Contacts of the helix formed by residues 44 - 57 (chain C) in PDB entry 5B6N
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 THR 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C PRO* 5.5 2.7 - - + -
41C ARG* 2.0 53.9 + - + +
42C ASP 4.2 1.3 - - - +
43C PHE* 1.3 78.5 - - - +
45C PRO* 1.3 69.0 - - + +
46C VAL 3.6 0.2 - - - -
47C CSD 3.1 24.4 - - - +
48C THR* 2.4 36.3 + - - -
82C TRP* 4.4 0.6 - - - +
191D PRO* 4.2 14.6 - - + -
217D TYR* 3.9 2.9 - - - -
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Residues in contact with PRO 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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44C THR* 1.3 90.1 - - + +
46C VAL* 1.3 64.8 + - + +
48C THR* 3.3 10.6 + - - +
49C THR* 3.4 18.0 + - - +
176D ALA* 6.1 0.9 - - + -
188D MET* 3.9 34.6 - - + +
189D VAL 3.9 17.5 - - - +
191D PRO* 3.6 27.4 - - + -
217D TYR* 3.4 28.0 - - + +
218D LEU* 5.0 4.4 - - + +
219D ARG 5.2 0.2 - - - +
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Residues in contact with VAL 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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45C PRO* 1.3 76.6 - - + +
47C CSD 1.3 58.1 + - - +
48C THR 3.0 4.9 - - - -
49C THR* 2.4 32.0 + - - +
50C GLU* 2.8 16.1 + - + +
132C ARG* 3.5 34.5 - - - +
152C THR 4.8 0.2 - - - +
154C GLY* 3.8 9.6 - - - -
176D ALA* 3.7 27.4 - - + -
177D THR 3.7 32.1 - - - +
178D PRO* 4.0 2.0 - - + -
188D MET* 3.9 11.7 - - + -
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Residues in contact with CSD 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 3.3 22.2 - - + +
40C PRO* 3.5 17.7 - - - +
41C ARG 3.6 12.6 - - - +
44C THR* 3.1 31.3 + - - +
45C PRO 3.3 0.6 - - - -
46C VAL* 1.3 75.4 + - - +
48C THR* 1.3 55.3 + - - +
50C GLU* 3.8 6.2 + - - -
51C LEU* 3.2 31.2 + - - +
82C TRP* 3.4 15.5 - - + -
132C ARG* 2.4 40.1 + - - -
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR 2.4 27.0 + - - -
45C PRO* 3.5 6.5 - - - -
46C VAL 3.0 0.8 - - - -
47C CSD 1.3 75.4 + - - -
49C THR* 1.3 65.8 + - - +
50C GLU 3.1 1.3 - - - -
52C GLY* 3.3 19.9 + - - -
82C TRP* 3.5 16.4 + - - +
85C ASP 4.4 8.1 - - - +
86C ILE* 3.9 18.1 - - + +
89C TYR* 4.1 23.9 - - + -
217D TYR* 3.5 18.1 - - - +
218D LEU* 4.4 13.0 - - + -
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Residues in contact with THR 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 PRO 3.4 14.8 - - - +
46C VAL* 2.4 24.6 + - - -
48C THR* 1.3 77.2 - - - +
50C GLU* 1.3 64.4 + - - +
52C GLY* 4.1 0.7 - - - -
53C ARG* 3.4 14.0 + - - +
89C TYR* 3.8 33.4 + - + +
178D PRO* 3.9 13.4 - - + +
179D VAL* 3.2 38.8 + - - +
188D MET* 4.7 7.9 - - + -
218D LEU* 5.3 2.0 - - + -
220D TYR* 4.2 12.8 - - - +
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Residues in contact with GLU 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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37C PHE* 5.3 0.3 - - - -
39C HIS* 5.1 0.5 - - - +
46C VAL* 2.8 18.9 + - + +
47C CSD 3.9 7.1 + - - +
48C THR 3.1 0.2 - - - -
49C THR* 1.3 77.6 + - - +
51C LEU* 1.3 63.4 + - + +
52C GLY 3.1 8.9 + - - -
53C ARG* 3.2 11.4 + - - +
54C ALA 3.3 7.8 + - - -
132C ARG* 3.4 14.7 + - - -
154C GLY* 3.3 8.5 - - - -
155C ARG* 2.6 70.9 + - - +
157C PHE* 3.6 19.9 - - + -
179D VAL* 3.8 24.0 - - + -
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Residues in contact with LEU 51 (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 PHE* 4.0 20.0 - - + -
39C HIS* 3.6 40.4 - - + +
47C CSD 3.2 25.1 + - - +
48C THR 3.6 0.2 + - - -
49C THR 3.6 0.2 - - - -
50C GLU* 1.3 82.4 - - + +
52C GLY* 1.3 57.6 + - - +
53C ARG 3.5 0.2 - - - -
54C ALA* 4.0 8.5 - - - -
55C ALA* 3.6 8.3 + - - +
70C ALA* 4.3 2.9 - - + -
82C TRP* 3.7 21.5 - - + -
86C ILE* 3.7 19.7 - - + +
98C LEU* 4.9 2.6 - - + +
100C PHE* 3.5 32.5 - - + -
102C ILE* 4.0 18.2 - - + -
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Residues in contact with GLY 52 (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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48C THR 3.3 12.9 + - - -
49C THR 4.1 1.3 - - - -
50C GLU 3.1 1.0 - - - -
51C LEU* 1.3 78.4 - - - +
53C ARG* 1.3 63.7 + - - +
54C ALA 3.3 0.2 - - - -
55C ALA* 3.7 1.3 - - - -
56C LYS* 3.3 12.5 + - - +
86C ILE* 3.7 11.4 - - - -
89C TYR* 4.5 4.5 - - - -
90C ASN* 2.7 41.3 + - - +
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Residues in contact with ARG 53 (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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49C THR 3.4 12.8 + - - +
50C GLU 3.2 9.3 + - - +
52C GLY* 1.3 76.2 - - - +
54C ALA* 1.3 59.4 + - - +
55C ALA 3.1 0.9 - - - -
56C LYS* 3.4 17.6 + - - +
57C LEU* 2.9 55.8 + - + +
89C TYR* 6.0 0.2 - - - -
90C ASN* 5.3 0.2 - - - -
157C PHE* 3.9 21.5 - - + -
158C ASP* 3.0 27.5 + - - -
179D VAL* 4.2 12.6 - - + -
180D ASP* 3.5 18.4 + - - +
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Residues in contact with ALA 54 (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 PHE* 4.6 4.5 - - + -
50C GLU 3.3 7.0 + - - +
51C LEU* 4.2 3.6 - - - +
53C ARG* 1.3 78.3 - - - +
55C ALA* 1.3 59.0 + - - +
57C LEU* 3.8 7.4 - - - +
58C ALA* 3.1 25.3 + - - +
61C PHE* 5.7 0.2 - - - -
68C LEU* 3.7 12.5 - - + +
100C PHE* 3.5 21.7 - - + -
157C PHE* 3.6 34.7 - - + -
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Residues in contact with ALA 55 (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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51C LEU 3.6 17.3 + - - +
52C GLY* 3.7 7.9 - - - +
54C ALA* 1.3 81.1 - - - +
56C LYS* 1.3 61.8 + - - +
58C ALA* 3.5 14.4 - - - +
59C PRO* 4.1 3.3 - - - +
86C ILE* 5.0 0.7 - - + -
87C ASN* 5.1 3.4 - - - +
90C ASN* 4.1 9.2 - - - +
98C LEU* 4.6 9.2 - - + -
99C PRO* 3.8 20.8 - - + +
100C PHE* 3.6 14.6 - - + -
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Residues in contact with LYS 56 (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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52C GLY 3.3 15.5 - - - +
53C ARG* 3.4 22.6 + - - +
55C ALA* 1.3 78.0 - - - +
57C LEU* 1.3 57.3 + - - +
58C ALA 3.1 4.5 - - - -
59C PRO* 3.3 16.5 - - - +
60C GLU* 5.2 3.1 - - - +
90C ASN* 3.5 33.9 + - - +
92C GLU* 2.3 39.3 + - - +
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Residues in contact with LEU 57 (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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53C ARG* 2.9 55.9 + - - +
54C ALA* 4.3 2.9 - - - -
55C ALA 3.4 0.2 - - - -
56C LYS* 1.3 75.2 - - - +
58C ALA* 1.3 63.5 + - - +
59C PRO* 3.4 1.1 - - - -
60C GLU* 3.1 24.8 + - + +
61C PHE* 3.0 27.7 - - + -
157C PHE* 3.2 33.4 - - + +
158C ASP* 3.9 7.0 - - - +
161C LEU* 3.8 25.6 - - + -
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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