Contacts of the helix formed by residues 17 - 27 (chain A) in PDB entry 2C8U
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 ALA 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.2 10.8 - - + -
10A TYR* 3.8 37.5 - - + -
12A ASN 4.0 4.2 + - - +
13A GLY 4.8 1.8 - - - +
15A GLY 3.2 1.8 - - - -
16A ARG* 1.3 75.0 - - - +
18A GLU* 1.3 64.8 + - - +
19A SER 3.2 0.4 - - - -
20A ILE* 3.0 11.5 + - - +
21A GLN* 2.9 36.7 + - - +
54A PRO* 3.6 11.4 - - + +
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Residues in contact with GLU 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 GLY 4.2 14.5 - - - +
14A ARG* 3.1 47.9 + - - +
15A GLY 3.5 11.8 - - - +
16A ARG 3.1 1.2 - - - -
17A ALA* 1.3 77.4 - - - +
19A SER* 1.3 59.1 + - - +
21A GLN* 3.6 12.2 - - - +
22A MET* 2.9 56.1 + - + +
165A ALA* 3.8 21.3 - - + +
168A ASP* 5.9 1.1 - - - +
169A HIS* 3.7 12.0 + - - -
202A TYR* 4.8 4.9 - - - +
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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
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16A ARG 3.8 7.9 + - - -
17A ALA 3.2 0.4 - - - -
18A GLU* 1.3 77.6 - - - +
20A ILE* 1.3 59.2 + - - +
22A MET* 4.4 4.8 - - - +
23A THR* 2.6 33.3 + - - -
71A SER 5.7 0.7 - - - -
72A LEU* 4.0 24.3 - - - +
75A ALA* 3.9 7.8 - - - +
158A LEU* 4.4 2.8 - - - +
161A LEU* 4.8 2.9 - - - +
162A VAL* 3.8 28.3 - - - +
165A ALA* 4.4 9.0 - - - +
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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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8A VAL* 4.1 11.0 - - + -
16A ARG 4.6 1.3 - - - +
17A ALA* 3.0 10.9 + - - +
19A SER* 1.3 75.2 - - - +
21A GLN* 1.3 65.9 + - - +
23A THR* 3.4 3.9 + - - -
24A LEU* 3.1 39.9 + - + +
54A PRO* 4.3 13.9 - - + -
56A VAL* 4.0 23.6 - - + -
71A SER* 3.6 46.0 - - - +
74A ILE* 4.1 27.8 - - + -
75A ALA* 4.4 6.3 - - - +
78A MET* 5.5 3.8 - - + +
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Residues in contact with GLN 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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8A VAL* 4.3 9.4 - - + +
10A TYR* 3.4 31.7 + - - -
13A GLY 5.1 3.6 + - - +
17A ALA* 2.9 24.9 + - - +
18A GLU* 3.6 11.9 - - - +
20A ILE* 1.3 76.8 - - - +
22A MET* 1.3 57.2 + - - +
24A LEU* 3.4 2.5 + - - +
25A VAL* 2.9 34.6 + - - +
31A TYR* 3.5 25.1 + - + +
33A ASP* 3.0 33.1 + - - +
202A TYR* 3.2 24.0 + - - +
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Residues in contact with MET 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 GLU* 2.9 49.0 + - + +
19A SER 4.4 0.4 - - - +
21A GLN* 1.3 72.5 - - - +
23A THR* 1.3 53.4 + - - +
25A VAL* 3.4 5.0 + - - +
26A ALA* 2.8 35.9 + - - +
161A LEU* 3.7 23.8 - - + +
164A ILE* 3.7 33.0 - - + -
165A ALA* 4.3 16.4 - - + -
168A ASP* 5.7 2.7 - - - +
199A LEU* 3.7 22.4 - - + +
202A TYR* 3.7 16.6 - - + +
203A LEU* 4.1 18.8 - - + -
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Residues in contact with THR 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 2.6 24.4 + - - -
20A ILE* 3.7 5.4 - - - -
22A MET* 1.3 75.8 - - - +
24A LEU* 1.3 57.6 + - - +
26A ALA* 3.2 2.3 + - - -
27A ALA* 2.8 30.9 + - + +
75A ALA* 3.9 5.9 - - - +
78A MET* 3.8 15.0 - - + -
79A ALA* 3.6 37.5 - - + +
84A MET* 3.7 10.1 - - + +
158A LEU* 3.5 19.9 - - - +
161A LEU* 3.5 12.7 - - + +
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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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6A ILE* 4.1 18.2 - - + -
8A VAL* 4.1 11.7 - - + -
20A ILE* 3.1 24.1 + - + +
21A GLN 3.8 1.1 - - - +
23A THR* 1.3 73.7 - - - +
25A VAL* 1.3 62.1 + - - +
27A ALA* 3.2 3.7 + - + -
28A GLY 3.0 5.2 + - - -
29A VAL* 2.9 55.9 + - + +
31A TYR* 3.7 43.1 - - + -
78A MET* 4.0 35.0 - - + -
82A HIS* 5.9 1.3 - - + +
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Residues in contact with VAL 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 GLN 2.9 21.0 + - - +
22A MET* 3.7 6.3 - - - +
24A LEU* 1.3 76.7 - - - +
26A ALA* 1.3 60.9 + - - +
28A GLY* 3.1 10.4 + - - -
29A VAL 4.9 2.2 - - - +
31A TYR* 3.4 24.5 - - + +
198A ARG* 3.2 48.5 - - + +
199A LEU* 4.0 6.5 - - + +
202A TYR* 3.7 30.3 - - + -
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Residues in contact with ALA 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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22A MET 2.8 20.6 + - - +
23A THR 3.8 3.4 - - - +
25A VAL* 1.3 74.9 - - - +
27A ALA* 1.3 53.8 + - - +
84A MET* 4.1 18.4 - - - +
156A VAL* 4.2 14.8 - - + -
161A LEU* 4.4 9.0 - - + -
196A SER* 4.2 21.7 + - - +
198A ARG* 2.8 24.4 + - - +
199A LEU* 5.2 4.0 - - + +
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Residues in contact with ALA 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 THR* 2.8 18.8 + - + +
24A LEU* 3.8 2.7 - - + +
26A ALA* 1.3 75.0 - - - +
28A GLY* 1.3 62.9 + - - +
29A VAL* 3.5 17.9 + - + +
78A MET 5.3 0.2 - - - +
82A HIS* 3.7 29.9 + - + -
84A MET* 3.5 19.2 - - + +
198A ARG* 3.4 6.2 + - - -
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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