Contacts of the helix formed by residues 11 - 21 (chain A) in PDB entry 1D02
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 1.3 67.2 - - - +
12A TRP* 1.3 64.5 + - - +
13A GLN* 3.5 11.3 + - - +
14A ALA* 2.9 30.1 + - - +
15A LEU 3.2 15.1 + - - -
33A ALA 3.8 5.6 - - - +
34A VAL* 2.8 30.1 + - - +
36A GLU* 2.8 39.1 + - - +
38A THR* 3.9 2.1 - - + +
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Residues in contact with TRP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.1 45.7 + - + +
11A ASN* 1.3 73.2 - - - +
13A GLN* 1.3 58.0 + - + +
15A LEU* 3.4 18.4 + - + +
16A ALA* 2.9 30.1 + - - +
34A VAL* 4.3 3.1 - - + -
187A GLU* 3.8 33.9 - - + -
190A VAL* 3.6 29.8 - - + -
191A GLN* 4.0 22.2 - - + -
194A ASN* 3.6 22.6 + - - -
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN* 3.1 8.9 + - - +
12A TRP* 1.3 79.3 - - + +
14A ALA* 1.3 63.1 + - - +
16A ALA* 3.2 8.7 + - - +
17A GLY* 3.0 19.1 + - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN* 2.9 22.8 + - - +
13A GLN* 1.3 76.2 - - - +
15A LEU* 1.3 62.9 + - - +
17A GLY* 3.1 4.0 + - - +
18A LEU* 3.0 20.1 + - - +
33A ALA* 3.2 30.1 - - + +
36A GLU* 3.7 18.6 - - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 3.2 3.8 + - - -
12A TRP* 3.7 20.0 - - + +
14A ALA* 1.3 79.9 - - - +
16A ALA* 1.3 62.2 + - - +
18A LEU* 3.0 13.1 + - + +
19A LYS* 3.0 21.7 + - + +
25A GLN* 4.1 16.8 - - - +
30A VAL* 3.9 30.5 - - + +
33A ALA* 4.1 7.3 - - + +
34A VAL* 3.9 29.4 - - + -
186A GLY 4.9 0.9 - - - -
187A GLU* 3.9 32.5 - - + +
190A VAL* 4.1 7.9 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP 2.9 17.3 + - - +
13A GLN* 3.2 8.2 + - - +
15A LEU* 1.3 77.4 - - - +
17A GLY* 1.3 57.0 + - - +
19A LYS* 3.4 12.5 + - + +
20A ALA* 2.8 30.2 + - - +
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Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN 3.0 13.2 + - - -
14A ALA* 3.1 4.9 + - - -
15A LEU 3.1 0.4 - - - -
16A ALA* 1.3 75.4 - - - +
18A LEU* 1.3 59.1 + - - +
20A ALA* 3.3 7.3 + - - +
21A SER* 2.9 30.1 + - - -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA 3.0 11.0 + - - +
15A LEU* 3.0 13.4 + - + +
17A GLY* 1.3 74.3 - - - +
19A LYS* 1.3 63.5 + - - +
21A SER* 2.6 26.1 + - - +
22A GLY 3.7 2.1 + - - -
23A ALA* 3.9 24.0 + - + +
25A GLN* 4.0 19.7 - - + +
29A ASN* 3.4 54.7 - - + +
30A VAL* 3.8 10.5 - - + -
33A ALA* 4.2 8.1 - - + -
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.0 11.2 + - + +
16A ALA* 3.6 14.1 - - + +
18A LEU* 1.3 77.9 - - - +
20A ALA* 1.3 61.4 + - - +
22A GLY* 3.1 15.8 + - - -
23A ALA 5.4 0.7 - - - -
25A GLN* 3.6 26.4 + - - +
185A SER* 3.9 25.9 - - - +
187A GLU* 6.2 0.9 - - + -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA 2.8 17.9 + - - +
17A GLY* 3.7 7.6 - - - +
18A LEU 3.3 0.2 - - - -
19A LYS* 1.3 71.3 - - - +
21A SER* 1.3 57.9 + - - +
22A GLY* 2.9 10.9 + - - -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 2.9 13.7 + - - -
18A LEU* 2.6 25.1 + - - +
20A ALA* 1.3 73.8 - - - +
22A GLY* 1.3 52.1 + - - +
23A ALA* 2.7 28.1 + - - +
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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