Contacts of the helix formed by residues 30 - 43 (chain C) in PDB entry 5D0A
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 PHE 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C THR* 5.0 1.1 - - + -
28C ASP 3.8 3.1 - - - -
29C THR* 1.3 71.5 - - - +
31C ASP* 1.3 59.4 + - - +
32C SER 3.6 1.8 - - - -
33C LEU* 3.8 20.4 - - + -
34C LYS* 3.1 20.6 + - - +
57C ARG 4.6 3.8 - - - -
58C VAL* 2.8 39.3 + - + +
60C PRO* 3.6 20.9 - - + -
70C ILE* 4.1 7.0 - - + -
138C LEU* 4.6 4.5 - - + -
142C ALA* 3.8 36.3 - - + -
143C VAL* 3.8 24.9 - - + -
146C ARG* 3.3 48.5 - - + +
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Residues in contact with ASP 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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29C THR* 2.8 32.1 + - - +
30C PHE* 1.3 68.9 - - - +
32C SER* 1.3 65.9 + - - +
33C LEU 3.2 1.1 - - - -
34C LYS* 3.2 20.4 + - + +
35C ASP* 3.2 20.5 + - - +
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASP* 1.3 78.6 - - - +
33C LEU* 1.3 63.5 + - - +
35C ASP* 3.4 11.2 + - - +
36C ARG* 3.0 22.3 + - - +
503C B12 3.1 23.4 + - - -
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Residues in contact with LEU 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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30C PHE* 3.7 22.1 - - + +
31C ASP 3.2 0.2 - - - -
32C SER* 1.3 80.4 - - - +
34C LYS* 1.3 56.0 + - - +
36C ARG* 3.2 3.5 + - + +
37C LEU* 2.8 50.9 + - + +
57C ARG* 4.2 9.9 - - + +
58C VAL* 4.0 15.0 - - + -
139C SER* 3.6 25.8 - - - +
142C ALA* 3.8 18.4 - - + -
503C B12 3.2 41.9 - - + +
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Residues in contact with LYS 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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353A GLU* 5.9 0.6 + - - -
356A LEU* 5.5 2.8 - - - +
369A GLU* 4.6 8.7 - - - -
372A ILE* 6.0 6.2 - - - +
373A GLU* 5.6 2.2 - - - +
376A LYS* 5.7 5.1 - - - +
30C PHE 3.1 14.8 + - - +
31C ASP* 3.2 16.8 + - + +
33C LEU* 1.3 76.1 - - - +
35C ASP* 1.3 67.8 + - - +
37C LEU* 3.8 1.4 - - - +
38C ILE* 3.2 42.3 + - + +
54C ILE* 4.1 15.9 - - + +
55C GLU* 3.6 28.0 + - - -
58C VAL* 3.8 20.5 - - + +
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Residues in contact with ASP 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 2.7 39.7 - - - +
376A LYS* 5.9 1.6 - - - -
31C ASP* 3.2 17.5 + - - +
32C SER* 3.7 8.5 - - - +
34C LYS* 1.3 80.7 - - - +
36C ARG* 1.3 58.1 + - - +
38C ILE* 3.4 2.3 + - - +
39C LEU* 2.9 30.0 + - - +
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Residues in contact with ARG 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 SER 3.0 17.6 + - - +
33C LEU* 3.6 5.2 - - + +
35C ASP* 1.3 75.8 - - - +
37C LEU* 1.3 54.0 + - - +
39C LEU* 3.2 24.6 + - - +
40C GLN* 2.8 58.6 + - + +
207C GLY 3.8 3.2 + - - -
208C GLN* 3.2 41.0 - - - +
503C B12 3.4 89.5 - - + +
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Residues in contact with LEU 37 (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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33C LEU* 2.8 38.9 + - + +
34C LYS 3.8 3.8 - - - +
36C ARG* 1.3 76.3 - - - +
38C ILE* 1.3 57.2 + - - +
40C GLN* 3.2 4.8 + - - +
41C GLU* 2.9 29.8 + - - +
46C LEU* 4.2 18.1 - - + +
50C GLU* 5.8 0.2 - - + -
54C ILE* 4.0 28.2 - - + +
57C ARG* 3.5 52.9 - - + +
58C VAL* 4.3 2.7 - - + -
503C B12 4.1 24.5 - - + -
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Residues in contact with ILE 38 (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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366A LEU 5.8 0.2 - - - +
369A GLU* 4.0 25.1 - - + +
370A LYS* 3.8 33.0 - - + +
373A GLU* 3.7 33.0 - - + +
34C LYS* 3.2 35.6 + - + +
35C ASP* 3.7 3.8 - - - +
37C LEU* 1.3 74.9 - - - +
39C LEU* 1.3 65.2 + - - +
41C GLU* 3.2 6.1 + - - +
42C SER* 2.9 23.4 + - - -
54C ILE* 3.8 20.6 - - + -
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Residues in contact with LEU 39 (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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35C ASP 2.9 18.2 + - - +
36C ARG* 3.5 36.6 - - - +
38C ILE* 1.3 77.1 - - - +
40C GLN* 1.3 66.7 + - - +
42C SER* 3.3 11.6 + - - +
43C LEU* 3.0 39.7 + - + +
208C GLN* 4.4 7.0 - - - +
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Residues in contact with GLN 40 (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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36C ARG* 2.8 37.9 + - + +
37C LEU 3.8 4.3 - - - +
39C LEU* 1.3 72.5 - - - +
41C GLU* 1.3 64.9 + - - +
43C LEU* 3.4 4.1 + - - +
44C GLY 3.2 3.3 + - - -
45C TYR* 2.9 41.2 + - + +
46C LEU* 3.8 19.4 - - + +
208C GLN* 2.9 39.2 + - - +
209C LEU* 3.1 30.3 + - - +
503C B12 4.0 22.9 - - + +
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Residues in contact with GLU 41 (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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366A LEU* 3.8 39.9 - - + +
370A LYS* 4.7 17.1 + - - +
37C LEU 2.9 15.9 + - - +
38C ILE* 3.6 7.2 - - - +
40C GLN* 1.3 72.9 - - - +
42C SER* 1.3 69.0 + - - +
44C GLY* 2.8 15.5 + - - -
45C TYR 5.0 0.2 - - - +
46C LEU* 3.1 31.0 - - + +
54C ILE* 5.3 2.1 - - + +
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Residues in contact with SER 42 (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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226A PRO* 5.8 0.7 - - - +
227A ASP* 2.7 52.1 + - - +
228A GLU 4.9 1.7 + - - -
370A LYS* 4.3 10.9 - - - +
38C ILE* 2.9 14.8 + - - -
39C LEU* 3.3 17.4 - - - +
41C GLU* 1.3 78.7 - - - +
43C LEU* 1.3 62.6 + - - +
44C GLY 3.3 0.3 + - - -
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Residues in contact with LEU 43 (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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228A GLU* 6.4 1.8 - - + -
39C LEU* 3.0 36.3 + - + +
40C GLN* 3.8 8.3 - - - +
41C GLU 3.1 0.4 - - - -
42C SER* 1.3 78.1 - - - +
44C GLY* 1.3 59.6 + - - +
45C TYR* 3.4 39.5 - - + +
208C GLN* 3.5 28.0 - - - +
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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