Contacts of the helix formed by residues 23 - 38 (chain C) in PDB entry 5DPR
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 SER 23 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 1.3 76.5 - - - +
24C PHE* 1.3 65.8 + - - +
25C ALA* 3.7 6.6 + - - +
26C ASP* 3.1 35.1 + - - +
27C ARG* 3.0 21.0 + - - -
20D GLN 3.6 5.8 - - - -
21D ARG 3.3 20.0 - - - -
22D ARG* 4.2 0.9 - - - -
23D SER* 3.8 23.2 - - - +
26D ASP* 5.1 3.8 - - - -
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Residues in contact with PHE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 1.3 73.1 - - - +
25C ALA* 1.3 66.0 + - - +
27C ARG* 3.4 28.0 + - - +
28C CYS* 3.1 41.4 + - - -
115C ASP* 5.0 0.9 - - - -
116C GLU* 4.0 20.6 - - + -
117C ASP* 3.8 25.8 - - + -
16D ARG* 3.3 57.7 - - - -
20D GLN 2.8 17.7 + - - +
21D ARG* 4.2 3.9 + - - +
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 3.2 7.9 + - - +
24C PHE* 1.3 85.8 - - + +
26C ASP* 1.3 65.1 + - - +
28C CYS* 3.3 7.7 + - - +
29C LYS* 3.1 38.8 + - - +
21D ARG 5.2 1.0 + - - +
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Residues in contact with ASP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 3.6 38.4 + - - +
23C SER* 3.1 30.2 + - - +
25C ALA* 1.3 79.8 - - - +
27C ARG* 1.3 63.1 + - - +
29C LYS* 3.4 24.1 + - - +
30C GLU* 3.0 23.7 + - - +
23D SER* 5.3 2.8 + - - -
26D ASP* 5.0 5.9 - - - +
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Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 3.6 32.1 - - + -
19C LYS* 3.2 49.5 + - - +
22C ARG* 3.1 30.7 + - + -
23C SER 3.0 9.6 + - - +
24C PHE* 3.5 42.1 - - - +
26C ASP* 1.3 73.5 - - - +
28C CYS* 1.3 65.9 + - - +
30C GLU* 3.4 3.8 + - - -
31C VAL* 3.1 29.8 + - - +
115C ASP* 4.2 2.0 + - - -
117C ASP* 2.9 29.8 + - + +
119C PHE* 3.6 9.4 - - + -
121C TYR* 3.4 5.9 + - - -
20D GLN* 3.5 13.1 + - - +
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Residues in contact with CYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 3.1 49.0 + - - +
25C ALA* 3.3 10.7 + - - +
27C ARG* 1.3 76.1 - - - +
29C LYS* 1.3 63.3 + - + +
31C VAL* 3.5 2.8 + - - +
32C GLN* 3.2 21.3 + - - +
116C GLU 4.6 2.2 - - - -
117C ASP* 3.7 24.8 - - - +
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Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 3.1 27.0 + - - +
26C ASP* 3.6 23.6 + - - +
27C ARG 3.2 0.2 - - - -
28C CYS* 1.3 76.5 - - + +
30C GLU* 1.3 63.2 + - - +
32C GLN* 2.9 17.7 + - - +
33C GLN* 3.1 24.0 + - + +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 4.3 7.3 - - - -
22C ARG* 3.9 26.4 + - - +
26C ASP 3.0 11.9 + - - +
27C ARG* 3.7 6.0 - - - +
29C LYS* 1.3 79.9 - - - +
31C VAL* 1.3 61.5 + - - +
33C GLN* 3.4 15.6 + - - +
34C ILE* 3.0 41.0 + - + +
62C LYS* 2.7 36.0 + - - -
119C PHE* 4.1 21.5 - - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ARG 3.1 17.8 + - - +
28C CYS 3.9 2.9 - - - +
30C GLU* 1.3 75.5 - - - +
32C GLN* 1.3 59.3 + - - +
34C ILE* 3.8 5.4 - - - +
35C ARG* 2.9 37.0 + - + +
43C PRO* 4.3 7.0 - - + -
110C TYR* 4.1 8.3 - - - +
117C ASP 3.5 13.0 - - - +
118C GLY* 3.8 23.8 - - - +
119C PHE* 3.4 44.0 - - + +
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C CYS 3.2 11.8 + - - +
29C LYS* 2.9 13.3 + - - +
31C VAL* 1.3 76.3 - - - +
33C GLN* 1.3 67.2 + - + +
35C ARG* 5.1 4.3 - - - +
36C ASP* 3.1 36.9 + - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.1 18.4 + - + +
30C GLU* 3.8 16.3 + - - +
32C GLN* 1.3 75.9 - - + +
34C ILE* 1.3 55.2 + - + +
36C ASP* 3.3 6.2 + - - +
37C GLN* 2.7 42.7 + - - +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU* 3.0 34.1 + - + +
31C VAL* 3.8 5.6 - - - +
33C GLN* 1.3 79.7 - - + +
35C ARG* 1.3 59.4 + - - +
37C GLN* 4.6 5.8 - - - +
38C HIS* 2.7 49.2 + - + +
41C LYS 5.4 0.4 - - - +
43C PRO* 4.2 17.9 - - + -
64C LEU* 3.5 36.6 - - + -
119C PHE* 6.2 1.6 - - + -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 2.9 29.2 + - + +
32C GLN* 4.4 6.3 - - - +
34C ILE* 1.3 73.3 - - + +
36C ASP* 1.3 66.0 + - - +
38C HIS 4.0 6.3 - - - -
39C PRO* 3.2 45.8 + - - +
41C LYS 4.4 8.8 + - - +
42C ILE* 4.2 15.5 - - - +
43C PRO* 4.4 12.7 - - + +
67C ASP* 4.7 2.0 + - - -
110C TYR* 3.4 41.2 - - - +
111C GLU* 3.8 12.3 + - - -
114C LYS* 5.0 1.6 - - - +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN* 3.1 29.5 + - + +
33C GLN* 3.4 7.5 - - - +
35C ARG* 1.3 81.0 - - - +
37C GLN* 1.3 64.5 + - - +
39C PRO* 3.6 11.7 - - - +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN* 2.7 24.0 + - - +
34C ILE* 4.8 6.6 - - - +
36C ASP* 1.3 78.3 + - - +
38C HIS* 1.3 91.7 + - + +
39C PRO* 3.5 6.5 - - - +
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 2.7 36.1 + - + +
35C ARG* 3.5 4.8 - - - +
37C GLN* 1.3 112.5 + - + +
39C PRO* 1.3 62.2 - - - +
40C SER* 3.0 13.2 + - - +
41C LYS* 3.2 40.0 + - + +
64C LEU* 3.8 25.9 - - + +
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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