Contacts of the helix formed by residues 10 - 20 (chain O) in PDB entry 6AH0
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 ASN 10 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8O LEU 3.6 4.0 - - - +
9O HIS* 1.3 79.6 + - - +
11O GLY* 1.3 65.9 + - - +
12O TRP 3.1 4.0 - - - +
13O GLN* 3.0 16.8 + - - +
14O VAL* 3.3 7.4 + - - -
65O GLU 5.8 1.6 - - - -
66O VAL* 5.9 2.7 - - - +
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Residues in contact with GLY 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N PRO* 4.9 14.2 - - - +
10O ASN* 1.3 70.8 - - - +
12O TRP* 1.3 55.8 + - - +
13O GLN 3.3 0.2 - - - -
14O VAL* 3.2 14.0 + - - -
15O ASP* 3.3 10.9 + - - -
66O VAL* 5.3 9.2 - - - +
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Residues in contact with TRP 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N PRO* 6.0 2.0 - - - -
10O ASN* 3.1 2.2 - - - +
11O GLY* 1.3 74.6 - - - +
13O GLN* 1.3 61.6 + - - +
14O VAL 3.2 0.4 - - - -
15O ASP* 4.3 1.1 - - - +
16O GLN* 3.4 17.8 + - - -
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Residues in contact with GLN 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N PHE 6.2 1.6 - - - -
9N LEU* 6.6 0.2 - - - +
8O LEU* 5.7 9.0 - - - +
9O HIS 5.8 0.4 - - - +
10O ASN* 3.0 15.5 + - - +
12O TRP* 1.3 73.5 - - - +
14O VAL* 1.3 65.9 + - - +
16O GLN* 5.6 0.2 - - - +
17O ALA* 3.3 17.0 + - - +
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Residues in contact with VAL 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O LEU* 5.8 1.3 - - - +
10O ASN 3.3 7.7 + - - -
11O GLY* 3.2 8.7 + - - -
12O TRP 3.2 0.8 - - - -
13O GLN* 1.3 79.8 - - - +
15O ASP* 1.3 61.5 + - - +
17O ALA* 3.7 1.0 - - - -
18O ILE* 3.1 19.2 + - - -
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Residues in contact with ASP 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N PRO* 5.9 3.4 - - - -
23N ARG* 6.0 4.9 - - - +
11O GLY 3.3 12.5 + - - -
12O TRP* 3.8 2.4 + - - +
13O GLN 3.4 0.2 - - - -
14O VAL* 1.3 74.1 - - - +
16O GLN* 1.3 64.0 + - - +
18O ILE* 3.3 3.0 + - - +
19O LEU* 3.2 16.3 + - - -
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Residues in contact with GLN 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O TRP 3.4 15.2 + - - -
13O GLN* 4.6 0.4 - - - +
15O ASP* 1.3 73.1 - - - +
17O ALA* 1.3 58.4 + - - +
19O LEU* 3.0 3.9 + - - +
20O SER* 2.9 28.9 + - - -
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Residues in contact with ALA 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O GLN 3.3 15.8 + - - -
14O VAL 3.7 4.3 - - - -
15O ASP 3.3 0.4 - - - -
16O GLN* 1.3 76.0 - - - +
18O ILE* 1.3 60.5 + - - +
20O SER* 4.2 4.0 + - - +
21O GLU* 4.2 8.0 + - - -
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Residues in contact with ILE 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O VAL 3.1 13.6 + - - -
15O ASP* 3.3 4.6 + - - +
16O GLN 3.2 0.6 - - - -
17O ALA* 1.3 76.2 - - - +
19O LEU* 1.3 62.5 + - - +
21O GLU 3.9 11.3 - - - +
26O VAL* 6.2 3.8 - - - +
86O ARG* 5.4 1.9 + - - -
87O ASN* 4.7 14.3 + - - -
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Residues in contact with LEU 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O ASP 3.2 9.5 + - - -
16O GLN* 3.0 6.5 + - - +
18O ILE* 1.3 76.1 - - - +
20O SER* 1.3 63.9 + - - +
21O GLU 3.1 9.6 + - - +
22O GLU* 4.4 2.9 + - - -
86O ARG* 6.2 0.2 - - - -
87O ASN* 5.8 2.9 - - - +
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Residues in contact with SER 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O GLN 2.9 14.3 + - - -
17O ALA* 4.2 1.3 + - - +
18O ILE 3.6 0.2 - - - -
19O LEU* 1.3 73.8 - - - +
21O GLU* 1.3 55.4 + - - +
22O GLU 3.6 4.4 + - - -
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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