Contacts of the helix formed by residues 12 - 25 (chain G) in PDB entry 6BZE
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 ASP 12 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G GLU* 2.8 48.9 + - - +
11G GLU* 1.3 78.5 - - - +
13G LEU* 1.3 64.8 + - - +
14G THR* 3.2 2.9 - - - -
15G GLU* 3.2 24.6 + - - +
16G VAL* 3.9 8.7 - - - +
113G HIS* 4.2 24.6 - - + +
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Residues in contact with LEU 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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10G GLU* 5.3 8.4 + - - +
11G GLU* 4.7 21.8 - - - +
12G ASP* 1.3 78.0 - - - +
14G THR* 1.3 74.5 + - + +
15G GLU 2.8 12.2 + - - -
16G VAL* 3.1 22.8 + - + +
17G LYS* 2.5 44.4 + - - +
76G PRO 5.5 1.1 - - - +
110G LYS* 5.4 11.9 - - + -
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Residues in contact with THR 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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11G GLU* 3.4 32.5 - - - +
13G LEU* 1.3 84.3 - - - +
15G GLU* 1.3 79.1 + - + +
17G LYS* 3.6 22.8 - - - +
18G LYS* 4.2 8.3 - - - +
73G GLN 4.8 1.2 + - - +
75G ASN 3.9 6.1 + - - +
76G PRO* 3.1 39.5 - - + +
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Residues in contact with GLU 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 GLU 5.4 0.4 - - - +
12G ASP* 3.5 14.8 - - - +
13G LEU 2.8 2.0 + - - -
14G THR* 1.3 96.7 + - + +
16G VAL* 1.3 65.1 + - + +
17G LYS 3.0 2.5 - - - -
18G LYS* 2.3 62.1 + - - +
19G ASP* 3.6 5.7 + - - +
73G GLN 5.2 1.4 - - - +
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Residues in contact with VAL 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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12G ASP 3.9 13.9 - - - +
13G LEU* 3.1 14.5 + - - +
15G GLU* 1.3 76.6 - - + +
17G LYS* 1.3 55.6 + - - +
19G ASP* 3.0 17.1 + - - +
20G ALA* 2.7 33.1 + - - +
106G LEU* 3.6 20.6 - - + -
109G ILE* 3.6 20.1 - - + +
110G LYS* 4.1 18.8 - - + -
113G HIS* 4.1 27.6 - - + +
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Residues in contact with LYS 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 LEU* 2.5 61.6 + - - +
14G THR* 3.6 15.9 - - - +
15G GLU 3.0 0.2 - - - -
16G VAL* 1.3 76.4 - - - +
18G LYS* 1.3 55.4 + - + +
20G ALA* 3.2 9.7 + - - +
21G LEU* 2.6 36.3 + - - +
76G PRO 4.0 12.8 - - - +
77G LYS 4.6 11.7 - - - +
78G GLY* 5.5 7.2 - - - +
79G LEU* 5.0 8.5 - - + -
106G LEU* 3.5 32.8 - - + +
110G LYS* 5.9 0.4 - - - +
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Residues in contact with LYS 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 THR 4.2 5.6 - - - +
15G GLU* 2.3 73.7 + - - +
17G LYS* 1.3 78.1 - - + +
19G ASP* 1.3 53.4 + - - +
21G LEU* 2.8 8.9 + - - +
22G GLU* 2.2 46.8 + - + +
73G GLN* 3.5 52.3 - - + +
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Residues in contact with ASP 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 GLU 4.0 4.7 - - - +
16G VAL* 3.0 26.6 + - - +
18G LYS* 1.3 77.2 + - - +
20G ALA* 1.3 54.7 + - - +
22G GLU* 3.8 11.2 - - - +
23G ASN* 2.4 46.3 + - - +
109G ILE* 3.6 17.3 - - + +
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Residues in contact with ALA 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 VAL 2.7 15.5 + - - +
17G LYS* 3.3 12.6 - - - +
19G ASP* 1.3 70.6 - - - +
21G LEU* 1.3 53.0 + - - +
23G ASN* 3.0 4.5 + - - +
24G LEU* 2.5 40.0 + - - +
102G GLU* 4.8 4.0 - - + +
105G LYS* 3.8 7.7 - - + +
106G LEU* 3.6 37.0 - - + +
109G ILE* 3.2 10.4 - - - +
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Residues in contact with LEU 21 (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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17G LYS 2.6 21.5 + - - +
18G LYS* 3.2 5.4 - - - +
20G ALA* 1.3 73.4 - - - +
22G GLU* 1.3 52.9 + - - +
24G LEU* 3.1 17.3 - - + -
25G ARG* 2.4 38.9 + - + +
69G LEU* 3.5 53.4 - - + +
72G LEU* 4.8 8.7 - - + -
73G GLN* 3.5 29.2 - - + +
102G GLU* 4.9 6.5 - - - +
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Residues in contact with GLU 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 LYS* 2.2 40.4 + - + +
19G ASP* 3.3 12.8 - - - +
21G LEU* 1.3 69.0 - - - +
23G ASN* 1.3 64.2 + - - +
25G ARG* 3.1 41.0 + - - +
26G VAL* 4.5 3.3 + - - +
73G GLN* 2.1 39.3 + - - +
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Residues in contact with ASN 23 (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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19G ASP* 2.4 33.7 + - - +
20G ALA* 3.2 2.0 - - - +
22G GLU* 1.3 77.7 + - - +
24G LEU* 1.3 58.2 + - - +
25G ARG 3.3 0.2 - - - -
26G VAL* 4.1 16.3 - - - +
105G LYS* 3.5 35.6 + - - +
109G ILE* 3.0 21.0 - - - +
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Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ALA 2.5 25.9 + - - +
21G LEU* 3.1 16.8 - - + +
23G ASN* 1.3 72.8 - - - +
25G ARG* 1.3 59.6 + - - +
26G VAL* 3.0 2.9 - - - -
27G TYR* 2.8 49.3 + - + +
69G LEU* 4.9 4.7 - - + +
95G LEU* 6.4 2.0 - - + -
98G LYS* 5.2 1.1 - - + +
101G ASP* 4.1 10.8 - - - +
102G GLU* 3.2 47.1 - - + +
105G LYS* 3.7 26.5 - - + -
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Residues in contact with ARG 25 (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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21G LEU* 2.4 24.0 + - - +
22G GLU* 3.1 41.4 + - - +
23G ASN 3.3 0.2 - - - -
24G LEU* 1.3 70.2 - - - +
26G VAL* 1.3 61.9 + - + +
27G TYR 3.2 1.2 + - - -
28G LEU* 3.3 31.7 + - + +
66G GLY* 3.9 29.1 + - - -
69G LEU* 4.9 17.3 - - - -
70G ASP* 4.4 19.8 + - - +
73G GLN* 5.7 2.2 - - - +
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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