Contacts of the helix formed by residues 15 - 25 (chain A) in PDB entry 2DDH
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PHE* 1.3 79.2 - - - +
16A PRO* 1.3 70.1 - - - +
17A GLU* 3.0 27.5 + - - +
18A LEU* 2.9 50.1 + - + +
19A ILE 3.9 0.7 + - - -
548A ASP* 5.4 0.4 + - - -
550A ALA* 5.3 0.8 - - - +
551A VAL* 4.4 0.5 - - - +
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Residues in contact with PRO 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 ALA* 5.5 0.9 - - + -
14A PHE* 3.2 29.1 - - + +
15A ASN* 1.3 86.3 - - - +
17A GLU* 1.3 63.3 + - - +
19A ILE* 2.9 15.3 + - - +
20A THR* 3.0 15.3 + - - -
605A ALA* 3.5 35.0 - - + +
608A ASP* 4.8 6.7 - - + -
609A ALA* 3.8 12.7 - - + +
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Residues in contact with GLU 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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15A ASN* 3.0 22.6 + - - +
16A PRO* 1.3 79.5 - - - +
18A LEU* 1.3 63.0 + - + +
20A THR* 3.2 8.5 + - - -
21A HIS* 3.0 50.9 + - + +
34A ARG* 2.6 46.5 + - - -
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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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15A ASN* 2.9 40.7 + - + +
17A GLU* 1.3 78.4 - - + +
19A ILE* 1.3 61.7 + - - +
21A HIS* 3.4 22.2 + - + +
22A ILE* 3.3 27.1 + - + +
548A ASP* 3.3 41.1 - - + +
551A VAL* 3.9 11.0 - - + -
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Residues in contact with ILE 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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14A PHE* 3.4 34.1 - - + -
16A PRO 2.9 8.5 + - - +
18A LEU* 1.3 75.0 - - - +
20A THR* 1.3 67.6 + - - +
22A ILE* 3.0 11.4 + - + +
23A LEU* 2.9 28.9 + - + +
339A TYR* 3.5 31.6 - - + +
343A PHE* 6.4 0.7 - - + -
551A VAL* 3.7 26.2 - - + -
554A VAL* 4.7 1.3 - - + -
555A LEU* 4.4 14.4 - - + -
606A LEU* 3.9 19.5 - - + -
609A ALA* 3.6 9.2 - - + -
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Residues in contact with THR 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 PRO 3.0 11.4 + - - -
17A GLU* 3.4 13.6 + - - -
19A ILE* 1.3 78.3 - - - +
21A HIS* 1.3 63.4 + - - +
23A LEU* 3.2 6.7 + - + +
24A ASP* 3.0 43.3 + - - +
30A THR* 3.7 13.2 - - + -
33A ARG* 3.5 16.2 - - - +
34A ARG* 4.0 9.7 + - - +
608A ASP 4.8 0.3 + - - -
609A ALA* 2.7 24.2 + - - +
610A PHE 5.3 0.4 - - - +
611A ASP* 3.8 13.9 - - + +
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Residues in contact with HIS 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 GLU* 3.0 44.6 + - + +
18A LEU* 3.6 26.3 - - + +
20A THR* 1.3 76.9 - - - +
22A ILE* 1.3 61.0 + - + +
24A ASP 3.4 0.3 + - - -
25A GLY 3.0 3.6 + - - -
26A SER* 2.9 29.9 + - - -
27A PRO* 3.5 44.6 - - + +
30A THR* 3.3 23.5 + - + +
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Residues in contact with ILE 22 (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* 3.3 15.2 + - + +
19A ILE* 3.0 11.1 + - + +
21A HIS* 1.3 78.2 - - + +
23A LEU* 1.3 64.5 + - + +
25A GLY* 3.0 15.7 + - - -
343A PHE* 3.9 29.8 - - + -
346A ARG* 3.6 10.6 + - - +
542A LYS* 4.6 13.2 - - - +
546A ILE* 3.7 28.3 - - + -
547A GLN 5.9 1.1 - - - +
551A VAL* 4.1 20.0 - - + -
555A LEU* 5.0 3.4 - - + -
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Residues in contact with LEU 23 (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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19A ILE* 2.9 26.0 + - + +
20A THR* 3.6 6.5 - - + +
22A ILE* 1.3 77.2 - - + +
24A ASP* 1.3 54.5 + - - +
291A GLN* 5.8 2.0 - - - +
339A TYR* 4.6 12.6 - - + -
342A HIS* 4.0 37.0 - - + +
343A PHE* 5.1 11.7 - - + -
346A ARG* 2.5 27.6 + - - +
609A ALA 3.8 18.8 - - - +
610A PHE* 3.8 32.1 - - + +
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Residues in contact with ASP 24 (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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20A THR* 3.0 14.1 + - - +
21A HIS 4.0 0.2 - - - +
23A LEU* 1.3 77.9 - - - +
25A GLY* 1.3 57.2 + - - +
26A SER 3.3 4.0 - - - +
29A ASN* 2.9 24.9 - - + +
30A THR* 2.7 44.5 + - - +
33A ARG* 2.8 47.8 + - - +
83A GLU* 4.2 7.6 - - - +
87A TRP* 4.8 7.1 + - + -
346A ARG* 3.3 5.9 + - - -
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Residues in contact with GLY 25 (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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21A HIS 3.0 5.6 + - - -
22A ILE* 3.0 13.9 + - - -
23A LEU 3.2 0.2 - - - -
24A ASP* 1.3 78.3 - - - +
26A SER* 1.3 65.4 + - - +
29A ASN* 4.2 3.4 - - - -
346A ARG* 3.6 14.6 - - - -
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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