Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 3V4R
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLN 3.4 0.4 + - - -
15A GLY* 1.4 71.6 - - - -
17A GLN* 1.3 62.4 + - - +
18A PRO* 3.5 2.0 - - - -
19A LYS* 3.7 11.5 + - + +
20A ALA* 3.2 24.3 + - - +
409A GLU* 4.0 7.8 - - - +
410A GLN* 3.4 16.2 - - - +
411A ILE* 3.0 27.1 + - - +
412A ILE* 3.1 45.4 + - + +
577A PHE* 5.9 0.4 - - + -
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Residues in contact with GLN 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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13A PRO* 3.5 11.8 - - + +
14A GLN* 3.3 20.8 + - - +
16A ASP* 1.3 76.3 - - - +
18A PRO* 1.4 67.7 - - + +
20A ALA* 3.2 1.9 + - - +
21A ILE* 3.0 32.1 + - + +
43A THR 3.0 19.8 + - - +
44A GLY 3.0 26.1 + - - -
47A PHE* 3.6 10.6 - - - -
48A THR* 3.4 14.6 + - - +
410A GLN* 3.6 11.7 - - + +
412A ILE 6.0 0.9 - - - +
414A PRO* 5.4 3.3 - - + +
701A ADP 3.2 41.8 + - - -
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Residues in contact with PRO 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 PRO* 3.4 27.1 - - + +
14A GLN 3.6 6.7 - - - +
15A GLY 3.5 17.0 - - - +
16A ASP 3.7 0.9 - - - -
17A GLN* 1.4 92.4 - - + +
19A LYS* 1.4 61.1 + - - +
21A ILE* 3.5 8.5 + - + +
22A GLU* 3.1 25.7 + - - +
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Residues in contact with LYS 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 ASP* 3.7 14.9 + - + +
17A GLN 3.4 0.2 - - - -
18A PRO* 1.4 79.2 - - - +
20A ALA* 1.4 61.5 + - - +
22A GLU* 3.8 4.7 - - - +
23A LYS* 3.1 26.1 + - - +
409A GLU 6.1 0.7 - - - +
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Residues in contact with ALA 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 ASP 3.2 19.3 + - - +
17A GLN 3.5 4.7 - - - +
19A LYS* 1.4 73.7 - - - +
21A ILE* 1.4 57.7 + - - +
23A LYS* 3.2 4.7 + - - +
24A LEU* 2.9 35.6 + - - +
37A LEU* 3.9 19.5 - - + -
48A THR* 4.3 2.7 - - + -
408A VAL* 4.0 13.2 - - + -
409A GLU 4.6 4.8 + - - +
410A GLN* 3.5 22.0 - - + +
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Residues in contact with ILE 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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13A PRO* 3.9 18.2 - - + -
17A GLN* 3.0 32.5 + - + +
18A PRO* 4.1 4.0 - - + +
20A ALA* 1.4 68.2 - - - +
22A GLU* 1.4 64.4 + - - +
24A LEU* 3.3 5.1 + - - +
25A VAL* 2.9 45.6 + - + +
48A THR* 3.9 21.5 - - + +
51A ASN* 3.6 45.8 - - + +
52A LEU* 4.0 9.2 - - + +
55A GLU* 4.2 10.8 - - + +
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Residues in contact with GLU 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 PRO 3.1 17.8 + - - +
19A LYS* 3.8 6.5 - - - +
21A ILE* 1.4 74.1 - - - +
23A LYS* 1.4 57.5 + - - +
25A VAL* 3.5 4.0 + - - +
26A LYS* 3.1 31.4 + - - +
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Residues in contact with LYS 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 LYS 3.1 18.2 + - - +
20A ALA 3.7 3.4 - - - +
22A GLU* 1.4 75.3 - - - +
24A LEU* 1.3 57.7 + - - +
26A LYS* 3.7 6.0 + - - +
27A GLY* 3.2 22.5 + - - -
35A GLN* 3.9 2.5 - - - +
408A VAL* 4.1 19.3 - - + -
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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 ALA 2.9 19.9 + - - +
21A ILE* 4.0 4.3 - - - +
23A LYS* 1.3 73.9 - - - +
25A VAL* 1.4 63.4 + - - +
28A ILE* 3.4 22.5 + - - +
35A GLN* 3.4 43.6 + - + +
36A THR 4.8 2.9 - - - +
37A LEU* 3.6 36.3 - - + -
48A THR* 4.7 8.7 - - + -
49A VAL* 6.5 0.4 - - + -
52A LEU* 4.0 19.7 - - + -
390A VAL* 4.2 20.2 - - + -
408A VAL* 3.9 19.3 - - + -
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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 ILE* 2.9 36.4 + - + +
22A GLU* 4.2 3.1 - - - +
24A LEU* 1.4 73.5 - - - +
26A LYS* 1.4 65.0 + - - +
28A ILE* 3.3 5.4 + - - +
29A GLN* 3.0 23.7 + - + +
52A LEU* 3.9 17.9 - - + -
55A GLU* 3.8 33.7 - - + +
56A VAL* 3.8 17.0 - - + -
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Residues in contact with LYS 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 GLU 3.1 18.9 + - - +
23A LYS* 3.9 6.7 - - - +
25A VAL* 1.4 75.9 - - - +
27A GLY* 1.3 52.1 + - - +
29A GLN* 3.3 7.9 + - - +
30A GLU* 2.7 38.5 + - + +
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Residues in contact with GLY 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 LYS 3.2 12.3 + - - -
24A LEU 3.6 0.2 + - - -
25A VAL 3.2 0.6 - - - -
26A LYS* 1.3 76.0 - - - +
28A ILE* 1.3 54.4 + - - +
30A GLU* 3.3 5.9 + - - +
31A GLY 3.2 5.0 + - - -
32A LYS* 2.8 40.8 + - - +
35A GLN* 3.4 20.6 - - - -
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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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24A LEU 3.4 7.7 + - - +
25A VAL 3.3 7.2 + - - +
27A GLY* 1.3 73.9 - - - +
29A GLN* 1.4 64.9 + - - +
31A GLY* 3.0 15.9 + - - -
32A LYS 4.0 4.7 - - - -
35A GLN* 3.5 15.3 - - - +
52A LEU* 3.7 28.9 - - + -
56A VAL* 3.8 23.6 - - + -
58A LYS* 4.4 10.8 - - - +
334A MET* 3.7 25.1 - - + -
388A ASN* 3.9 33.0 + - + +
390A VAL* 4.5 6.5 - - + -
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Residues in contact with GLN 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 VAL* 3.0 15.7 + - + +
26A LYS* 3.6 11.0 - - - +
28A ILE* 1.4 77.6 - - - +
30A GLU* 1.4 57.6 + - - +
31A GLY 3.1 4.4 + - - -
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Residues in contact with GLU 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 LYS* 2.7 22.4 + - + +
27A GLY* 3.3 5.8 + - - +
28A ILE 3.3 0.2 - - - -
29A GLN* 1.4 71.1 - - - +
31A GLY* 1.3 58.4 + - - +
32A LYS* 3.5 3.0 + - + +
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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