Contacts of the helix formed by residues 15 - 36 (chain A) in PDB entry 3RTC
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 ASP 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 5.3 1.1 - - - -
13A GLY 3.3 6.6 + - - -
14A VAL* 1.3 75.7 - - - +
16A SER* 1.3 70.7 + - - +
17A ARG* 2.9 58.6 + - - +
18A ILE* 3.0 42.4 + - + +
19A LEU* 3.4 5.2 + - - +
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Residues in contact with SER 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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9A ILE* 4.0 35.4 - - - +
14A VAL 3.3 3.0 + - - -
15A ASP* 1.3 77.9 + - - +
17A ARG* 1.3 62.4 + - - +
19A LEU* 3.3 7.1 + - - +
20A MET* 3.1 21.5 + - - +
82A ASP* 2.4 35.0 + - - +
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Residues in contact with ARG 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 ASP* 2.9 31.9 + - - +
16A SER* 1.3 78.1 + - - +
18A ILE* 1.3 57.6 + - + +
20A MET* 3.4 7.5 + - - +
21A GLU* 2.9 27.9 + - - +
82A ASP* 3.5 22.7 - - + +
85A TYR* 3.5 61.5 + - + -
86A ASN* 5.1 4.4 + - - +
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Residues in contact with ILE 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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14A VAL* 3.8 16.8 - - + -
15A ASP* 3.0 33.1 + - + +
17A ARG* 1.3 73.7 - - + +
19A LEU* 1.3 61.5 + - + +
21A GLU* 3.3 6.0 + - - +
22A ARG* 3.0 45.7 + - + +
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Residues in contact with LEU 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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5A ASP* 4.3 9.0 - - - +
8A THR* 4.2 23.1 - - + -
9A ILE* 4.1 30.3 - - + -
14A VAL* 4.1 20.9 - - + -
15A ASP 3.4 3.0 + - - +
16A SER 3.3 9.4 + - - +
18A ILE* 1.3 75.7 - - + +
20A MET* 1.3 57.7 + - - +
22A ARG* 3.4 5.4 + - - +
23A ALA* 2.9 28.6 + - - +
196A ILE* 3.3 42.7 - - + +
197A GLY 4.6 4.0 - - - -
198A HIS* 4.3 14.6 - - - +
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Residues in contact with MET 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 SER 3.1 15.9 + - - +
17A ARG* 3.7 6.3 - - - +
18A ILE 3.3 0.2 - - - -
19A LEU* 1.3 74.5 - - - +
21A GLU* 1.3 65.0 + - - +
23A ALA* 3.2 1.6 + - - +
24A GLY* 3.0 20.3 + - - -
51A ASN* 3.4 45.1 - - + +
54A GLY* 3.6 15.5 - - - +
55A ASP* 3.3 18.7 - - - +
58A VAL* 3.8 11.6 - - + +
82A ASP* 3.6 32.8 - - + +
86A ASN* 3.1 29.8 - - - +
493A NAD 5.5 1.3 - - - +
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Residues in contact with GLU 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 ARG 2.9 17.7 + - - +
18A ILE* 3.3 6.9 + - - +
20A MET* 1.3 75.9 - - - +
22A ARG* 1.3 63.5 + - + +
24A GLY* 3.2 2.3 + - - -
25A ILE* 2.9 37.7 + - + +
58A VAL* 3.5 14.6 - - - +
61A ARG* 2.8 43.2 + - - -
62A ASN* 3.2 13.7 + - - +
86A ASN* 4.4 2.8 - - - +
89A LEU* 5.4 0.9 - - - +
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Residues in contact with ARG 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 ILE* 3.0 31.8 + - + +
19A LEU 3.6 3.1 - - - +
21A GLU* 1.3 77.0 - - + +
23A ALA* 1.3 60.5 + - - +
25A ILE* 3.3 20.8 - - - +
26A SER* 3.1 25.1 + - - -
195A ASN* 3.1 27.1 + - - +
196A ILE* 3.5 29.9 + - + +
197A GLY* 3.4 22.6 - - - +
3B TRP* 3.4 34.5 - - - -
4B LEU* 5.7 2.2 - - - +
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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 LEU 2.9 16.9 + - - +
20A MET* 3.6 5.6 - - - +
21A GLU 3.2 0.2 - - - -
22A ARG* 1.3 72.3 - - - +
24A GLY* 1.3 63.6 + - - +
26A SER* 2.9 19.1 + - - -
27A VAL* 3.2 11.8 + - - +
55A ASP* 3.6 21.3 - - - +
172A PHE* 3.5 30.5 - - + -
196A ILE* 3.7 16.3 - - + +
493A NAD 6.0 0.9 - - - +
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Residues in contact with GLY 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 MET 3.0 11.9 + - - -
23A ALA* 1.3 78.4 - - - +
25A ILE* 1.3 61.0 + - - +
27A VAL* 3.1 14.5 + - - +
28A VAL* 3.3 13.0 + - - +
55A ASP* 4.0 5.3 + - - -
58A VAL* 3.5 24.0 - - - -
59A VAL* 3.5 20.9 - - - +
62A ASN* 5.1 0.2 - - - -
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Residues in contact with ILE 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 GLU* 2.9 39.6 + - + +
22A ARG* 3.3 33.2 - - - +
24A GLY* 1.3 76.2 - - - +
26A SER* 1.3 67.3 + - - +
28A VAL* 3.2 10.6 + - + +
29A LEU* 3.0 36.7 + - + +
58A VAL* 4.1 0.2 - - - +
62A ASN* 3.8 16.6 - - - +
4B LEU* 6.3 2.2 - - + -
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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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22A ARG 3.1 17.1 + - - -
23A ALA 2.9 13.5 + - - -
25A ILE* 1.3 78.0 - - - +
27A VAL* 1.3 56.2 + - - +
29A LEU* 3.4 3.3 + - - +
30A ALA* 2.9 32.1 + - - +
170A VAL* 4.0 2.3 - - - +
172A PHE* 3.4 10.2 - - - -
194A ALA* 3.3 32.7 - - - +
196A ILE* 4.6 2.5 - - - -
4B LEU* 4.2 17.0 - - - -
5B PHE* 3.4 10.2 - - - -
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Residues in contact with VAL 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 ALA 3.2 13.9 + - - +
24A GLY* 3.1 9.2 + - - +
26A SER* 1.3 77.7 + - - +
28A VAL* 1.3 61.6 + - - +
30A ALA* 3.4 1.9 + - - +
31A MET* 3.0 31.8 + - + +
59A VAL* 3.7 22.4 - - + -
113A VAL* 4.9 1.3 - - + -
144A VAL* 4.1 25.1 - - + -
146A VAL* 4.4 18.4 - - + -
170A VAL* 3.9 19.7 - - + -
172A PHE* 3.8 20.6 - - + -
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Residues in contact with VAL 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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24A GLY 3.6 13.0 - - - +
25A ILE* 3.2 9.8 + - + +
27A VAL* 1.3 75.1 - - - +
29A LEU* 1.3 66.8 + - + +
31A MET* 3.2 12.7 + - + +
32A GLU* 3.0 25.3 + - - +
38A LEU* 3.9 17.0 - - + +
59A VAL* 4.2 21.8 - - + +
62A ASN* 4.2 27.8 - - + +
63A LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.0 32.2 + - + +
26A SER* 3.9 3.1 - - - +
28A VAL* 1.3 77.2 - - + +
30A ALA* 1.3 64.5 + - - +
32A GLU* 3.3 22.6 + - - +
33A GLU* 3.0 24.9 + - - +
4B LEU* 3.6 31.0 - - + -
5B PHE* 4.2 4.6 - - + -
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Residues in contact with ALA 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 2.9 18.2 + - - +
27A VAL 3.6 1.1 - - - +
29A LEU* 1.3 75.8 - - - +
31A MET* 1.3 62.7 + - - +
33A GLU* 3.4 4.4 - - - +
34A GLU* 3.0 24.3 + - - +
168A LEU* 4.1 3.6 - - + -
170A VAL* 3.5 28.3 - - + -
192A LYS* 3.7 18.7 - - + +
5B PHE* 3.6 20.6 - - + -
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Residues in contact with MET 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 VAL* 3.0 21.4 + - + +
28A VAL* 3.2 13.2 + - - +
30A ALA* 1.3 76.3 - - - +
32A GLU* 1.3 53.2 + - - +
34A GLU* 3.2 1.2 + - - -
35A LEU* 2.6 46.6 + - + +
38A LEU* 4.0 12.1 - - + -
43A PHE* 3.9 30.5 - - + -
59A VAL* 4.0 27.4 - - + -
63A LEU* 4.2 9.4 - - + -
111A VAL* 4.5 0.4 - - - -
113A VAL* 4.0 10.1 - - + -
144A VAL* 3.7 44.4 - - + -
168A LEU* 4.2 7.0 - - + -
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Residues in contact with GLU 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 VAL* 3.0 14.4 + - - +
29A LEU* 3.5 31.0 - - - +
30A ALA 3.3 0.2 - - - -
31A MET* 1.3 78.6 - - - +
33A GLU* 1.3 56.0 + - - +
36A GLY* 2.7 50.6 + - - +
37A ASN* 5.0 6.9 + - - +
38A LEU* 4.0 16.0 + - + +
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Residues in contact with GLU 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 LEU 3.0 15.3 + - - +
30A ALA* 3.4 4.4 - - - +
32A GLU* 1.3 76.2 - - - +
34A GLU* 1.3 59.7 + - - +
36A GLY* 4.6 1.0 + - - -
192A LYS* 3.1 39.4 + - - +
5B PHE* 3.6 28.4 - - - +
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Residues in contact with GLU 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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30A ALA 3.0 16.7 + - - +
31A MET* 3.8 2.5 - - - +
33A GLU* 1.3 78.1 - - - +
35A LEU* 1.3 74.7 + - + +
36A GLY 3.6 0.4 + - - -
142A VAL* 6.2 1.3 - - + -
167A ASP* 5.0 9.7 - - + +
168A LEU* 4.2 24.0 - - + -
190A LYS* 2.8 42.9 + - - +
192A LYS* 4.4 6.9 + - - +
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Residues in contact with LEU 35 (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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31A MET* 2.6 32.2 + - + +
34A GLU* 1.3 88.9 - - + +
36A GLY* 1.3 60.3 + - - +
37A ASN 4.3 0.2 - - - +
38A LEU* 4.0 19.7 - - + -
41A TYR* 3.4 36.2 + - + +
43A PHE* 5.0 1.1 - - + -
111A VAL* 4.0 29.8 - - + -
142A VAL* 4.1 29.2 - - + -
144A VAL* 5.2 2.0 - - + -
168A LEU* 6.4 0.4 - - + -
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Residues in contact with GLY 36 (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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32A GLU* 2.7 37.7 + - - +
33A GLU 4.5 1.4 + - - -
34A GLU 3.6 1.8 - - - -
35A LEU* 1.3 76.0 - - - +
37A ASN* 1.3 67.6 + - - -
38A LEU* 3.3 5.4 + - - +
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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