Contacts of the helix formed by residues 23 - 34 (chain A) in PDB entry 1D5C
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 GLY 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA 3.3 1.0 - - - -
22A VAL* 1.3 80.8 - - - +
24A LYS* 1.3 60.9 + - - +
25A THR 3.4 2.0 - - - -
26A SER 3.3 0.7 + - - -
27A ILE* 2.8 40.3 + - - +
90A VAL* 4.8 0.4 - - - -
124A ASN* 3.7 9.0 - - - -
201A GDP 3.0 31.5 + - - -
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Residues in contact with LYS 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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16A PHE* 3.6 30.0 - - + +
17A LEU 3.6 17.7 - - - +
18A GLY 3.2 10.1 + - - +
19A GLU 3.0 25.3 + - - -
20A GLN* 4.2 2.4 + - - +
22A VAL* 3.9 10.5 - - + +
23A GLY* 1.3 72.4 - - - +
25A THR* 1.3 63.1 + - - +
27A ILE* 3.8 7.1 - - - +
28A ILE* 3.1 27.6 + - - +
66A ASP* 3.7 10.8 - - - +
67A THR* 3.5 29.2 - - - -
69A GLY 4.7 4.1 - - - +
90A VAL* 4.2 15.0 - - + +
201A GDP 2.7 38.5 + - - +
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Residues in contact with THR 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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24A LYS* 1.3 75.1 - - - +
26A SER* 1.3 57.7 + - - +
28A ILE* 3.4 4.2 + - + +
29A THR* 2.9 41.0 + - - +
40A TYR* 4.1 21.8 + - + +
43A THR* 5.3 0.3 + - - -
66A ASP* 2.8 26.1 + - - +
201A GDP 3.0 17.2 + - - -
300A MG 2.2 28.5 - - - -
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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
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23A GLY 3.8 1.6 - - - -
24A LYS 3.2 0.2 - - - -
25A THR* 1.3 74.5 - - - +
27A ILE* 1.3 60.6 - - - +
29A THR* 3.2 6.7 + - - -
30A ARG* 2.8 30.3 + - - +
35A THR 4.9 0.9 - - - +
36A PHE* 3.9 12.2 - - - -
40A TYR* 4.5 7.3 - - - -
155A ALA* 3.8 8.5 - - - +
201A GDP 2.9 64.4 + - - -
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Residues in contact with ILE 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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16A PHE* 4.6 9.9 - - + -
23A GLY 2.8 25.4 + - - +
24A LYS* 3.8 3.8 - - - +
26A SER* 1.3 72.0 - - - +
28A ILE* 1.3 63.4 + - - +
30A ARG* 3.2 5.7 + - - +
31A PHE* 3.0 21.8 + - - +
90A VAL* 3.9 35.0 - - + -
122A VAL* 4.2 6.5 - - + -
124A ASN* 4.0 18.2 - - + +
153A THR* 3.9 17.7 - - + +
155A ALA* 4.0 9.0 - - + -
161A ILE* 4.1 15.8 - - + +
164A LEU* 4.9 7.0 - - + -
165A PHE* 4.2 22.2 - - + -
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Residues in contact with ILE 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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16A PHE* 3.7 43.3 - - + -
24A LYS 3.1 15.0 + - - +
25A THR* 3.6 5.2 - - - +
27A ILE* 1.3 76.5 - - - +
29A THR* 1.3 57.2 + - - +
31A PHE* 3.3 6.1 + - - +
32A MSE 2.9 48.1 + - + +
49A LEU* 4.2 16.6 - - + -
64A LEU* 4.1 17.0 - - + -
65A TRP 4.6 0.7 - - - -
66A ASP* 3.6 41.7 - - + +
165A PHE* 4.9 3.4 - - - -
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Residues in contact with THR 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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25A THR* 2.9 30.3 + - - +
26A SER* 3.6 7.8 - - - -
28A ILE* 1.3 76.8 - - - +
30A ARG* 1.3 64.5 + - - +
32A MSE 3.9 5.6 - - - +
33A TYR* 2.9 35.4 + - + -
34A ASP 3.5 2.3 + - - -
35A THR* 3.6 31.9 - - + +
36A PHE* 5.1 2.5 - - - +
37A ASP* 5.7 2.0 - - + +
49A LEU* 6.0 1.9 - - - +
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Residues in contact with ARG 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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26A SER 2.8 17.7 + - - +
27A ILE 3.2 6.0 + - - +
29A THR* 1.3 78.6 - - - +
31A PHE* 1.3 58.1 + - - +
34A ASP* 2.8 68.9 + - - +
35A THR* 3.5 19.8 + - - +
36A PHE* 3.4 12.1 - - - +
155A ALA* 2.7 26.5 + - + +
156A LYS 2.9 27.7 + - - -
157A ALA 4.0 3.2 + - - -
158A GLY* 3.7 19.4 - - - +
161A ILE* 3.7 27.6 - - + -
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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 ILE 3.0 13.1 + - - +
28A ILE 3.7 5.4 - - - +
29A THR 3.2 0.2 - - - -
30A ARG* 1.3 78.4 - - - +
32A MSE 1.3 60.9 + - - +
34A ASP* 4.4 1.6 + - - +
51A LYS* 3.0 54.2 + - + -
53A LEU* 3.7 37.9 - - + -
62A LEU* 4.5 5.8 - - + -
64A LEU* 4.0 15.5 - - + -
161A ILE* 4.4 6.7 - - + +
162A LYS* 5.1 17.0 - - + -
165A PHE* 3.5 64.4 - + + -
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Residues in contact with MSE 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 ILE* 2.9 34.6 + - + +
29A THR* 4.5 0.2 - - - -
31A PHE* 1.3 80.1 - - - +
33A TYR* 1.3 99.6 + - + +
34A ASP 3.7 0.2 - - - -
49A LEU* 3.7 30.3 - - + -
50A SER 3.7 16.6 - - - +
51A LYS* 3.8 39.9 + - + +
64A LEU* 3.9 19.1 - - + -
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Residues in contact with TYR 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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29A THR* 2.9 27.5 + - + -
32A MSE 1.3 108.2 - - + +
34A ASP* 1.3 73.5 + - - +
35A THR* 3.1 19.8 + - + -
49A LEU* 3.9 29.2 - - + +
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Residues in contact with ASP 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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29A THR 3.5 0.2 + - - -
30A ARG* 2.8 50.2 + - - +
31A PHE 4.4 1.9 + - - +
32A MSE 3.7 0.8 - - - -
33A TYR* 1.3 80.5 - - - +
35A THR* 1.3 57.6 + - - +
158A GLY* 5.7 0.7 - - - -
162A LYS* 4.7 21.5 + - - -
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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