Contacts of the helix formed by residues 50 - 70 (chain C) in PDB entry 2PI8
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 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 2.8 21.3 + - - +
49C SER* 1.3 80.8 - - - +
51C PRO* 1.3 59.0 - - - +
52C ARG* 3.0 35.2 + - - +
53C LEU* 3.5 16.0 - - - +
54C TYR 3.1 13.5 + - - -
248C SER 4.8 3.8 + - - -
250C VAL* 3.9 23.8 - - - -
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Residues in contact with PRO 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 5.3 2.5 - - - +
143B ASP 5.5 0.7 - - - +
144B LYS* 3.5 40.3 - - + +
146B ILE 5.2 5.4 - - - +
46C ILE 3.6 1.9 - - - +
47C ARG 4.0 12.1 - - - +
48C ASN 3.8 11.9 - - - +
49C SER 3.7 4.7 - - - +
50C SER* 1.3 87.0 - - - +
52C ARG* 1.3 64.4 + - - +
54C TYR* 4.1 11.0 - - + +
55C GLY* 3.0 24.8 + - - -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.7 36.8 - - - +
144B LYS* 4.5 23.1 - - + +
49C SER 3.6 15.8 + - - -
50C SER* 3.3 25.2 + - - +
51C PRO* 1.3 83.5 - - - +
53C LEU* 1.3 69.7 - - + +
55C GLY* 3.5 6.4 + - - -
56C ASN* 3.5 20.6 - - - +
248C SER 5.3 1.6 + - - -
249C ALA* 5.2 11.9 - - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.9 7.6 - - + -
50C SER* 3.3 20.2 + - - +
52C ARG* 1.3 78.2 - - + +
54C TYR* 1.3 66.6 + - - +
56C ASN* 3.2 5.9 + - + +
57C GLN* 3.1 43.7 + - + +
248C SER* 5.0 6.1 - - - +
250C VAL* 5.7 0.9 - - + -
267C PRO* 3.6 47.6 - - + +
268C GLY* 4.0 7.2 - - - +
296C LEU* 4.7 11.2 - - + -
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Residues in contact with TYR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.5 32.7 - - + +
46C ILE* 3.4 31.8 - - + +
47C ARG* 3.2 50.1 + - + -
50C SER 3.1 6.7 + - - +
51C PRO* 4.1 7.0 - - + -
53C LEU* 1.3 78.8 - - - +
55C GLY* 1.3 56.5 + - - +
57C GLN* 4.3 3.6 - - - +
58C SER* 2.7 58.3 + - - -
61C TYR* 3.5 26.8 - + + +
62C ASN* 4.4 11.4 + - - -
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Residues in contact with GLY 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PRO 3.0 21.0 + - - -
52C ARG 3.5 3.3 + - - -
53C LEU 3.2 0.6 - - - -
54C TYR* 1.3 79.8 - - - +
56C ASN* 1.3 64.9 + - - +
57C GLN 3.6 0.2 - - - -
58C SER* 4.4 7.7 + - - -
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Residues in contact with ASN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ARG 3.5 15.1 + - - +
53C LEU* 3.2 8.0 + - + +
54C TYR 3.0 0.4 - - - -
55C GLY* 1.3 81.9 + - - +
57C GLN* 1.3 73.7 + - - +
58C SER 3.6 0.9 - - - -
59C ASN* 3.2 13.2 - - - +
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Residues in contact with GLN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.1 39.6 + - + +
54C TYR 3.0 1.6 + - - -
56C ASN* 1.3 90.7 + - - +
58C SER* 1.3 65.8 + - - +
59C ASN* 3.2 6.3 - - - -
60C VAL* 3.1 27.5 + - - +
61C TYR* 3.3 34.7 + - + +
266C PRO* 6.4 0.2 - - - +
267C PRO 4.7 3.7 + - - -
268C GLY* 3.4 23.7 - - - +
269C THR* 4.6 3.9 + - - -
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Residues in contact with SER 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 2.7 48.2 + - - -
55C GLY* 4.4 7.9 + - - -
56C ASN 3.6 0.8 - - - -
57C GLN* 1.3 78.4 - - - +
59C ASN* 1.3 56.3 + - - +
61C TYR* 3.0 11.4 + - - -
62C ASN* 2.7 51.9 + - - -
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Residues in contact with ASN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASN 3.2 24.3 + - - +
57C GLN* 3.3 7.4 - - - -
58C SER* 1.3 74.7 + - - +
60C VAL* 1.3 67.1 + - - +
62C ASN* 4.1 8.4 - - - +
63C ALA* 3.5 16.1 + - - +
335C THR* 3.3 43.0 + - + +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN* 3.1 20.1 + - - +
59C ASN* 1.3 93.4 - - - +
61C TYR* 1.3 61.1 + - + +
63C ALA* 3.3 3.9 + - - +
64C VAL* 3.0 33.3 + - + +
268C GLY 5.9 0.4 - - - +
270C THR* 3.4 24.0 - - - +
333C LEU 3.3 27.4 - - - +
334C LYS* 4.2 15.9 - - + +
335C THR* 3.9 11.9 - - + +
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Residues in contact with TYR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 4.5 2.9 - + - -
43C ILE* 3.9 32.3 - - + -
46C ILE* 3.4 29.1 - - + +
54C TYR* 3.5 37.2 - + + +
57C GLN* 3.3 33.1 - - + +
58C SER* 3.0 6.1 + - - +
60C VAL* 1.3 74.8 - - + +
62C ASN* 1.3 57.5 + - - +
64C VAL* 3.1 5.8 - - - +
65C GLN* 2.7 42.4 + - + +
268C GLY* 2.8 31.5 + - - -
270C THR* 3.3 25.4 - - - -
294C VAL* 3.9 13.1 - - + +
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Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TYR* 4.4 12.5 + - - -
58C SER* 2.7 38.7 + - - +
59C ASN* 4.1 7.7 - - - +
61C TYR* 1.3 74.3 - - - +
63C ALA* 1.3 56.7 + - - +
65C GLN* 4.0 6.0 - - - +
66C GLU* 3.1 30.7 + - - +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN 3.5 13.0 + - - +
60C VAL* 3.3 10.5 + - - +
61C TYR 3.1 0.4 - - - -
62C ASN* 1.3 79.0 - - - +
64C VAL* 1.3 59.1 + - + +
65C GLN 3.2 0.2 - - - -
66C GLU* 3.6 3.0 + - - +
67C TRP* 3.2 26.5 + - - +
80C PHE* 3.6 26.5 - - - +
81C GLY 3.9 14.6 - - - +
82C ILE* 3.5 11.4 - - + +
334C LYS 5.6 0.7 - - - +
335C THR* 4.7 2.2 - - + -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 3.5 34.2 - - + -
60C VAL* 3.0 23.0 + - + +
61C TYR* 3.1 20.4 - - - +
63C ALA* 1.3 74.8 - - - +
65C GLN* 1.3 60.2 + - + +
67C TRP* 3.8 10.9 - - + -
68C LEU* 3.3 25.3 + - - +
77C MSE 5.3 0.4 - - + -
82C ILE* 3.9 20.0 - - + -
270C THR* 4.2 8.7 - - + -
292C LEU* 5.2 3.4 - - + +
333C LEU* 4.0 28.5 - - + -
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Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 4.3 4.5 - - - -
40C ALA* 4.0 14.2 + - - +
43C ILE* 3.8 31.9 - - + +
47C ARG* 6.0 1.4 - - - +
61C TYR* 2.7 24.8 + - + +
62C ASN* 4.0 6.3 - - - +
64C VAL* 1.3 76.8 - - - +
66C GLU* 1.3 59.4 + - - +
67C TRP 3.1 1.6 - - - -
68C LEU* 3.2 11.6 + - - +
69C ARG* 2.8 79.9 + - - +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLN* 5.3 6.6 + - - +
62C ASN 3.1 21.5 + - - +
63C ALA* 3.6 5.8 + - - +
65C GLN* 1.3 76.7 - - - +
67C TRP* 1.3 57.0 + - - +
69C ARG* 4.0 7.7 - - - +
70C ALA* 3.1 30.5 + - - +
80C PHE* 3.5 20.9 - - + -
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Residues in contact with TRP 67 (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 PRO* 3.6 35.0 - - + -
63C ALA 3.2 18.1 + - - +
64C VAL* 3.8 17.5 - - + +
65C GLN 3.1 0.2 - - - -
66C GLU* 1.3 76.2 - - - +
68C LEU* 1.3 70.3 + - + +
70C ALA 3.2 21.2 - - - +
72C GLY* 3.3 28.8 + - - -
73C ASP 2.7 24.8 + - - +
74C THR* 3.6 20.2 - - + -
76C ASN* 4.1 1.1 - - + -
77C MSE 3.5 47.1 - - + +
80C PHE* 3.5 33.8 - + + -
82C ILE* 3.7 12.6 - - + -
272C ILE* 4.3 2.0 - - + -
292C LEU* 4.2 15.9 - - + -
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Residues in contact with LEU 68 (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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34A ILE* 4.4 14.1 - - + -
289A GLU* 6.0 1.6 - - - +
33C PRO* 6.2 0.7 - - + -
36C ALA* 3.6 45.1 - - + +
39C PHE* 4.4 11.2 - - + -
64C VAL 3.3 16.5 + - - +
65C GLN* 3.2 15.4 + - - +
67C TRP* 1.3 82.0 - - + +
69C ARG* 1.3 93.2 + - - +
70C ALA 3.3 0.2 + - - -
71C GLY 3.2 21.8 + - - +
72C GLY* 4.2 9.0 - - - -
292C LEU* 4.7 7.4 - - + -
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 4.1 15.4 - - + +
287A GLN* 2.9 34.7 - - - +
288A TYR 4.0 10.0 - - - +
289A GLU* 5.5 7.2 + - - -
36C ALA 5.0 0.4 + - - -
40C ALA* 4.0 15.8 - - - +
65C GLN* 2.8 73.4 + - - +
66C GLU* 4.0 9.9 - - - +
68C LEU* 1.3 101.6 - - - +
70C ALA* 1.3 56.8 + - - +
71C GLY 3.0 6.4 + - - -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLN* 4.2 17.0 - - - +
66C GLU* 3.1 20.9 + - + +
67C TRP* 3.2 4.8 - - - +
68C LEU 3.2 0.4 - - - -
69C ARG* 1.3 72.9 - - - +
71C GLY* 1.3 57.1 + - - +
72C GLY 3.1 7.6 + - - -
73C ASP 4.8 1.4 + - - -
76C ASN* 6.1 0.2 - - - +
80C PHE* 3.6 27.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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