Contacts of the helix formed by residues 26 - 35 (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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU* 4.1 9.6 + - + +
25A GLN* 1.3 75.2 - - - +
27A LEU* 1.3 64.2 + - - +
28A TYR* 3.0 20.3 + - + +
29A ASN* 2.7 63.5 + - - +
30A VAL* 3.1 10.7 + - - +
101A ARG* 6.3 1.6 - - - +
180A TRP* 3.7 10.3 - - - -
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Residues in contact with LEU 27 (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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26A ASN* 1.3 74.0 - - - +
28A TYR* 1.3 66.1 + - + +
30A VAL* 3.7 0.5 - - - +
31A PHE* 3.0 49.1 + - + +
42A LEU* 4.4 4.5 - - + -
84A PHE* 3.6 52.9 - - + -
99A ILE* 4.0 23.1 - - + -
151A VAL* 3.9 23.8 - - + -
153A GLU* 4.6 3.8 + - - +
180A TRP* 3.5 18.3 - - + -
189A LEU* 4.0 13.9 - - + -
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Residues in contact with TYR 28 (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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26A ASN* 3.0 17.1 + - + +
27A LEU* 1.3 78.0 - - + +
29A ASN* 1.3 65.8 + - - +
32A ASN* 2.9 35.7 + - - +
42A LEU* 3.7 20.3 - - + +
44A GLU* 3.4 54.7 + - + +
83A ALA* 2.6 37.5 + - - +
84A PHE* 3.9 9.9 - - + -
99A ILE* 3.8 20.9 - - + +
101A ARG* 5.0 8.5 - - - -
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Residues in contact with ASN 29 (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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18A LEU* 3.4 24.4 - - + +
23A ALA* 5.2 1.2 - - - +
24A GLU* 2.9 31.9 + - - -
25A GLN* 3.4 4.9 - - - -
26A ASN* 2.7 59.7 + - - +
28A TYR* 1.3 74.1 - - - +
30A VAL* 1.3 61.7 + - - +
32A ASN* 3.8 6.8 - - - +
33A ALA* 3.0 31.2 + - - +
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Residues in contact with VAL 30 (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* 3.9 7.8 - - + +
18A LEU* 3.8 8.7 - - + -
25A GLN* 3.6 31.9 - - + +
26A ASN 3.1 19.8 + - - +
27A LEU* 3.7 5.2 - - - +
29A ASN* 1.3 84.9 + - - +
31A PHE* 1.3 62.0 + - - +
33A ALA* 3.8 1.7 - - - +
34A VAL* 3.1 22.9 + - - +
180A TRP* 4.3 2.7 - - + -
186A GLY* 3.8 25.6 - - - +
189A LEU* 4.3 9.2 - - + -
190A VAL* 3.5 28.5 - - + -
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Residues in contact with PHE 31 (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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27A LEU* 3.0 41.5 + - + +
30A VAL* 1.3 74.1 - - - +
32A ASN* 1.3 67.3 + - - +
34A VAL* 3.7 6.0 - - + +
35A PHE* 2.9 64.2 + + + -
42A LEU* 4.0 22.7 - - + -
84A PHE* 5.3 0.2 - + - -
86A ILE* 4.1 5.6 - - + -
149A TRP* 3.7 33.0 - + - -
189A LEU* 3.7 33.0 - - + -
190A VAL* 4.1 15.0 - - + -
193A PHE* 4.0 21.3 - + + -
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Residues in contact with ASN 32 (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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28A TYR* 2.9 31.0 + - - +
29A ASN* 3.8 6.3 - - - +
31A PHE* 1.3 77.7 - - - +
33A ALA* 1.3 62.8 + - - +
35A PHE* 4.0 4.1 - - - +
36A GLU* 3.3 23.0 + - - +
41A VAL* 6.0 0.4 - - - +
42A LEU* 3.7 32.4 + - - +
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Residues in contact with ALA 33 (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* 3.8 0.7 - - - +
14A ALA* 3.2 40.6 - - + +
15A LEU* 4.1 7.4 - - - -
18A LEU* 4.2 13.9 - - + -
29A ASN 3.0 18.7 + - - +
30A VAL 3.8 3.6 - - - +
32A ASN* 1.3 77.7 - - - +
34A VAL* 1.3 62.0 + - - +
35A PHE 3.2 1.2 + - - -
36A GLU* 3.2 24.8 + - - +
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Residues in contact with VAL 34 (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* 3.8 12.3 - - + -
11A ASN* 2.8 49.0 + - - +
12A TRP* 4.2 6.1 - - + +
15A LEU* 3.9 24.0 - - + +
30A VAL 3.1 15.5 + - - +
31A PHE* 3.7 14.8 - - + +
33A ALA* 1.3 78.1 - - - +
35A PHE* 1.3 78.4 + - + +
36A GLU 3.4 0.2 - - - -
38A THR* 3.5 3.5 - - - +
190A VAL* 3.8 30.3 - - + -
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Residues in contact with PHE 35 (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* 4.1 10.5 - - + -
31A PHE* 2.9 52.2 + + + +
32A ASN* 4.0 4.5 - - - +
33A ALA 3.1 0.4 - - - -
34A VAL* 1.3 90.5 - - + +
36A GLU* 1.3 66.4 + - - +
37A GLY 3.1 1.2 + - - -
38A THR* 2.7 25.7 + - - +
40A TYR* 3.5 33.1 - - + +
41A VAL* 3.9 7.9 - - - -
42A LEU* 3.8 20.0 - - + +
86A ILE* 3.6 40.2 - - + -
193A PHE* 4.0 19.3 - + - -
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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