Contacts of the helix formed by residues 9 - 22 (chain B) in PDB entry 6MOL
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 PRO 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ASP* 1.3 96.2 - - + +
10B LYS* 1.3 60.9 + - + +
12B GLU* 3.7 11.0 + - + +
13B SER* 3.8 11.1 + - - -
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASP 3.3 1.5 - - - +
9B PRO* 1.3 80.4 - - + +
11B PHE* 1.3 63.9 + - - +
12B GLU 3.2 0.4 - - - -
13B SER* 2.7 23.3 + - - +
14B LYS* 3.0 19.1 + - + +
31B GLU* 4.9 8.7 - - - +
122B ASP* 5.3 8.5 - - - +
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASP* 3.3 42.7 + - - +
10B LYS* 1.3 79.6 - - - +
12B GLU* 1.3 71.0 + - + +
14B LYS* 3.4 5.1 + - - +
15B ALA* 3.0 35.3 + - + +
29B PHE* 3.5 24.7 - + + -
31B GLU* 4.6 11.5 + - - +
37B VAL* 3.8 26.5 - - + -
39B PHE* 5.2 2.0 - + - -
80B ARG* 5.3 7.2 - - - -
82B TRP* 3.9 43.3 - + + -
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASP 3.1 16.3 + - - +
9B PRO* 3.9 7.2 - - + +
11B PHE* 1.3 88.9 - - + +
13B SER* 1.3 63.3 + - - +
15B ALA* 3.3 5.9 + - - +
16B ALA* 3.1 24.8 + - + +
74B THR* 3.6 17.5 + - - -
80B ARG* 3.4 22.8 + - - -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO 3.8 6.0 + - - -
10B LYS* 2.7 30.3 + - - +
12B GLU* 1.3 78.8 - - - +
14B LYS* 1.3 62.0 + - - +
16B ALA* 3.5 8.5 + - - +
17B LEU* 3.5 17.5 + - - +
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 3.0 21.9 + - + +
11B PHE 3.8 4.5 - - - +
13B SER* 1.3 78.7 + - - +
15B ALA* 1.3 64.7 + - - +
17B LEU* 3.2 17.4 + - + +
18B LEU* 3.4 16.1 + - - +
29B PHE* 4.3 10.5 - - + -
31B GLU* 3.4 34.4 - - + +
120B LEU* 3.0 47.3 + - + +
121B LEU 3.6 13.4 + - - -
122B ASP* 3.4 38.8 + - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 3.0 28.0 + - + +
12B GLU 3.3 0.6 + - - +
14B LYS* 1.3 77.2 - - - +
16B ALA* 1.3 57.7 + - - +
18B LEU* 3.4 1.1 + - - -
19B ALA* 3.0 27.9 + - - +
29B PHE* 4.9 2.4 - - + -
39B PHE* 3.4 36.5 - - + -
80B ARG* 3.3 26.7 - - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU* 3.1 17.5 + - + +
13B SER* 3.8 9.9 - - - +
14B LYS 3.2 0.4 - - - -
15B ALA* 1.3 77.7 - - - +
17B LEU* 1.3 62.1 + - - +
19B ALA* 4.0 2.0 - - - +
20B ALA* 3.2 24.6 + - - +
80B ARG* 4.2 12.3 - - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER 3.5 9.3 + - - +
14B LYS* 3.2 13.0 + - + +
16B ALA* 1.3 80.4 - - - +
18B LEU* 1.3 63.1 + - + +
20B ALA* 3.6 5.9 + - + +
21B ARG* 3.4 31.5 + - + +
120B LEU* 4.5 13.2 - - + -
197B ARG* 5.8 5.4 - - - +
209B TRP 3.6 24.0 - - - +
210B SER 4.1 1.8 - - - +
211B ALA* 3.9 29.8 - - + +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS 3.4 7.8 + - - +
15B ALA 3.4 1.4 + - - +
16B ALA 3.4 0.2 - - - -
17B LEU* 1.3 77.2 - - + +
19B ALA* 1.3 66.0 + - - +
21B ARG* 3.2 9.1 + - + +
22B GLY 3.0 20.3 + - - -
27B LEU* 3.5 31.0 - - + +
28B CYS 5.0 0.9 - - - +
29B PHE* 3.7 42.8 - - + -
39B PHE* 3.9 13.5 - - + -
120B LEU* 4.0 14.8 - - + -
208B PHE* 3.6 43.1 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 3.0 17.3 + - - +
16B ALA* 4.0 3.8 - - - +
17B LEU 3.4 0.2 - - - -
18B LEU* 1.3 76.4 - - - +
20B ALA* 1.3 62.4 + - - +
22B GLY 4.6 0.4 - - - -
23B PRO* 3.4 31.2 - - + +
27B LEU* 3.9 11.3 - - + +
39B PHE* 4.4 6.5 - - + -
41B GLU* 3.2 35.4 - - + +
80B ARG* 4.3 2.0 - - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.2 17.5 + - - +
17B LEU* 3.9 6.7 - - + +
18B LEU 3.3 0.2 - - - -
19B ALA* 1.3 77.1 - - - +
21B ARG* 1.3 63.5 + - + +
23B PRO* 4.3 5.1 - - - +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.4 22.9 + - + +
18B LEU* 3.2 14.6 + - + +
20B ALA* 1.3 81.8 - - + +
22B GLY* 1.3 57.5 + - - +
23B PRO* 3.8 3.7 - - - +
197B ARG* 3.2 31.9 - - - +
209B TRP* 6.2 1.4 - - - +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU 3.0 8.8 + - - -
19B ALA 3.7 2.7 - - - -
21B ARG* 1.3 80.7 - - - +
23B PRO* 1.3 67.1 - - - +
25B GLU* 3.3 31.8 - - - +
27B LEU* 3.4 18.6 - - - +
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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