Contacts of the helix formed by residues 7 - 19 (chain E) in PDB entry 6H25
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 SER 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LEU* 1.3 77.0 - - - +
8E GLU* 1.3 67.6 + - - +
9E ALA* 3.5 12.8 + - - +
10E GLU* 2.4 40.3 + - - +
11E LYS* 3.2 17.8 - - - +
138H GLY 3.5 16.9 + - - -
139H ASP* 2.3 39.0 + - - +
140H LEU* 4.7 3.6 - - - -
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Residues in contact with GLU 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E SER* 1.3 82.1 + - - +
9E ALA* 1.3 61.6 + - + +
10E GLU 3.3 1.3 - - - -
11E LYS* 3.2 21.4 - - + +
12E VAL* 2.9 27.7 + - - +
136H GLN* 5.1 14.9 - - + +
139H ASP* 4.2 5.2 + - - +
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Residues in contact with ALA 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E SER* 3.5 8.1 + - - +
8E GLU* 1.3 84.8 - - + +
10E GLU* 1.3 56.8 + - - +
12E VAL* 3.2 13.7 + - - +
13E TYR 3.0 22.3 + - - -
166H LEU 5.2 1.1 - - - +
167H GLY 3.3 26.2 - - - +
168H GLN* 3.3 15.9 - - + +
221H ALA* 5.9 3.1 - - + -
223H LEU* 4.4 14.1 - - + -
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Residues in contact with GLU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 3.3 21.1 - - + +
7E SER* 2.4 48.4 + - - +
9E ALA* 1.3 74.9 - - - +
11E LYS* 1.3 59.6 + - - +
13E TYR* 3.8 4.0 - - - +
14E ILE* 2.9 41.9 + - + +
87H ARG* 3.4 11.6 + - - -
140H LEU* 3.4 20.5 - - - +
168H GLN 3.4 19.8 + - - +
169H GLY 4.6 4.5 - - - +
170H VAL* 5.3 1.4 - - - -
171H LEU* 4.8 6.9 + - - +
204H TRP* 4.1 7.3 - - + -
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL 5.8 3.0 - - - +
6E LEU* 3.7 15.7 + - + -
7E SER 3.2 23.3 + - - +
8E GLU* 3.2 21.2 + - + +
9E ALA 3.2 0.6 - - - -
10E GLU* 1.3 77.0 - - - +
12E VAL* 1.3 57.1 + - - +
14E ILE* 3.1 2.9 + - - +
15E VAL* 2.9 35.7 + - + +
220E ALA* 4.0 18.8 + - - -
221E CYS* 3.6 32.0 - - + +
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Residues in contact with VAL 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU 2.9 13.5 + - - +
9E ALA 3.2 14.8 + - - +
11E LYS* 1.3 76.5 - - - +
13E TYR* 1.3 57.6 + - - +
15E VAL* 3.7 10.1 - - + -
16E HIS* 2.7 60.1 + - + +
168H GLN* 3.5 13.2 - - - +
223H LEU* 3.9 33.4 - - + +
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Residues in contact with TYR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA 3.0 15.5 + - - +
10E GLU* 3.8 4.3 - - - +
11E LYS 3.2 0.2 - - - -
12E VAL* 1.3 79.7 - - - +
14E ILE* 1.3 66.4 + - + +
16E HIS* 3.4 3.2 + - - -
17E GLY* 2.9 24.9 + - - -
24E VAL* 5.0 12.8 - - + -
168H GLN* 3.7 32.3 - - + +
169H GLY* 3.2 30.3 - - - +
170H VAL* 4.7 8.3 - - + -
207H PRO* 5.8 2.0 - - + -
226H VAL* 4.7 11.0 - - + -
231H ARG* 3.3 52.4 + - + +
234H ILE* 3.6 29.6 - - + +
235H SER* 5.6 1.2 - - - -
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Residues in contact with ILE 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 5.0 3.4 - - + -
10E GLU* 2.9 28.7 + - + +
11E LYS 3.7 3.4 - - - +
13E TYR* 1.3 82.0 - - + +
15E VAL* 1.3 59.5 + - + +
17E GLY* 3.2 3.0 + - - -
18E VAL* 2.9 37.8 + - + +
23E ARG* 6.0 1.0 - - + -
24E VAL* 3.9 27.1 - - + -
206E ILE* 5.5 1.6 - - + -
217E GLN* 4.0 24.5 - - + -
218E GLU* 4.6 18.2 - - + -
221E CYS* 3.7 30.7 - - + -
170H VAL* 6.3 1.6 - - + -
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Residues in contact with VAL 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LYS* 2.9 17.6 + - + +
12E VAL* 3.3 22.4 - - + +
14E ILE* 1.3 76.4 - - - +
16E HIS* 1.3 70.1 + - + +
18E VAL* 3.1 2.6 + - - +
19E GLN* 3.0 39.9 + - + +
206E ILE* 3.6 35.9 - - + +
207E GLY* 5.7 1.6 - - - -
221E CYS* 4.6 16.8 - - + +
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Residues in contact with HIS 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E VAL* 2.7 52.2 + - + +
13E TYR* 4.0 1.1 - - - +
15E VAL* 1.3 80.0 - - + +
17E GLY* 1.3 64.1 + - - +
19E GLN* 3.8 14.4 + - - +
20E GLU* 3.8 18.9 + - - +
168H GLN* 5.8 0.2 + - - -
223H LEU 5.0 6.1 - - - -
225H PRO* 3.5 42.6 - - + +
231H ARG* 3.5 27.6 + - - +
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Residues in contact with GLY 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E TYR* 2.9 13.9 + - - -
14E ILE* 3.2 4.5 + - - -
16E HIS* 1.3 77.9 - - - +
18E VAL* 1.3 62.2 + - - +
20E GLU 3.5 5.2 + - - -
21E ASP 3.6 0.2 + - - -
22E LEU* 2.9 39.3 + - - +
23E ARG* 4.8 1.6 - - - -
231H ARG* 3.4 22.8 - - - +
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Residues in contact with VAL 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ILE* 2.9 27.9 + - + +
15E VAL 3.1 5.4 + - - +
17E GLY* 1.3 77.1 - - - +
19E GLN* 1.3 66.0 + - + +
20E GLU 3.1 1.4 + - - -
21E ASP* 3.4 12.3 + - - +
23E ARG* 4.2 28.9 - - + -
206E ILE* 3.8 33.0 - - + -
207E GLY 4.8 2.0 - - - +
209E ARG* 4.6 21.4 - - + +
211E VAL* 3.7 25.5 - - + +
218E GLU* 5.7 1.8 - - + -
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Residues in contact with GLN 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E VAL* 3.0 25.0 + - - +
16E HIS* 3.8 16.8 + - + +
17E GLY 3.4 0.4 - - - -
18E VAL* 1.3 81.0 - - + +
20E GLU* 1.3 66.0 + - + +
21E ASP* 3.6 1.8 - - - +
207E GLY* 4.2 10.1 - - - -
208E TYR* 3.3 49.7 - - + +
209E ARG* 4.8 22.4 + - + +
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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