Contacts of the helix formed by residues 50 - 66 (chain C) in PDB entry 2W93
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 ASN 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.4 12.5 - - - +
48C ASN* 3.5 1.6 - - - +
49C ALA* 1.3 80.5 - - - +
51C GLU* 1.3 60.0 + - - +
52C LEU* 3.4 9.1 + - - +
53C ASN* 2.8 54.4 + - - +
54C ALA* 2.9 26.9 + - - +
449C LEU 5.2 1.2 + - - -
452C GLN* 3.6 10.3 + - - +
453C GLU* 3.7 2.4 + - - -
50D ASN* 5.1 7.5 - - - +
52D LEU* 5.9 7.7 - - + +
449D LEU* 2.9 40.2 + - + +
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.6 25.2 - - + +
50C ASN* 1.3 71.9 - - - +
52C LEU* 1.3 65.8 + - - +
54C ALA* 3.3 7.7 + - - +
55C ALA* 3.0 23.2 + - - +
70C ILE* 3.9 0.3 - - - +
72C THR* 3.9 17.5 - - + -
73C THR* 5.0 0.7 - - - +
77C GLY* 3.6 34.7 - - - +
80C SER* 3.7 10.8 + - - -
81C ALA* 3.9 7.2 - - - +
449D LEU* 3.8 9.2 - - - +
600D TPP 2.5 50.2 + - - +
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Residues in contact with LEU 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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50C ASN* 3.4 9.4 + - - +
51C GLU* 1.3 76.6 - - - +
53C ASN* 1.3 65.6 + - - +
55C ALA* 3.1 3.3 + - - +
56C TYR* 3.0 57.1 + - + +
80C SER* 3.5 23.1 + - - +
81C ALA* 4.3 2.0 - - - +
83C ASN* 3.9 9.6 - - + -
84C GLY 3.6 27.1 - - - +
449C LEU* 5.5 3.6 - - + +
450C THR* 5.0 7.0 - - + -
50D ASN* 5.9 7.2 - - + +
52D LEU* 5.9 11.0 - - + -
80D SER* 4.1 21.3 - - - +
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Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASN* 2.8 29.7 + - - +
52C LEU* 1.3 76.2 - - - +
54C ALA* 1.3 52.5 + - - +
56C TYR* 3.3 9.9 + - - +
57C ALA* 2.8 34.9 + - - +
420C GLY* 3.9 3.9 - - - -
449C LEU 4.6 0.3 - - - +
450C THR* 3.2 40.1 + - - +
452C GLN* 3.2 31.1 + - - +
453C GLU* 3.0 37.6 + - + +
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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
----------------------------------------------------------
23C PHE* 3.7 4.3 - - - +
24C GLY* 3.6 21.3 - - - +
48C ASN* 3.3 34.2 - - + +
50C ASN 2.9 14.9 + - - +
51C GLU* 3.5 10.5 - - - +
52C LEU 3.2 0.2 - - - -
53C ASN* 1.3 77.0 - - - +
55C ALA* 1.3 56.8 + - - +
57C ALA* 3.2 2.5 + - - +
58C ALA* 2.8 28.6 + - - +
70C ILE* 3.7 6.5 - - + -
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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
----------------------------------------------------------
51C GLU 3.0 12.5 + - - +
52C LEU 3.1 7.2 + - - +
54C ALA* 1.3 71.9 - - - +
56C TYR* 1.3 67.8 + - - +
58C ALA* 3.3 6.1 + - - +
59C ASP* 2.9 23.0 + - - +
70C ILE* 3.5 16.5 - - + +
81C ALA* 3.6 25.8 - - + +
84C GLY* 3.6 16.0 - - - -
85C ILE* 4.2 7.4 - - + +
88C SER* 4.7 2.8 + - - -
95C VAL* 5.1 1.4 - - - +
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Residues in contact with TYR 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 LEU* 3.0 45.0 + - + +
53C ASN* 3.4 11.2 - - - +
55C ALA* 1.3 78.4 - - - +
57C ALA* 1.3 59.9 + - - +
59C ASP* 3.3 8.8 + - + +
60C GLY 3.1 18.0 + - - -
83C ASN* 2.9 16.5 + - - -
84C GLY* 4.0 17.5 - - - -
409C GLN* 5.1 2.7 - - - -
412C TRP* 5.7 0.2 - - - -
414C SER* 2.8 27.9 + - - -
415C ILE 4.2 4.3 + - - -
416C GLY* 3.9 6.1 - - - -
417C PHE* 3.5 54.3 - + + +
420C GLY* 3.8 6.7 - - - -
421C ALA* 3.5 8.0 - - - -
450C THR* 3.6 23.6 - - + -
600C TPP 5.0 1.2 - - - +
80D SER* 4.5 0.2 + - - -
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Residues in contact with ALA 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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23C PHE* 3.7 24.2 - - + -
53C ASN 2.8 16.6 + - - +
54C ALA* 3.5 6.7 - - - +
55C ALA 3.2 0.2 - - - -
56C TYR* 1.3 75.5 - - - +
58C ALA* 1.3 59.0 + - - +
60C GLY 3.2 1.0 + - - -
61C TYR* 2.9 26.3 + - - +
420C GLY* 3.0 23.3 + - - +
423C LEU* 4.0 11.7 - - + -
424C GLY* 3.2 13.3 - - - +
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Residues in contact with ALA 58 (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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23C PHE* 3.7 23.3 - - + -
54C ALA 2.8 20.0 + - - +
55C ALA 3.3 6.0 + - - +
57C ALA* 1.3 72.6 - - - +
59C ASP* 1.3 57.8 + - - +
61C TYR 3.4 0.2 + - - -
62C ALA* 2.9 20.8 + - - +
68C SER* 2.8 31.0 + - - +
69C CYS 4.5 1.1 - - - +
70C ILE* 4.2 13.0 - - + -
95C VAL* 3.9 15.7 - - + -
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Residues in contact with ASP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA 2.9 11.7 + - - +
56C TYR* 3.3 11.4 - - - +
58C ALA* 1.3 75.8 - - - +
60C GLY* 1.3 61.3 + - - +
62C ALA 3.1 2.1 + - - -
63C ARG* 2.7 55.2 + - - +
84C GLY 4.6 2.4 - - - +
87C GLY 4.2 2.9 - - - -
88C SER* 2.7 38.7 + - - +
93C VAL* 3.6 17.7 - - - +
95C VAL* 4.1 3.7 - - - +
409C GLN* 4.7 1.4 + - - -
417C PHE* 3.5 21.0 - - + -
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Residues in contact with GLY 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR 3.1 10.9 + - - -
57C ALA 3.7 2.2 - - - -
59C ASP* 1.3 76.0 + - - +
61C TYR* 1.3 63.4 + - - +
63C ARG* 3.3 8.3 + - - +
64C ILE* 3.3 27.9 + - - +
407C ILE* 4.5 6.3 - - - -
421C ALA* 3.8 28.2 - - - +
425C ALA 3.9 7.0 - - - -
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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
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18C ASN 3.7 0.2 + - - -
19C VAL* 4.3 14.4 - - + -
20C ASN 2.9 20.4 + - - -
21C THR* 3.8 20.9 - - - -
23C PHE* 3.5 24.2 - + + -
57C ALA 2.9 16.5 + - - +
58C ALA 3.6 2.7 - - - +
60C GLY* 1.3 76.3 - - - +
62C ALA* 1.3 57.7 + - - +
64C ILE* 3.1 2.9 + - - +
65C LYS* 2.8 52.0 + - + +
67C MET 3.4 22.2 - - - -
68C SER* 3.8 8.3 - - - -
424C GLY 3.4 24.9 - - - +
427C PHE* 4.0 1.6 - - + -
428C ALA* 3.7 17.7 - - + +
431C GLU* 2.5 31.0 + - - -
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Residues in contact with ALA 62 (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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58C ALA 2.9 18.4 + - - +
59C ASP 3.1 0.2 + - - -
61C TYR* 1.3 76.0 - - - +
63C ARG* 1.3 60.4 + - - +
66C GLY* 2.8 31.3 + - - +
67C MET* 3.6 17.5 - - - -
68C SER* 3.6 12.3 - - - +
93C VAL* 3.5 23.1 - - + -
94C GLY 3.6 15.5 - - - +
160C GLN* 5.0 0.3 - - - +
224C ARG* 4.5 3.5 + - - -
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Residues in contact with ARG 63 (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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59C ASP* 2.7 37.8 + - - +
60C GLY* 3.5 9.0 - - - +
62C ALA* 1.3 77.9 - - - +
64C ILE* 1.3 60.7 + - - +
66C GLY* 4.7 0.7 + - - -
91C GLU* 2.8 41.2 + - - +
93C VAL* 3.8 11.8 - - + +
224C ARG* 3.4 36.5 + - - +
247C MET 5.8 2.0 + - - -
405C TYR* 3.2 35.7 + - + +
406C GLY 5.4 1.4 + - - -
407C ILE* 4.0 40.3 - - + +
408C SER 4.6 8.7 + - - +
409C GLN* 4.3 11.1 - - - +
417C PHE* 4.1 5.8 - - - -
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Residues in contact with ILE 64 (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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60C GLY 3.3 13.4 + - - +
61C TYR 3.1 1.6 + - - -
63C ARG* 1.3 79.5 - - - +
65C LYS* 1.3 59.9 + - - +
383C VAL* 3.9 23.1 - - + -
405C TYR* 3.5 43.1 - - + -
407C ILE* 4.3 3.8 - - + -
425C ALA* 3.9 19.3 - - + +
428C ALA* 3.6 22.9 - - + -
429C ALA* 4.2 11.0 - - + +
432C ILE* 3.7 25.0 - - + +
436C LYS* 5.2 3.4 - - - +
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Residues in contact with LYS 65 (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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17C VAL 5.7 0.2 - - - +
18C ASN* 2.9 54.6 + - - +
20C ASN* 2.8 28.9 + - - -
61C TYR* 2.8 36.5 + - + +
64C ILE* 1.3 75.1 - - - +
66C GLY* 1.3 56.6 + - - +
67C MET 3.7 2.9 + - - +
428C ALA* 4.0 19.1 - - + +
431C GLU* 2.9 36.4 + - - +
432C ILE* 4.2 15.3 - - + -
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Residues in contact with GLY 66 (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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62C ALA 2.8 19.9 + - - +
63C ARG 4.6 1.1 + - - -
64C ILE 3.7 0.6 - - - -
65C LYS* 1.3 74.5 - - - +
67C MET* 1.3 59.3 + - - +
157C TYR* 3.7 15.6 - - - -
160C GLN* 2.9 33.3 + - - +
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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
------------------------------------------------------------
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