Contacts of the helix formed by residues 15 - 32 (chain A) in PDB entry 4AVM
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 LYS 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 GLN* 1.4 65.8 + - - +
17A VAL* 3.2 6.1 - - - +
18A GLN* 3.5 13.4 + - + +
19A LYS* 3.2 27.0 + - + +
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Residues in contact with GLN 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 LYS* 1.4 76.5 - - - +
17A VAL* 1.4 62.1 - - - +
19A LYS* 3.8 8.3 + - - +
20A LYS* 3.5 18.0 + - - +
23A ARG* 5.3 1.4 + - - -
1249A EPE 6.3 0.9 - - - +
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Residues in contact with VAL 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 LYS 3.2 2.8 - - - +
16A GLN* 1.4 75.8 - - - +
18A GLN* 1.3 65.6 + - - +
20A LYS* 3.1 17.2 + - - +
21A PHE* 3.2 27.3 + - + -
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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 LYS* 3.5 15.1 + - + +
17A VAL* 1.3 74.4 - - - +
19A LYS* 1.4 65.1 + - - +
21A PHE* 3.1 24.2 + - - +
22A SER* 3.0 33.6 + - - +
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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
----------------------------------------------------------
15A LYS* 3.2 17.9 + - + +
16A GLN* 3.9 9.6 - - - +
17A VAL 3.3 0.2 - - - -
18A GLN* 1.4 74.6 - - - +
20A LYS* 1.4 56.8 + - - +
22A SER* 3.2 8.8 + - - -
23A ARG* 2.9 40.7 + - - +
145A LYS* 6.0 3.1 - - - +
148A ASP* 4.3 25.1 - - - +
176A GLU* 6.5 1.3 - - - -
179A LYS* 6.1 5.6 - - - -
1249A EPE 6.2 3.1 - - + -
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Residues in contact with LYS 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 GLN 3.5 9.8 + - - +
17A VAL* 3.1 13.5 + - - +
19A LYS* 1.4 76.8 - - - +
21A PHE* 1.3 59.8 + - + +
23A ARG* 3.7 25.4 + - - +
24A ALA* 3.1 27.9 + - - +
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Residues in contact with PHE 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 VAL* 3.2 34.3 + - + -
18A GLN* 3.1 29.7 + - - +
20A LYS* 1.3 78.3 - - + +
22A SER* 1.4 58.4 + - - +
24A ALA* 3.4 4.8 + - + +
25A GLN* 3.0 30.9 + - - +
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 3.0 22.6 + - - +
19A LYS* 3.6 10.2 - - - -
21A PHE* 1.4 73.1 - - - +
23A ARG* 1.3 57.7 + - - +
25A GLN* 3.5 13.1 + - - +
26A GLU* 3.0 28.9 + - - +
151A SER* 3.5 22.0 + - - -
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Residues in contact with ARG 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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16A GLN 5.3 1.8 + - - -
19A LYS* 2.9 22.8 + - - +
20A LYS* 3.7 28.9 - - - +
22A SER* 1.3 73.6 - - - +
24A ALA* 1.4 66.6 + - - +
26A GLU* 3.3 2.6 + - - -
27A LYS* 3.0 19.6 + - - +
144A ARG* 3.1 58.1 - - - +
147A VAL* 3.3 21.5 - - + +
148A ASP* 2.9 51.1 + - - +
151A SER* 4.7 3.1 - - - -
1249A EPE 4.0 23.0 + - - +
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Residues in contact with ALA 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 LYS 3.1 15.9 + - - +
21A PHE* 3.9 5.2 - - + +
23A ARG* 1.4 78.1 - - - +
25A GLN* 1.3 61.3 + - - +
27A LYS* 3.3 7.8 + - - +
28A VAL* 3.1 25.2 + - - +
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Residues in contact with GLN 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 PHE 3.0 17.4 + - - +
22A SER* 3.8 11.6 - - - +
23A ARG 3.3 0.2 - - - -
24A ALA* 1.3 72.1 - - - +
26A GLU* 1.3 65.4 + - - +
28A VAL* 3.4 10.3 - - + +
29A LEU* 3.0 42.3 + - + +
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Residues in contact with GLU 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 SER 3.0 17.8 + - - +
23A ARG 3.5 5.6 - - - +
25A GLN* 1.3 75.9 - - - +
27A LYS* 1.4 61.8 + - - +
29A LEU* 3.2 9.1 + - - +
30A GLN* 3.1 54.2 + - - +
35A ALA* 4.1 4.1 - - - +
36A VAL 3.8 0.7 - - - +
147A VAL* 4.0 7.6 - - + +
150A ASP* 3.4 16.9 - - + +
151A SER* 3.6 22.5 - - - +
154A HIS* 3.3 27.7 + - - +
1245A EDO 2.7 23.3 + - - -
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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
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23A ARG 3.0 13.1 + - - +
24A ALA* 3.7 11.2 - - - +
26A GLU* 1.4 75.9 - - - +
28A VAL* 1.3 61.5 + - - +
30A GLN* 3.3 17.5 + - - +
31A LYS* 3.1 39.2 + - - +
147A VAL* 4.3 11.6 - - + +
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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 ALA 3.1 15.3 + - - +
25A GLN* 3.4 17.7 - - + +
27A LYS* 1.3 76.9 - - - +
29A LEU* 1.4 68.8 + - + +
31A LYS* 3.2 15.2 + - + +
32A LEU* 3.0 46.3 + - + +
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Residues in contact with LEU 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 GLN* 3.0 43.7 + - + +
26A GLU* 3.7 7.4 - - - +
28A VAL* 1.4 80.0 - - + +
30A GLN* 1.3 58.3 + - - +
32A LEU* 3.4 7.1 + - + +
33A GLY 3.3 3.1 + - - -
34A LYS* 2.8 60.9 + - + +
35A ALA* 3.2 13.6 + - + -
154A HIS* 4.1 26.7 - - + +
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Residues in contact with GLN 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 GLU* 3.1 50.1 + - - +
27A LYS* 3.4 13.7 - - - +
28A VAL 3.2 0.2 - - - -
29A LEU* 1.3 76.5 - - - +
31A LYS* 1.4 63.3 + - + +
33A GLY* 3.0 15.2 + - - -
35A ALA* 3.5 24.4 - - + +
37A GLU* 3.4 44.3 - - + +
147A VAL* 5.1 8.4 - - - +
150A ASP* 3.6 12.3 + - - +
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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 29.4 + - - +
28A VAL* 3.2 15.7 + - + +
30A GLN* 1.4 74.5 - - + +
32A LEU* 1.3 62.6 + - + +
33A GLY 3.3 1.3 + - - -
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Residues in contact with LEU 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 37.7 + - + +
29A LEU* 3.9 9.2 - - + +
30A GLN 3.2 0.6 - - - -
31A LYS* 1.3 79.8 - - + +
33A GLY* 1.3 62.6 + - - +
34A LYS* 3.2 24.7 + - + +
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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