Contacts of the helix formed by residues 17 - 32 (chain B) in PDB entry 5DPS
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 PRO 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B LYS 4.9 0.9 - - - +
14B GLU 5.8 0.2 - - - +
15B GLU 4.1 5.2 - - - +
16B HIS* 1.3 88.8 - - + +
18B PHE* 1.3 66.8 + - - +
19B GLU* 4.6 4.7 - - + +
20B LYS* 3.2 27.7 + - + +
21B ARG* 3.1 17.7 + - - +
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 1.3 71.7 - - - +
19B GLU* 1.3 62.8 + - + +
21B ARG* 3.0 38.3 + - - +
22B ARG* 2.8 71.1 + - + +
108B GLU* 4.0 27.6 - - + -
109B ASP* 3.9 26.0 - - + -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.3 4.2 - - + +
18B PHE* 1.3 86.6 - - + +
20B LYS* 1.3 62.4 + - + +
22B ARG* 3.3 29.8 + - - +
23B SER* 3.1 24.8 + - - -
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B HIS* 5.2 3.4 - - + -
17B PRO* 3.2 33.6 + - + +
19B GLU* 1.3 76.7 - - + +
21B ARG* 1.3 65.6 + - + +
23B SER* 3.5 7.0 + - - -
24B GLU* 3.1 23.1 + - - +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.9 21.3 - - + -
13B LYS* 3.0 39.8 + - - +
16B HIS* 2.9 35.6 + - + +
17B PRO* 3.1 12.7 + - - +
18B PHE* 3.0 44.0 + - - +
20B LYS* 1.3 76.7 - - - +
22B ARG* 1.3 51.6 + - - +
24B GLU* 3.1 6.8 + - - +
25B GLY* 2.7 33.4 + - - -
107B GLU* 4.8 3.2 + - - -
109B ASP* 2.8 31.8 + - + +
111B PHE* 3.7 13.3 - - + -
113B TYR* 3.3 13.9 + - - -
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 2.8 47.0 + - + +
19B GLU* 3.3 36.5 + - - +
21B ARG* 1.3 75.4 - - - +
23B SER* 1.3 59.7 + - - +
26B GLU* 2.8 41.6 + - - +
108B GLU* 3.8 26.5 + - - +
109B ASP* 3.6 17.9 - - + +
110B PHE* 3.8 15.2 - - + -
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU 3.1 19.0 + - - -
20B LYS* 3.7 8.3 - - - -
22B ARG* 1.3 78.9 - - - +
24B GLU* 1.3 62.1 + - - +
26B GLU* 3.7 8.8 - - - +
27B LYS* 3.1 39.1 + - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.6 17.0 + - - -
20B LYS 3.1 14.3 + - - +
21B ARG* 3.6 7.9 - - - +
23B SER* 1.3 76.2 - - - +
25B GLY* 1.3 64.7 + - - +
27B LYS* 3.3 8.1 + - - +
28B ILE* 3.0 26.8 + - + +
55B LYS* 2.7 29.3 + - - -
111B PHE* 4.1 12.8 - - + -
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG 2.7 14.8 + - - -
24B GLU* 1.3 70.9 - - - +
26B GLU* 1.3 64.5 + - - +
28B ILE* 3.5 3.1 - - - +
29B ARG* 3.2 29.3 + - - +
109B ASP 3.4 18.4 - - - -
110B PHE* 3.6 8.3 - - - -
111B PHE* 3.4 19.9 - - - -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 2.8 32.5 + - - +
23B SER* 3.7 8.1 - - - +
25B GLY* 1.3 70.7 - - - +
27B LYS* 1.3 64.4 + - + +
29B ARG* 3.3 4.6 + - - +
30B LYS* 3.1 22.9 + - - +
110B PHE* 3.6 35.5 - - + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER* 3.1 28.1 + - - +
24B GLU* 3.7 5.4 - - - +
26B GLU* 1.3 80.5 - - + +
28B ILE* 1.3 57.9 + - - +
30B LYS* 3.3 8.5 + - - +
31B LYS* 2.9 28.7 + - - +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.0 19.9 + - + +
25B GLY* 3.5 13.9 - - - +
27B LYS* 1.3 76.4 - - - +
29B ARG* 1.3 61.1 + - - +
31B LYS* 4.3 12.8 - - + +
32B TYR* 2.8 50.0 + - + +
37B PRO* 4.0 31.0 - - + -
57B LEU* 4.1 25.2 - - + +
111B PHE* 4.5 3.4 - - + -
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLY 3.2 21.1 + - - +
26B GLU* 3.7 5.2 - - - +
27B LYS 3.2 0.2 - - - -
28B ILE* 1.3 76.3 - - - +
30B LYS* 1.3 63.3 + - - +
32B TYR 4.2 1.6 - - - -
33B PRO* 3.3 51.0 + - - +
34B ASP 5.0 0.4 - - - -
35B ARG 3.0 25.4 + - - -
36B VAL* 4.4 6.9 - - - +
37B PRO* 3.9 16.2 - - + -
60B SER* 6.1 0.4 - - - -
102B TYR* 3.5 54.4 + - - +
110B PHE* 4.2 13.9 - - + +
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 3.1 13.8 + - + +
27B LYS* 3.7 10.1 - - - +
29B ARG* 1.3 75.7 - - - +
31B LYS* 1.3 64.9 + - - +
32B TYR 3.5 0.2 + - - -
33B PRO* 3.6 11.7 - - - +
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 2.9 17.5 + - - +
28B ILE* 3.7 16.0 - - + +
30B LYS* 1.3 79.1 - - - +
32B TYR* 1.3 100.5 + - + +
33B PRO* 3.6 5.4 - - - +
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 2.8 24.0 + - + +
29B ARG* 3.5 7.1 + - - +
31B LYS* 1.3 121.0 + - + +
33B PRO* 1.3 68.2 - - - +
34B ASP 3.0 3.4 + - - -
35B ARG* 3.2 67.2 + - + +
57B LEU* 3.9 15.9 - - + -
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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