Contacts of the helix formed by residues 15 - 27 (chain A) in PDB entry 3DI3
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 VAL 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLN 3.5 11.7 + - - +
12A TYR 3.2 1.2 + - - -
14A SER* 1.3 85.0 - - - +
16A LEU* 1.3 64.5 + - - +
17A MET 3.3 1.1 - - - -
18A VAL* 2.8 31.3 + - - +
19A SER* 3.8 4.0 + - - -
80B LEU 3.6 23.1 - - - +
81B LEU* 3.6 27.4 - - + +
82B ILE* 3.8 9.0 - - + -
104B THR* 4.6 0.4 - - + -
139B TYR* 4.1 10.6 - - + +
192B TYR* 4.1 23.6 - - + +
193B PHE* 4.1 11.2 - - + -
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Residues in contact with LEU 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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11A GLN 3.4 3.3 + - - +
12A TYR* 2.9 32.6 + - + +
15A VAL* 1.3 79.7 - - - +
17A MET* 1.3 61.8 + - - +
18A VAL 3.0 1.0 + - - -
19A SER* 3.3 16.0 + - - -
20A ILE* 3.5 33.4 + - + +
81A LYS* 4.7 2.7 - - - +
82A VAL* 4.4 11.2 - - + +
85A GLY* 3.2 41.1 - - - +
86A THR* 3.4 20.4 - - - +
89A LEU* 4.3 12.1 - - + -
142A TRP* 3.9 5.4 - - + +
82B ILE* 4.7 7.4 - - + -
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Residues in contact with MET 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 2.6 62.4 + - + +
13A GLU* 3.5 26.0 - - + +
16A LEU* 1.3 72.9 - - - +
18A VAL* 1.3 62.4 + - - +
20A ILE* 3.7 9.8 - - + +
21A ASP* 3.0 40.0 + - - +
139A LYS* 3.4 25.4 - - + +
143A ASN* 5.0 7.9 - - + +
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Residues in contact with VAL 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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13A GLU 4.0 5.4 - - - +
14A SER 3.4 23.6 - - - +
15A VAL 2.8 19.2 + - - +
17A MET* 1.3 78.2 - - - +
19A SER* 1.3 58.4 + - - +
21A ASP* 3.3 5.2 + - - +
22A GLN* 3.1 23.9 + - - +
78A HIS* 5.3 4.0 - - + -
138B LYS* 3.9 35.0 - - + +
139B TYR* 3.5 36.8 - - + +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL 4.6 2.9 + - - -
16A LEU* 3.3 7.3 + - - -
18A VAL* 1.3 74.9 - - - +
20A ILE* 1.3 66.2 + - - +
22A GLN* 3.3 2.1 + - - +
23A LEU* 3.0 28.9 + - - +
78A HIS* 2.9 38.2 + - - +
81A LYS* 3.7 20.7 - - - +
82A VAL* 3.5 21.3 - - - -
139B TYR* 4.2 5.7 + - - -
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Residues in contact with ILE 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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12A TYR* 4.0 21.5 - - + +
16A LEU* 3.5 32.5 + - + +
17A MET* 3.4 8.7 + - + +
18A VAL 3.3 0.6 - - - -
19A SER* 1.3 76.5 - - - +
21A ASP* 1.3 63.3 + - - +
23A LEU* 3.4 6.5 + - - +
24A LEU* 3.1 41.4 + - + +
82A VAL* 3.6 21.3 - - + -
135A LEU* 4.2 20.5 - - + +
138A ILE* 4.1 21.8 - - + -
139A LYS* 4.3 12.1 - - + -
142A TRP* 4.5 0.4 - - + -
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Residues in contact with ASP 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 MET* 3.0 33.9 + - - +
18A VAL* 3.9 4.8 - - - +
19A SER 3.2 0.2 - - - -
20A ILE* 1.3 75.3 - - - +
22A GLN* 1.3 59.8 + - - +
23A LEU 3.1 1.6 - - - -
24A LEU* 3.1 8.3 + - - +
25A ASP* 2.9 40.0 + - - +
139A LYS* 2.9 30.1 + - - +
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Residues in contact with GLN 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 VAL* 3.1 18.0 + - + +
19A SER 3.3 4.2 + - - +
21A ASP* 1.3 78.3 - - - +
23A LEU* 1.3 61.8 + - - +
25A ASP* 3.6 16.0 + - - +
26A SER* 3.4 21.3 + - - -
78A HIS* 3.8 30.3 - - + +
138B LYS* 3.4 35.0 + - - +
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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 SER 3.0 21.6 + - - +
20A ILE* 3.6 4.9 - - - +
22A GLN* 1.3 76.4 - - - +
24A LEU* 1.3 64.1 + - - +
26A SER* 2.6 22.5 + - - -
27A MET* 3.4 13.4 + - + +
75A PHE* 3.5 43.1 - - + +
78A HIS* 3.6 30.1 - - + -
79A LEU* 3.6 27.4 - - + +
82A VAL* 4.1 11.4 - - + -
135A LEU* 3.9 22.0 - - + -
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Residues in contact with LEU 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 ILE* 3.1 26.7 + - + +
21A ASP* 3.1 10.5 + - - +
23A LEU* 1.3 76.0 - - - +
25A ASP* 1.3 66.0 + - - +
27A MET* 3.0 16.4 + - + +
28A LYS* 3.2 10.9 + - - +
132A LYS* 4.0 34.2 - - + +
135A LEU* 3.9 25.4 - - + -
136A GLN* 4.6 14.1 - - + +
139A LYS* 4.1 27.4 - - + -
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Residues in contact with ASP 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 ASP* 2.9 24.6 + - - +
22A GLN* 3.8 18.9 + - - +
23A LEU 3.2 0.2 - - - -
24A LEU* 1.3 73.5 - - - +
26A SER* 1.3 63.2 + - - +
27A MET 2.8 5.8 + - - -
28A LYS* 2.9 22.7 + - - +
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 3.4 9.5 + - - -
23A LEU* 2.6 23.8 + - - -
25A ASP* 1.3 77.1 - - - +
27A MET* 1.3 59.4 + - - +
28A LYS 3.5 0.6 + - - -
29A GLU* 4.8 7.4 + - - +
75A PHE* 3.6 24.1 - - - -
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Residues in contact with MET 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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23A LEU* 3.6 15.9 - - + +
24A LEU* 3.0 13.3 + - - +
25A ASP 2.8 1.6 - - - -
26A SER* 1.3 84.7 + - - +
28A LYS* 1.3 63.2 + - - +
29A GLU* 3.1 3.4 - - - +
30A ILE* 3.1 37.9 + - + +
75A PHE* 4.7 7.6 - - + -
128A LEU* 3.8 29.6 - - + +
131A LEU* 3.5 32.5 - - + -
132A LYS* 3.5 30.6 + - + -
135A LEU* 3.6 23.6 - - + -
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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