Contacts of the helix formed by residues 11 - 19 (chain G) in PDB entry 6R7H
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 LEU 11 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G SER* 3.9 28.3 - - - +
9G SER 3.3 1.2 - - - +
10G ASN* 1.3 80.4 - - + +
12G LEU* 1.3 64.3 + - + +
13G GLU 3.3 0.2 - - - -
14G GLN* 3.5 32.1 + - - +
15G PHE* 3.2 36.7 + - + -
37G ALA* 6.1 2.7 - - + -
38G PRO 4.1 18.2 - - - +
39G GLY* 5.1 0.4 - - - -
40G VAL* 4.7 7.6 - - + -
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Residues in contact with LEU 12 (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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254F HIS* 4.7 20.9 - - + +
255F GLU* 4.7 3.6 - - - +
258F ARG* 3.4 32.1 - - - +
8G SER 3.8 15.7 - - - +
9G SER* 3.9 11.9 - - - +
10G ASN 3.3 1.0 - - - -
11G LEU* 1.3 79.6 - - + +
13G GLU* 1.3 59.4 + - - +
14G GLN 3.5 0.5 + - - -
15G PHE* 3.9 3.9 + - + +
16G ILE* 3.4 30.3 + - - +
39G GLY 4.6 1.3 - - - +
40G VAL* 3.8 34.8 - - + -
41G TYR 4.8 0.4 - - - +
42G VAL* 3.8 28.5 - - + -
45G GLU* 4.5 10.3 - - - +
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Residues in contact with GLU 13 (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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254F HIS* 4.8 13.2 - - + +
9G SER 4.1 13.0 - - - +
10G ASN* 3.7 18.1 + - - +
11G LEU 3.3 0.4 - - - -
12G LEU* 1.3 77.8 - - - +
14G GLN* 1.3 62.1 + - + +
16G ILE* 3.7 23.1 - - + +
17G LEU* 3.6 23.3 - - + +
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Residues in contact with GLN 14 (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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10G ASN* 3.5 33.1 + - - +
11G LEU* 3.5 27.9 + - - +
12G LEU 3.3 0.8 - - - -
13G GLU* 1.3 80.1 - - + +
15G PHE* 1.3 69.1 + - + +
16G ILE 3.3 2.0 - - - -
17G LEU* 3.6 5.7 + - - +
18G LEU* 3.4 33.7 + - + +
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Residues in contact with PHE 15 (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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11G LEU* 3.2 32.3 + - + +
12G LEU* 3.9 4.9 + - - +
14G GLN* 1.3 83.8 - - + +
16G ILE* 1.3 63.5 + - + +
17G LEU 3.3 0.4 - - - -
18G LEU* 4.2 9.2 - - + +
19G ALA* 3.6 22.7 + - - +
30G LEU* 4.2 22.2 - - + +
33G GLN* 4.7 12.8 - - + -
34G VAL* 3.7 40.4 - - + -
37G ALA* 4.9 9.9 - - + -
40G VAL* 3.7 29.2 - - + -
46G LEU* 4.1 15.7 - - + +
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Residues in contact with ILE 16 (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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254F HIS* 4.5 18.4 - - + +
12G LEU 3.4 22.0 - - - +
13G GLU* 3.7 21.8 - - + +
15G PHE* 1.3 79.3 - - + +
17G LEU* 1.3 66.0 + - + +
19G ALA* 4.3 3.6 - - - +
20G LYS* 4.0 25.1 + - - +
45G GLU* 3.8 33.4 - - + +
46G LEU* 4.6 11.7 - - + -
49G LEU* 5.4 5.8 - - + +
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Residues in contact with LEU 17 (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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13G GLU* 3.6 21.1 - - + +
14G GLN* 3.6 6.8 + - - +
15G PHE 3.3 0.4 - - - -
16G ILE* 1.3 86.6 - - + +
18G LEU* 1.3 66.9 + - + +
19G ALA 3.4 0.4 - - - -
20G LYS* 3.7 7.2 + - + +
21G GLY* 3.7 15.1 + - - -
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Residues in contact with LEU 18 (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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14G GLN* 3.4 24.7 + - + +
15G PHE* 4.0 8.9 + - + -
17G LEU* 1.3 79.0 - - + +
19G ALA* 1.3 63.7 + - - +
20G LYS 3.3 0.6 + - - -
21G GLY* 3.6 5.5 + - - -
22G THR* 3.4 24.5 + - + +
30G LEU* 4.5 27.3 - - + +
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Residues in contact with ALA 19 (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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15G PHE 3.6 18.0 + - - +
16G ILE 4.8 2.9 - - - +
17G LEU 3.4 0.2 - - - -
18G LEU* 1.3 80.6 - - - +
20G LYS* 1.3 55.8 + - - +
21G GLY 3.4 0.2 - - - -
22G THR* 3.1 18.7 - - - +
27G LEU* 4.0 16.1 - - + +
30G LEU* 4.0 16.5 - - + +
46G LEU* 4.7 12.3 - - + -
49G LEU* 4.8 7.0 - - + -
51G ASN* 3.2 25.4 + - + +
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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