Contacts of the helix formed by residues 18 - 34 (chain A) in PDB entry 5V6Y
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 5.0 2.1 - - - +
17A LYS* 1.3 74.7 - - - +
19A TYR* 1.3 58.2 + - - -
21A GLY 3.4 1.4 + - - -
22A LEU* 3.0 25.9 + - - +
295A VAL* 3.8 19.4 - - - +
298A ASP* 3.1 24.0 - - - -
299A LYS* 3.6 19.8 + - - +
301A LEU* 5.9 1.0 - - - +
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.7 23.1 - - + +
14A ASN 4.2 6.3 - - - -
15A GLY 3.3 24.7 + - - -
17A LYS 3.1 15.5 + - - -
18A GLY* 1.3 71.2 - - - +
20A ASN* 1.3 100.4 + - - +
22A LEU* 3.3 8.3 + - - +
23A ALA* 2.8 29.5 + - - +
39A VAL* 3.9 14.6 - - + +
41A HIS* 3.4 48.0 + + - +
298A ASP* 3.6 0.6 + - - -
299A LYS* 6.6 0.2 - - - -
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 1.3 108.0 + - - +
21A GLY* 1.3 59.5 + - - +
23A ALA* 3.3 9.4 + - - +
24A GLU* 3.1 29.6 + - - +
298A ASP* 3.2 18.3 + - - +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.4 3.5 + - - -
20A ASN* 1.3 74.6 - - - +
22A LEU* 1.3 63.9 + - - +
24A GLU* 3.2 22.0 + - - +
25A VAL* 3.2 16.6 + - - +
294A ALA* 3.4 23.7 - - - +
295A VAL* 4.1 6.7 - - - -
298A ASP* 3.1 17.8 + - - -
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Residues in contact with LEU 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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11A ILE* 3.7 30.3 - - + -
13A ILE* 4.1 20.2 - - + -
18A GLY 3.0 14.7 + - - +
19A TYR* 3.3 8.7 + - - +
21A GLY* 1.3 72.2 - - - +
23A ALA* 1.3 64.7 + - - +
25A VAL* 3.1 6.5 + - + +
26A GLY* 3.1 17.8 + - - -
39A VAL* 4.2 15.1 - - + +
63A PHE* 3.9 12.6 - - + -
281A PHE* 4.1 15.7 - - + -
286A LEU* 3.7 36.8 - - + -
295A VAL* 3.9 11.0 - - + +
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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 TYR 2.8 20.5 + - - +
20A ASN* 3.5 10.1 - - - +
21A GLY 3.2 0.2 - - - -
22A LEU* 1.3 72.5 - - - +
24A GLU* 1.3 58.2 + - + +
26A GLY* 3.1 3.8 + - - +
27A LYS* 2.8 38.4 + - + +
37A VAL* 5.7 2.4 - - - +
39A VAL* 3.9 20.8 - - + +
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Residues in contact with GLU 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 ASN* 3.1 18.6 + - - +
21A GLY* 3.2 12.6 + - - +
23A ALA* 1.3 73.7 - - + +
25A VAL* 1.3 60.4 + - - +
27A LYS* 3.1 12.8 + - + +
28A LYS* 3.0 27.7 + - - +
294A ALA* 4.4 19.1 - - + +
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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 GLY 3.3 15.5 - - - +
22A LEU* 3.1 14.3 + - + +
24A GLU* 1.3 75.0 - - - +
26A GLY* 1.3 58.1 + - - +
28A LYS* 3.4 9.5 + - + +
29A PHE* 3.0 22.0 + - - +
281A PHE* 3.5 25.3 - - + -
285A TYR* 3.8 32.7 - - + +
286A LEU* 4.0 7.6 - - + +
291A GLY* 3.7 25.6 - - - +
294A ALA* 4.0 9.0 - - + -
295A VAL* 4.2 4.3 - - + -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 3.1 12.2 + - - -
23A ALA* 3.1 5.5 + - - -
25A VAL* 1.3 74.7 - - - +
27A LYS* 1.3 59.7 + - - +
29A PHE* 3.4 2.5 + - - +
30A GLU* 3.0 29.9 + - - +
37A VAL* 3.8 31.1 - - - +
281A PHE* 3.7 14.4 - - - -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 2.8 27.3 + - + +
24A GLU* 3.1 13.6 + - + +
26A GLY* 1.3 77.9 - - - +
28A LYS* 1.3 62.7 + - - +
30A GLU* 3.4 18.2 + - - +
31A LYS* 3.1 32.7 + - + +
37A VAL 5.5 6.7 - - - +
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Residues in contact with LYS 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 GLU 3.0 12.4 + - - +
25A VAL* 3.8 11.4 - - + +
27A LYS* 1.3 73.5 - - - +
29A PHE* 1.3 64.7 + - - +
31A LYS* 3.4 10.5 + - + +
32A ASP* 3.2 39.5 + - - +
285A TYR* 4.3 26.9 + - + +
288A THR* 5.9 0.4 + - - -
290A GLU* 4.3 25.3 - - - +
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Residues in contact with PHE 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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9A LEU* 4.0 10.3 - - + -
25A VAL 3.0 17.2 + - - +
26A GLY 3.6 4.9 - - - +
27A LYS 3.3 0.2 - - - -
28A LYS* 1.3 77.6 - - - +
30A GLU* 1.3 59.4 + - - +
32A ASP* 3.5 0.7 + - - -
33A THR* 2.8 52.6 + - + +
35A ILE* 3.6 34.3 - - + -
37A VAL* 3.8 10.8 - - + -
277A LEU* 3.8 24.5 - - + -
280A GLU* 3.8 14.4 - - + -
281A PHE* 3.6 28.7 - + + -
285A TYR* 3.5 41.5 - + + -
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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 GLY 3.0 15.5 + - - +
27A LYS* 3.7 20.3 - - - +
29A PHE* 1.3 78.1 - - - +
31A LYS* 1.3 59.8 + - + +
34A GLY* 2.7 35.3 + - - +
35A ILE 3.4 24.0 + - - +
36A LYS* 3.7 27.0 - - - +
37A VAL 4.3 3.8 + - - +
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Residues in contact with LYS 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 LYS* 3.1 21.4 + - + +
28A LYS* 3.8 11.9 - - + +
29A PHE 3.3 0.4 - - - -
30A GLU* 1.3 78.7 - - + +
32A ASP* 1.3 68.1 + - - +
34A GLY 4.8 0.3 + - - -
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Residues in contact with ASP 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 LYS* 3.2 30.2 + - - +
29A PHE 4.1 1.6 - - - +
30A GLU 3.2 0.8 - - - -
31A LYS* 1.3 87.3 - - - +
33A THR* 1.3 61.1 + - + +
285A TYR* 3.2 34.9 + - - +
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Residues in contact with THR 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 PHE* 2.8 46.5 + - + +
32A ASP* 1.3 81.2 - - + +
34A GLY* 1.3 62.1 + - - +
35A ILE* 3.3 21.1 + - - +
277A LEU* 6.1 1.3 - - + -
280A GLU* 5.3 5.6 - - + +
285A TYR* 4.1 16.6 - - + +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 2.7 28.8 + - - +
31A LYS 4.6 0.6 + - - -
32A ASP 3.8 0.4 - - - -
33A THR* 1.3 71.3 - - - +
35A ILE* 1.3 64.5 + - - +
36A LYS* 3.7 3.9 + - - +
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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