.2 13.8 + - - +
18G ALA* 1.3 80.7 - - - +
20G LEU* 1.3 56.9 + - - +
22G GLN* 4.6 4.3 + - - +
23G LEU* 3.0 21.3 + - - +
65G TYR* 4.0 20.5 + - + -
66G GLU* 3.6 41.8 + - + +
69G ALA* 3.9 13.6 - - + +
70G ASP* 4.9 13.7 - - - +
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 3.5 20.8 + - + +
17G ASP* 3.1 6.1 + - - +
18G ALA 3.1 0.6 - - - -
19G GLN* 1.3 78.0 - - - +
21G ARG* 1.3 65.0 + - - +
22G GLN 3.3 0.9 - - - -
23G LEU* 3.3 24.9 + - + +
24G VAL* 3.8 5.5 + - - +
35G ILE* 3.4 35.2 - - + +
38G ASP* 3.6 31.4 - - + +
39G ALA* 4.3 2.9 - - - +
65G TYR* 3.1 28.0 - - + +
893G LEU* 4.1 36.1 - - + +
896G PRO* 4.9 1.3 - - + -
897G TYR* 4.8 4.0 - - - +
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Residues in contact with ARG 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ASP* 3.3 31.5 + - - +
18G ALA* 2.9 12.1 + - - +
20G LEU* 1.3 77.8 - - - +
22G GLN* 1.3 62.0 + - - +
23G LEU 3.2 0.2 - - - -
24G VAL* 2.6 29.3 - - - +
35G ILE* 3.4 42.0 - - + +
36G GLU* 5.2 6.7 - - - +
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ALA 3.6 7.9 + - - +
19G GLN* 4.6 3.5 - - - +
20G LEU 3.3 0.6 - - - -
21G ARG* 1.3 85.1 + - - +
23G LEU* 1.3 61.9 + - - +
24G VAL 3.5 2.9 + - - -
25G PRO* 5.9 2.8 - - - +
73G GLY* 5.2 8.4 - - - -
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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