Contacts of the helix formed by residues 15 - 25 (chain A) in PDB entry 2R6C
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 GLU 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 1.3 69.1 + - - +
17A GLU* 3.2 10.0 - - - +
18A GLN* 3.5 25.0 + - - +
19A ALA 3.2 16.1 + - - -
48A HIS* 6.2 0.2 - - - -
68B VAL* 3.4 26.8 - - + +
71B THR* 2.9 35.5 + - - +
72B ALA* 5.6 1.3 - - + -
75B ALA* 5.5 1.4 - - - +
80B LEU* 4.1 11.4 - - - +
86B VAL* 3.2 31.5 - - - +
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Residues in contact with ALA 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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15A GLU* 1.3 79.2 - - - +
17A GLU* 1.3 64.3 + - - +
19A ALA* 3.2 15.7 + - - +
20A VAL* 3.3 14.0 + - - +
105A TYR* 4.3 7.9 - - + +
108A ILE* 3.5 38.1 - - + -
109A VAL* 4.0 9.4 - - + -
68B VAL* 3.5 17.6 - - + +
72B ALA* 5.4 2.9 - - + +
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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 GLU 3.2 6.3 - - - +
16A ALA* 1.3 76.4 - - - +
18A GLN* 1.3 66.0 + - - +
20A VAL* 3.2 13.4 + - - +
21A LEU* 3.4 16.3 + - - +
43A PHE* 3.3 25.5 - - + -
44A TYR* 2.6 37.0 + - - +
45A ARG* 3.6 10.9 + - - +
48A HIS* 2.8 42.2 + - + +
109A VAL* 3.7 23.7 - - + +
116A ARG* 5.5 0.2 + - - -
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Residues in contact with GLN 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 GLU* 3.5 24.2 + - - +
16A ALA 3.3 0.2 - - - -
17A GLU* 1.3 79.2 - - - +
19A ALA* 1.3 54.2 + - - +
21A LEU* 3.4 1.3 + - - +
22A GLY* 2.8 34.7 + - - -
45A ARG* 5.0 5.5 - - - +
48A HIS* 3.8 8.5 - - + -
88A TYR* 3.0 40.5 + - - +
91A GLU* 5.5 1.8 + - - -
92A LEU* 3.7 22.0 - - + +
96A VAL* 4.5 4.1 - - + +
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Residues in contact with ALA 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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15A GLU 3.2 13.1 + - - +
16A ALA 3.3 11.0 - - - +
17A GLU 3.1 0.6 - - - -
18A GLN* 1.3 75.2 - - - +
20A VAL* 1.3 57.3 + - - +
22A GLY 3.8 0.3 - - - -
23A ALA* 2.9 31.5 + - - +
96A VAL* 3.7 21.1 - - + +
105A TYR* 3.6 40.0 - - + -
68B VAL* 4.2 4.9 - - + +
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Residues in contact with VAL 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 ALA 3.3 13.0 + - - +
17A GLU 3.2 7.2 + - - +
19A ALA* 1.3 71.4 - - - +
21A LEU* 1.3 68.5 + - - +
23A ALA* 2.9 16.8 + - - +
24A VAL* 3.0 12.7 + - + +
34A ALA* 3.7 30.1 - - + -
38A LEU* 4.2 11.4 - - + -
43A PHE* 4.4 5.2 - - + -
52A PHE* 4.1 16.2 - - + -
102A VAL* 4.1 8.9 - - + +
105A TYR* 3.8 7.6 - - + +
106A ALA* 3.7 30.5 - - - +
109A VAL* 4.6 3.8 - - + -
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Residues in contact with LEU 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 3.4 9.9 + - - +
18A GLN 3.8 4.3 - - - +
20A VAL* 1.3 77.0 - - - +
22A GLY* 1.3 64.0 + - - +
24A VAL* 2.9 16.1 + - - +
25A PHE* 3.3 16.1 + - + -
43A PHE* 4.0 7.4 - - + -
48A HIS* 3.7 45.8 - - + +
51A ILE* 4.0 20.6 - - + -
52A PHE* 3.8 30.7 - - + +
55A MET* 3.7 28.8 - - + +
92A LEU* 4.0 16.6 - - + -
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Residues in contact with GLY 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 GLN 2.8 20.8 + - - -
19A ALA 3.9 0.9 - - - -
21A LEU* 1.3 71.6 - - - +
23A ALA* 1.3 59.9 + - - +
25A PHE* 3.3 16.2 + - - +
26A LEU* 3.4 13.3 + - - +
92A LEU* 3.6 32.5 - - - +
93A ALA* 4.2 4.3 - - - -
96A VAL* 4.3 9.4 - - - -
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Residues in contact with ALA 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 ALA 2.9 23.0 + - - +
20A VAL* 2.9 5.1 + - - +
22A GLY* 1.3 70.0 - - - +
24A VAL* 1.3 65.2 - - - +
26A LEU* 3.1 6.5 + - - +
27A ASP 3.0 19.9 + - - -
30A ALA* 3.4 7.4 - - + +
96A VAL* 4.1 8.4 - - + +
98A THR 4.5 1.3 - - - +
99A ALA* 3.7 25.2 - - + +
102A VAL* 3.9 21.5 - - + +
105A TYR* 6.2 0.9 - - + -
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Residues in contact with VAL 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 VAL* 3.0 13.1 + - + +
21A LEU 2.9 10.3 + - - +
23A ALA* 1.3 71.8 - - - +
25A PHE* 1.3 56.5 + - + +
26A LEU 2.8 14.7 + - - -
28A PRO* 2.9 33.6 - - + +
30A ALA* 3.9 8.5 - - + +
31A LEU* 3.7 36.6 - - + +
34A ALA* 4.7 5.8 - - + -
55A MET* 3.4 47.3 - - + -
65A VAL* 4.3 12.8 - - + +
102A VAL* 5.4 0.2 - - + -
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Residues in contact with PHE 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 LEU* 3.3 14.7 + - + -
22A GLY 3.3 8.1 + - - +
24A VAL* 1.3 78.3 - - + +
26A LEU* 1.3 60.7 + - - +
28A PRO* 5.2 1.6 - - - -
51A ILE* 4.5 6.7 - - + -
55A MET* 4.9 7.2 - - - -
65A VAL 5.5 2.9 - - - -
66A ASP* 4.2 5.4 - - - +
67A LEU* 3.8 34.8 + - + +
70A VAL* 3.9 30.7 - - + -
89A LEU* 3.6 55.2 - - + -
92A LEU* 4.0 12.3 - - + -
93A ALA* 4.0 23.1 - - + -
588G ILE* 4.3 16.3 - - + +
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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