Contacts of the helix formed by residues 30 - 48 (chain C) in PDB entry 1F15
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 ALA 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 2.9 20.9 - - + +
29C ASP* 1.3 68.3 - - - +
31C ASN* 1.3 67.3 + - - +
32C PHE 3.1 1.1 - - - -
33C ARG* 3.0 20.9 - - - +
34C VAL* 2.9 23.1 + - + +
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Residues in contact with ASN 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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29B ASP* 3.0 35.4 + - - +
30B ALA 3.4 10.7 + - - +
32B PHE* 2.8 65.8 - - + +
29C ASP 2.7 10.9 + - - +
30C ALA* 1.3 75.3 - - - +
32C PHE* 1.3 59.9 + - + +
34C VAL* 3.2 15.8 - - - +
35C LEU* 3.6 1.6 - - - +
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Residues in contact with PHE 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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32B PHE* 4.2 26.5 - + - -
29C ASP* 2.9 37.2 + - + +
31C ASN* 1.3 77.0 - - + +
33C ARG* 1.3 57.5 + - - +
34C VAL 2.7 17.1 + - - -
35C LEU* 2.8 24.0 + - + +
36C SER* 3.0 11.4 + - - -
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Residues in contact with ARG 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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28C ALA* 3.6 30.3 - - - +
29C ASP 3.7 11.8 - - - +
30C ALA* 3.0 34.2 - - - +
32C PHE* 1.3 79.3 - - - +
34C VAL* 1.3 56.0 + - + +
36C SER* 2.7 16.2 + - - +
37C GLN* 3.0 22.1 + - - +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 3.7 20.2 - - - +
32B PHE* 4.9 2.5 - - + +
33B ARG* 5.7 0.4 - - - +
36B SER* 4.4 15.3 - - - +
30C ALA* 2.9 17.8 + - + +
31C ASN 3.2 18.4 - - - +
32C PHE 2.7 6.3 + - - -
33C ARG* 1.3 77.0 - - + +
35C LEU* 1.3 71.7 + - + +
36C SER 3.2 1.8 - - - -
37C GLN* 3.1 12.7 + - + +
38C GLN* 3.1 27.4 + - - +
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Residues in contact with LEU 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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32B PHE* 3.4 33.9 - - + +
35B LEU* 4.3 24.0 - - + -
36B SER* 4.3 22.2 - - - +
39B LEU* 4.7 9.9 - - + -
31C ASN 3.6 11.7 - - - +
32C PHE* 2.8 16.9 + - + +
34C VAL* 1.3 74.3 - - + +
36C SER* 1.3 68.3 + - - +
38C GLN* 3.0 9.4 + - - +
39C LEU* 2.8 33.1 + - + +
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Residues in contact with SER 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 PHE 3.0 9.4 + - - -
33C ARG* 2.7 29.6 + - - +
35C LEU* 1.3 74.5 - - - +
37C GLN* 1.3 65.8 + - - +
39C LEU* 2.8 24.2 + - - +
40C SER* 2.9 17.7 + - - -
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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
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33C ARG* 3.0 27.0 + - - +
34C VAL* 3.1 14.1 + - + +
36C SER* 1.3 84.1 + - - +
38C GLN* 1.3 71.6 + - - +
40C SER* 3.5 8.3 + - - -
41C ARG* 3.4 21.7 + - - +
44C LYS* 5.4 1.2 + - - -
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Residues in contact with GLN 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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36B SER* 3.4 38.1 - - - +
39B LEU* 3.9 23.3 - - + -
40B SER* 3.9 6.9 + - - -
34C VAL* 3.1 18.0 + - - +
35C LEU* 3.0 7.3 + - - +
37C GLN* 1.3 78.6 - - - +
39C LEU* 1.3 67.7 + - - +
41C ARG* 2.7 57.6 + - - +
42C LEU* 3.0 16.5 + - + +
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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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39B LEU* 3.5 33.2 - - + -
35C LEU* 2.8 23.9 + - + +
36C SER* 2.8 18.3 + - - +
38C GLN* 1.3 73.3 - - - +
40C SER* 1.3 61.9 + - - +
42C LEU* 3.1 12.6 + - + +
43C ASN* 2.9 21.3 + - - +
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER 2.9 15.1 + - - -
37C GLN* 3.6 11.2 - - - -
39C LEU* 1.3 73.2 - - - +
41C ARG* 1.3 53.2 + - - +
43C ASN* 2.7 29.6 + - - +
44C LYS* 2.8 38.0 + - - +
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Residues in contact with ARG 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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40B SER* 3.1 25.5 + - - +
43B ASN* 3.0 21.0 - - - +
37C GLN 3.4 9.8 + - - -
38C GLN* 2.7 69.1 + - - +
40C SER* 1.3 77.9 - - - +
42C LEU* 1.3 66.1 + - - +
44C LYS* 3.2 24.8 + - + +
45C THR* 3.0 27.6 + - + +
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Residues in contact with LEU 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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39B LEU* 3.8 23.8 - - + +
42B LEU* 4.4 11.2 - - + -
43B ASN* 3.1 38.8 + - + +
46B LEU* 3.4 31.4 - - + -
38C GLN* 3.0 24.8 + - - +
39C LEU* 3.1 14.3 + - + +
41C ARG* 1.3 74.0 - - + +
43C ASN* 1.3 68.3 + - - +
45C THR* 2.8 13.8 + - - -
46C LEU* 2.9 22.4 + - + +
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Residues in contact with ASN 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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39C LEU 2.9 11.3 + - - +
40C SER* 2.7 13.9 + - - +
42C LEU* 1.3 78.8 - - - +
44C LYS* 1.3 66.4 + - + +
46C LEU* 2.9 10.0 + - - +
47C ALA* 2.7 29.8 + - - +
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Residues in contact with LYS 44 (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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37C GLN 5.4 1.0 + - - -
40C SER* 2.8 42.5 + - - +
41C ARG* 3.4 26.6 - - + +
43C ASN* 1.3 76.6 - - + +
45C THR* 1.3 66.9 + - + +
47C ALA* 2.9 18.4 + - - +
48C ALA* 2.9 10.9 + - - +
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Residues in contact with THR 45 (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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43B ASN* 3.2 33.5 + - - +
46B LEU* 4.7 6.2 - - - +
47B ALA* 4.3 21.8 - - + -
50B ARG* 2.8 29.4 + - - +
41C ARG* 3.0 18.6 + - + +
42C LEU* 2.8 17.2 + - - -
44C LYS* 1.3 71.2 - - + +
46C LEU* 1.3 53.4 + - - +
48C ALA* 3.0 15.5 + - - +
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Residues in contact with LEU 46 (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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46B LEU* 4.2 28.7 - - + -
50B ARG* 4.6 4.0 + - - +
42C LEU* 2.9 30.7 + - + +
43C ASN* 2.9 11.3 + - - +
45C THR* 1.3 70.5 - - - +
47C ALA* 1.3 64.6 + - - +
48C ALA* 2.7 15.5 + - - +
50C ARG* 3.6 18.1 + - - +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASN* 2.7 22.8 + - - +
44C LYS* 3.0 17.5 - - - +
46C LEU* 1.3 71.9 - - - +
48C ALA* 1.3 60.1 - - - +
50C ARG* 2.9 43.1 + - - +
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Residues in contact with ALA 48 (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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50B ARG* 3.9 21.1 - - - +
44C LYS 2.9 10.5 + - - +
45C THR* 3.1 15.9 - - - +
46C LEU 2.7 11.5 - - - +
47C ALA* 1.3 84.0 - - - +
49C GLY* 1.3 60.8 + - - +
50C ARG* 3.8 10.3 + - + -
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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