Contacts of the helix formed by residues 50 - 66 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.4 12.2 - - - +
48A ASN* 3.5 1.1 - - - +
49A ALA* 1.3 78.4 - - - +
51A GLU* 1.3 59.9 + - - +
52A LEU* 3.3 8.6 + - - +
53A ASN* 2.8 36.2 + - - +
54A ALA* 2.9 26.7 + - - +
449A LEU 5.3 0.6 + - - -
452A GLN* 3.6 19.0 + - - +
453A GLU* 3.7 2.4 + - - -
50B ASN* 5.1 7.9 - - - +
52B LEU* 5.8 8.6 - - + +
449B LEU* 2.9 40.5 + - + +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY 5.3 0.2 - - - -
25A LEU* 3.5 26.2 - - + +
50A ASN* 1.3 73.2 - - - +
52A LEU* 1.3 67.3 + - - +
54A ALA* 3.2 7.7 + - - +
55A ALA* 3.0 23.0 + - - +
70A ILE* 4.0 0.7 - - - +
72A THR* 3.9 18.3 - - + -
73A THR* 5.1 0.5 - - - +
77A GLY* 3.5 37.9 - - - +
80A SER* 3.7 12.5 - - - -
81A ALA* 3.9 6.4 - - - +
449B LEU* 3.7 10.4 - - - +
600B TPP 2.6 45.6 + - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN* 3.3 9.2 + - - +
51A GLU* 1.3 77.6 - - - +
53A ASN* 1.3 61.1 - - - +
55A ALA* 3.1 5.2 + - - +
56A TYR* 3.0 62.6 + - + +
80A SER* 3.5 24.2 + - - +
81A ALA* 4.3 2.2 - - - +
83A ASN* 3.9 9.6 - - + -
84A GLY 3.5 27.1 - - - +
449A LEU* 5.6 3.4 - - + +
450A THR* 5.1 4.3 - - + -
50B ASN* 5.8 7.4 - - + +
52B LEU* 5.9 10.3 - - + -
80B SER* 4.1 21.5 - - - +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 2.8 25.6 + - - +
52A LEU* 1.3 78.2 - - - +
54A ALA* 1.3 58.0 + - - +
56A TYR* 3.3 10.1 + - - +
57A ALA* 2.8 30.9 + - - +
420A GLY* 3.9 4.5 - - - -
449A LEU 4.6 0.5 - - - +
450A THR* 3.1 40.6 + - - +
452A GLN* 3.3 29.7 + - - +
453A GLU* 2.9 39.2 + - + +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.7 4.9 - - - +
24A GLY* 3.6 21.3 - - - +
48A ASN* 3.3 33.4 - - + +
50A ASN 2.9 18.2 + - - +
51A GLU* 3.5 8.5 - - - +
52A LEU 3.2 0.2 - - - -
53A ASN* 1.3 77.8 - - - +
55A ALA* 1.4 51.7 + - - +
57A ALA* 3.3 2.8 + - - +
58A ALA* 2.8 33.4 + - - +
70A ILE* 3.8 7.2 - - + -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU 3.0 11.9 + - - +
52A LEU 3.1 7.8 + - - +
54A ALA* 1.4 71.4 - - - +
56A TYR* 1.3 67.7 + - - +
58A ALA* 3.3 5.9 + - - +
59A ASP* 3.0 23.2 + - - +
70A ILE* 3.6 15.9 - - + +
81A ALA* 3.5 27.4 - - + +
84A GLY* 3.7 15.3 - - - -
85A ILE* 4.2 7.1 - - + +
88A SER* 4.8 2.3 + - - -
95A VAL* 5.1 1.4 - - - +
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.0 46.3 + - + +
53A ASN* 3.5 11.4 - - - +
55A ALA* 1.3 76.5 - - - +
57A ALA* 1.3 55.6 + - - +
59A ASP* 3.2 9.0 + - + +
60A GLY 3.0 22.2 + - - -
83A ASN* 3.0 13.8 + - - -
84A GLY* 4.0 17.7 - - - -
409A GLN* 5.2 3.1 - - - -
414A SER* 2.9 27.7 + - - -
415A ILE 4.1 5.2 + - - -
416A GLY 3.9 4.9 - - - -
417A PHE* 3.6 54.1 - + + +
420A GLY* 3.8 4.9 - - - -
421A ALA* 3.5 10.1 - - - -
450A THR* 3.6 25.4 - - + -
600A TPP 4.9 1.0 - - - +
80B SER* 4.6 0.5 + - - -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.7 24.2 - - + -
53A ASN 2.8 16.8 + - - +
54A ALA* 3.4 7.0 - - - +
56A TYR* 1.3 72.8 - - - +
58A ALA* 1.3 59.4 + - - +
59A ASP 3.1 1.6 - - - -
60A GLY 3.2 0.9 + - - -
61A TYR* 2.8 26.9 + - - +
420A GLY* 3.1 23.5 - - - +
423A LEU* 3.9 14.1 - - + -
424A GLY* 3.2 11.5 - - - +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.7 21.0 - - + -
54A ALA 2.8 19.6 + - - +
55A ALA 3.3 5.4 + - - +
57A ALA* 1.3 72.3 - - - +
59A ASP* 1.3 56.9 + - - +
61A TYR 3.4 0.2 + - - -
62A ALA* 3.0 19.6 + - - +
68A SER* 2.7 31.0 + - - +
69A CYS 4.5 1.8 - - - -
70A ILE* 4.1 13.9 - - + -
95A VAL* 3.9 17.5 - - + -
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 3.0 11.3 + - - +
56A TYR* 3.3 11.0 - - + +
57A ALA 3.1 0.2 - - - -
58A ALA* 1.3 73.6 - - - +
60A GLY* 1.3 65.2 + - - +
62A ALA 3.2 2.1 + - - -
63A ARG* 2.7 55.5 + - - +
84A GLY 4.6 1.8 - - - +
87A GLY 4.2 2.8 - - - -
88A SER* 2.6 39.3 + - - +
93A VAL* 3.5 12.1 - - - +
95A VAL* 4.0 9.8 - - - +
409A GLN* 4.6 1.6 + - - -
417A PHE* 3.5 19.0 - - + -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR 3.0 12.1 + - - -
57A ALA 3.2 3.1 + - - -
59A ASP* 1.3 76.0 + - - +
61A TYR* 1.3 62.3 + - - +
63A ARG* 3.2 17.6 + - - +
64A ILE* 3.3 20.1 + - - +
407A ILE* 4.7 4.4 - - - +
421A ALA* 3.7 28.2 - - - +
425A ALA 3.9 6.1 - - - -
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN 3.7 0.5 + - - -
19A VAL* 4.3 14.6 - - + -
20A ASN 2.9 20.4 + - - -
21A THR* 3.5 22.4 + - - -
23A PHE* 3.5 24.0 - + + -
57A ALA 2.8 21.2 + - - +
58A ALA 3.7 2.9 - - - +
60A GLY* 1.3 73.6 - - - +
62A ALA* 1.3 51.4 + - - +
64A ILE* 3.2 1.7 + - - -
65A LYS* 2.7 57.8 + - + +
67A MET 3.3 22.2 - - - -
68A SER* 3.7 8.7 - - - -
424A GLY 3.5 23.4 - - - +
427A PHE* 4.0 1.3 - - + -
428A ALA* 3.7 18.6 - - + +
431A GLU* 2.5 31.6 + - - -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA 3.0 17.0 + - - +
59A ASP 3.2 0.2 + - - -
61A TYR* 1.3 76.1 - - - +
63A ARG* 1.3 60.3 + - - +
66A GLY* 2.8 30.6 + - - +
67A MET* 3.6 16.2 - - - +
68A SER* 3.5 5.8 - - - +
93A VAL* 3.5 20.6 - - + -
94A GLY 3.5 27.1 - - - +
160A GLN* 5.0 2.3 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 2.7 39.4 + - - +
60A GLY* 3.6 8.1 - - - +
61A TYR 3.2 0.2 - - - -
62A ALA* 1.3 77.9 - - - +
64A ILE* 1.3 62.9 + - - +
66A GLY* 4.7 0.7 + - - -
91A GLU* 2.8 38.6 + - - +
93A VAL* 3.8 19.6 - - + +
224A ARG* 3.8 30.1 - - - +
247A MET* 6.0 0.2 - - - +
405A TYR* 3.3 37.0 + - + +
406A GLY 5.3 1.6 + - - -
407A ILE* 4.0 43.5 - - + +
408A SER 4.7 6.3 + - - +
409A GLN* 4.2 6.8 - - - +
417A PHE* 4.0 10.9 - - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLY 3.5 13.7 - - - +
61A TYR 3.2 1.2 + - - -
62A ALA 3.2 0.2 - - - -
63A ARG* 1.3 80.3 - - - +
65A LYS* 1.3 59.2 + - - +
383A VAL* 4.0 21.8 - - + -
405A TYR* 3.3 42.2 - - + -
407A ILE* 4.2 3.4 - - + -
425A ALA* 3.9 20.0 - - + +
428A ALA* 3.7 19.1 - - + -
429A ALA* 4.2 10.8 - - + +
432A ILE* 3.6 29.1 - - + +
436A LYS* 5.2 3.6 - - - -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 3.0 65.4 + - + +
20A ASN* 3.0 14.1 + - - -
61A TYR* 2.7 39.6 + - + +
64A ILE* 1.3 73.5 - - - +
66A GLY* 1.3 56.3 + - - +
67A MET 3.7 2.9 - - - +
428A ALA* 4.0 11.2 - - + +
431A GLU* 2.9 40.5 + - - +
432A ILE* 4.1 24.0 - - + -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 2.8 15.6 + - - +
63A ARG 4.6 0.9 - - - -
64A ILE 3.6 1.0 - - - -
65A LYS* 1.3 78.8 - - - +
67A MET* 1.3 59.8 + - - +
157A TYR* 3.5 17.1 - - - -
160A GLN* 2.9 33.4 + - - +
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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