Contacts of the helix formed by residues 36 - 50 (chain C) in PDB entry 6P59
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 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C ASP 4.6 0.9 - - - +
35C ARG* 1.3 93.1 - - + +
37C HIS* 1.3 66.1 + - - +
38C GLU* 4.5 6.5 - - + +
39C GLU* 3.1 25.5 + - + +
40C ARG* 3.1 18.7 + - - +
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Residues in contact with HIS 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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35C ARG 3.7 0.6 + - - -
36C PRO* 1.3 71.1 - - - +
38C GLU* 1.3 67.2 + - - +
40C ARG* 3.0 19.0 + - - +
41C GLN* 2.9 59.3 + - + +
117C GLN* 2.5 32.2 + - + +
118C ARG* 3.9 18.6 - - - -
119C LEU* 4.3 8.5 - - + -
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Residues in contact with GLU 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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36C PRO* 3.3 5.0 - - + +
37C HIS* 1.3 79.5 - - - +
39C GLU* 1.3 61.1 + - - +
41C GLN* 3.6 17.8 + - - +
42C ALA* 3.5 18.4 + - - +
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Residues in contact with GLU 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 ARG* 2.9 55.5 + - + +
36C PRO* 3.1 26.9 + - + +
38C GLU* 1.3 76.5 - - - +
40C ARG* 1.3 61.8 + - - +
42C ALA* 3.3 7.0 + - + +
43C ARG* 2.9 52.7 + - + +
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Residues in contact with ARG 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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29C TYR* 2.7 30.3 + - + -
30C THR* 4.7 0.4 - - - +
31C GLY 2.3 34.6 + - - +
32C PHE* 3.0 38.5 + - + +
33C ARG* 3.3 14.7 - - - +
35C ARG* 3.8 13.5 - - + +
36C PRO 3.1 9.1 + - - +
37C HIS* 3.0 19.0 + - - +
39C GLU* 1.3 77.4 - - - +
41C GLN* 1.3 57.1 + - - +
43C ARG* 3.0 8.3 + - - +
44C PHE* 2.9 33.4 + - - +
119C LEU* 3.8 30.1 - - + +
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Residues in contact with GLN 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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37C HIS* 2.9 53.4 + - + +
38C GLU* 3.6 19.7 - - - +
39C GLU 3.3 0.2 - - - -
40C ARG* 1.3 75.8 - - - +
42C ALA* 1.3 57.0 + - - +
44C PHE* 4.2 2.3 - - - +
45C GLN* 3.2 27.9 + - - +
116C LEU 4.1 13.8 - - - +
117C GLN* 3.1 34.5 + - - +
119C LEU* 4.7 8.7 - - + -
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Residues in contact with ALA 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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38C GLU 3.5 9.6 + - - +
39C GLU* 3.3 9.6 + - + +
40C ARG 3.2 0.4 - - - -
41C GLN* 1.3 78.6 - - - +
43C ARG* 1.3 59.5 + - + +
45C GLN* 4.5 4.7 - - - -
46C ASN* 2.9 45.5 + - - +
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Residues in contact with ARG 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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29C TYR* 4.3 3.3 + - - +
32C PHE* 4.0 37.0 - - + -
35C ARG* 2.9 32.3 - - - +
39C GLU* 2.9 40.4 + - + +
40C ARG* 3.0 6.7 + - - +
42C ALA* 1.3 78.3 - - + +
44C PHE* 1.3 57.8 + - - +
46C ASN* 4.0 3.1 - - - +
47C ALA* 3.0 29.5 + - - +
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Residues in contact with PHE 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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29C TYR* 3.3 44.8 + + + -
40C ARG 2.9 15.4 + - - +
41C GLN 4.4 1.8 - - - +
43C ARG* 1.3 74.7 - - - +
45C GLN* 1.3 70.5 + - + +
47C ALA* 3.4 3.2 + - - +
48C CYS* 3.2 45.7 + - - -
55C ILE* 4.8 4.3 - - + -
57C PHE* 3.4 37.0 - + - -
88C LEU* 5.2 2.0 - - + -
95C VAL* 3.9 30.5 - - + -
114C ILE* 4.4 7.0 - - + -
116C LEU* 4.7 13.9 - - + -
119C LEU* 3.9 23.1 - - + -
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Residues in contact with GLN 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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41C GLN 3.2 19.0 + - - +
42C ALA* 4.0 5.9 - - - +
44C PHE* 1.3 86.8 - - + +
46C ASN* 1.3 68.5 + - - +
47C ALA 3.4 0.2 + - - -
48C CYS* 3.5 11.0 + - - +
49C ARG* 3.5 19.4 + - + +
88C LEU* 5.1 9.3 - - + +
116C LEU* 4.2 26.0 - - + +
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Residues in contact with ASN 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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42C ALA* 2.9 27.7 + - - +
43C ARG* 4.2 3.1 - - - +
45C GLN* 1.3 86.3 - - - +
47C ALA* 1.3 53.3 + - - +
49C ARG* 3.1 6.0 + - - +
50C ASP* 2.6 39.7 + - + +
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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
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29C TYR* 5.0 5.4 - - - +
43C ARG 3.0 20.6 + - - +
44C PHE* 3.7 5.6 - - - +
45C GLN 3.2 0.6 - - - -
46C ASN* 1.3 77.3 - - - +
48C CYS* 1.3 59.8 + - - +
49C ARG 3.4 0.5 + - - -
50C ASP 3.7 0.9 + - - -
53C SER* 3.2 34.2 - - - +
54C GLU 4.1 9.0 - - - +
55C ILE* 3.5 23.0 - - + +
4F LYS* 3.6 9.0 + - - -
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Residues in contact with CYS 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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44C PHE* 3.2 44.6 + - - -
45C GLN* 4.0 3.6 - - - +
46C ASN 3.3 0.8 - - - -
47C ALA* 1.3 76.4 - - - +
49C ARG* 1.3 59.2 + - - +
55C ILE* 3.9 24.5 - - + -
86C VAL* 4.7 9.9 - - + -
88C LEU* 3.5 29.5 - - + +
95C VAL* 5.3 0.9 - - - -
4F LYS* 3.3 5.9 + - - +
6F TRP* 3.2 31.2 - - - -
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Residues in contact with ARG 49 (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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45C GLN* 3.5 18.5 + - + +
46C ASN* 3.1 8.8 + - - +
48C CYS* 1.3 78.6 - - - +
50C ASP* 1.3 67.6 + - - +
51C GLY* 3.5 2.1 + - - -
88C LEU* 4.4 23.6 - - + +
89C GLU* 3.1 46.6 + - - +
4F LYS* 4.5 5.2 - - - +
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Residues in contact with ASP 50 (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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46C ASN* 2.6 23.5 + - + +
47C ALA 3.7 1.8 + - - +
48C CYS 3.7 0.4 - - - -
49C ARG* 1.3 73.2 - - - +
51C GLY* 1.3 71.6 + - - +
52C ARG* 3.1 21.0 + - - +
53C SER* 3.0 29.1 + - - +
4F LYS* 2.9 25.5 + - - -
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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