Contacts of the helix formed by residues 6 - 24 (chain F) in PDB entry 6X0A
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 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F ARG* 1.3 79.2 - - - +
7F PRO* 1.3 68.7 - - - +
8F ALA* 3.5 8.1 + - - +
9F ALA* 2.8 24.6 + - - +
10F GLU 3.1 10.2 + - - -
80F ILE 3.1 9.4 + - - -
81F VAL* 2.6 34.7 + - - +
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Residues in contact with PRO 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 3.9 19.5 - - - +
6F SER* 1.3 85.8 - - - +
8F ALA* 1.3 61.0 + - - +
10F GLU* 3.3 9.8 - - + +
11F GLY* 3.1 18.5 + - - -
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Residues in contact with ALA 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F SER* 3.1 9.7 + - - +
7F PRO* 1.3 78.8 - - - +
9F ALA* 1.3 53.5 + - - +
11F GLY* 3.1 3.1 + - - -
12F ASP* 2.7 40.8 + - - +
81F VAL 4.3 0.2 - - - +
82F ARG* 4.0 33.7 - - + +
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Residues in contact with ALA 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 4.2 7.9 - - + -
6F SER* 2.8 18.4 + - - +
8F ALA* 1.3 75.1 - - - +
10F GLU* 1.3 64.4 + - - +
12F ASP* 3.2 12.3 + - - +
13F LEU* 3.1 27.6 + - + +
80F ILE* 3.7 15.0 - - + +
81F VAL 3.3 22.6 + - - +
83F ILE* 3.9 13.8 - - + +
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Residues in contact with GLU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 2.7 48.6 + - - +
6F SER 3.1 7.7 + - - -
7F PRO* 3.3 14.5 - - - +
9F ALA* 1.3 76.2 - - - +
11F GLY* 1.3 63.5 + - - +
13F LEU* 3.2 9.3 + - - +
14F VAL* 2.9 33.8 + - + +
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Residues in contact with GLY 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PRO 3.1 9.8 + - - -
8F ALA* 3.1 4.9 + - - -
10F GLU* 1.3 85.3 - - - +
12F ASP* 1.3 63.4 + - - +
14F VAL* 3.0 11.7 - - - +
15F ASP* 3.0 32.4 + - - -
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Residues in contact with ASP 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ALA 2.7 24.9 + - - +
9F ALA* 3.4 6.9 - - - +
10F GLU 3.2 0.2 - - - -
11F GLY* 1.3 75.3 - - - +
13F LEU* 1.3 58.7 + - - +
15F ASP* 3.3 6.2 + - - +
16F ILE* 2.8 33.4 + - - +
82F ARG* 2.6 45.2 + - - +
83F ILE* 2.7 46.7 + - + +
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Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA 3.1 14.5 + - - +
10F GLU* 3.8 8.1 - - - +
12F ASP* 1.3 76.1 - - - +
14F VAL* 1.3 56.5 + - - +
16F ILE* 3.3 8.8 + - + +
17F TRP* 2.7 33.4 + - - +
32F LEU* 3.7 21.2 - - + +
35F ILE* 3.8 38.8 - - + -
80F ILE* 6.3 0.4 - - + -
83F ILE* 3.9 32.1 - - + -
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Residues in contact with VAL 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F GLU* 2.9 19.4 + - + +
11F GLY* 3.0 28.0 - - - +
13F LEU* 1.3 72.7 - - - +
15F ASP* 1.3 66.0 + - - +
17F TRP* 3.1 8.0 + - + +
18F LEU* 2.9 44.9 + - + +
32F LEU* 5.4 1.1 - - - -
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Residues in contact with ASP 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLY 3.0 23.6 + - - +
12F ASP* 3.6 5.6 - - - +
14F VAL* 1.3 81.3 - - - +
16F ILE* 1.3 63.6 + - + +
18F LEU* 3.1 14.9 + - - +
19F ALA* 2.9 24.6 + - - +
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Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ASP 2.8 25.5 + - - +
13F LEU* 3.5 15.9 - - + +
14F VAL 3.3 0.2 - - - -
15F ASP* 1.3 72.6 - - + +
17F TRP* 1.3 66.1 + - - +
19F ALA* 3.4 5.8 + - - +
20F ILE* 3.3 25.2 + - + +
31F PHE* 4.0 29.2 - - + -
32F LEU* 4.2 9.6 - - + -
35F ILE* 4.7 4.5 - - + -
67F TYR* 4.3 25.8 - - + +
83F ILE* 3.5 39.3 - - + +
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Residues in contact with TRP 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU 2.7 20.9 + - - +
14F VAL* 3.1 10.7 + - + +
16F ILE* 1.3 75.3 - - - +
18F LEU* 1.3 79.1 + - + +
20F ILE 3.3 0.7 + - - -
21F ALA* 2.9 48.3 + - + +
25F PRO* 3.6 30.7 - - + -
28F ALA* 3.4 22.8 - - + +
29F ASP* 2.8 28.8 + - - +
32F LEU* 3.5 35.4 - - + -
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Residues in contact with LEU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F VAL* 2.9 33.1 + - + +
15F ASP* 3.7 14.4 - - - +
17F TRP* 1.3 96.8 - - + +
19F ALA* 1.3 63.7 + - - +
21F ALA* 2.8 16.0 + - + +
22F ASN* 3.1 18.0 + - - +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ALA* 6.0 3.3 - - - +
22C ASN* 6.1 4.3 - - + +
15F ASP 2.9 16.1 + - - +
16F ILE* 3.7 7.6 - - - +
18F LEU* 1.3 78.8 - - - +
20F ILE* 1.3 65.9 + - + +
22F ASN* 3.3 19.2 + - - +
23F ASP* 4.2 1.4 + - - +
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Residues in contact with ILE 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.5 19.1 - - + +
17F TRP 3.3 1.7 + - - +
18F LEU 3.3 0.2 - - - -
19F ALA* 1.3 77.2 - - + +
21F ALA* 1.3 62.6 + - - +
23F ASP* 3.0 12.6 + - + +
24F SER 3.0 18.0 + - - -
27F ALA* 3.8 13.9 - - + -
28F ALA* 3.4 33.9 - - + +
31F PHE* 3.8 40.2 - - + -
32F LEU* 5.1 0.9 - - + -
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 3.6 15.1 + - - -
17F TRP* 2.9 47.7 + - + +
18F LEU* 2.8 15.5 + - + +
20F ILE* 1.3 73.4 - - - +
22F ASN* 1.3 67.1 + - - +
23F ASP 3.4 0.2 + - - -
24F SER 3.5 17.3 + - - -
25F PRO* 3.7 8.4 - - + +
28F ALA* 3.9 0.9 - - + +
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Residues in contact with ASN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ALA* 5.9 4.6 - - - +
67C TYR* 4.1 7.8 + - - +
85C HIS* 3.0 12.4 - - - -
88C ARG* 2.6 29.7 + - - +
18F LEU* 3.1 14.3 + - - +
19F ALA* 3.5 12.3 + - - +
20F ILE 3.2 0.2 - - - -
21F ALA* 1.3 76.9 - - - +
23F ASP* 1.3 58.3 + - - +
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Residues in contact with ASP 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ASN* 3.1 34.6 + - - +
67C TYR* 4.0 20.9 + - + +
85C HIS* 3.0 23.0 + - - -
19F ALA 4.2 0.8 + - - +
20F ILE* 3.0 12.7 + - + +
21F ALA 3.8 0.4 - - - -
22F ASN* 1.3 78.4 - - - +
24F SER* 1.3 64.7 + - - +
25F PRO* 4.5 1.0 - - - +
27F ALA* 5.1 5.4 - - - +
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Residues in contact with SER 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ASN* 4.0 16.4 - - - -
26D ARG* 3.9 14.0 + - - -
20F ILE 3.0 13.8 + - - +
21F ALA* 3.5 1.6 + - - -
23F ASP* 1.3 84.5 - - - +
25F PRO* 1.3 70.1 - - - +
26F ARG* 3.5 11.1 + - - +
27F ALA* 3.3 26.7 + - - +
28F ALA 3.1 16.8 + - - -
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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