Contacts of the helix formed by residues 50 - 66 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN* 5.1 7.9 - - - +
52A LEU* 5.8 7.8 - - + +
449A LEU* 2.9 40.6 + - + +
25B LEU* 3.3 13.3 - - - +
48B ASN* 3.5 1.4 - - - +
49B ALA* 1.3 77.6 - - - +
51B GLU* 1.3 60.2 + - - +
52B LEU* 3.3 8.4 + - - +
53B ASN* 2.8 45.8 + - - +
54B ALA* 2.9 27.9 + - - +
449B LEU 5.3 0.4 + - - -
452B GLN* 3.5 19.6 + - - +
453B GLU* 3.7 2.4 + - - -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A LEU* 3.8 10.7 - - - +
600A TPP 2.7 43.9 + - - +
25B LEU* 3.6 27.3 - - + +
50B ASN* 1.3 72.2 - - - +
52B LEU* 1.3 67.8 + - - +
54B ALA* 3.2 8.2 + - - +
55B ALA* 3.0 23.2 + - - +
70B ILE* 3.9 2.9 - - - +
72B THR* 3.9 16.6 - - + -
73B THR* 5.1 0.7 - - - +
77B GLY* 3.6 37.5 - - - +
80B SER* 3.7 13.4 - - - -
81B ALA* 4.0 3.7 - - - +
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Residues in contact with LEU 52 (chain B).
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* 5.8 7.6 - - + +
52A LEU* 5.9 10.1 - - + -
80A SER* 4.1 21.1 - - - +
50B ASN* 3.3 8.8 + - - +
51B GLU* 1.3 78.7 - - - +
53B ASN* 1.3 66.9 + - - +
55B ALA* 3.1 5.9 + - - +
56B TYR* 3.0 54.1 + - + +
80B SER* 3.4 23.6 + - - +
81B ALA* 4.3 1.8 - - - +
83B ASN* 3.8 11.2 - - + -
84B GLY* 3.5 28.3 - - - +
449B LEU* 5.5 3.1 - - + +
450B THR* 5.0 3.8 - - + -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASN* 2.8 24.9 + - - +
52B LEU* 1.3 79.7 - - - +
54B ALA* 1.3 57.4 + - - +
56B TYR* 3.3 10.3 + - - +
57B ALA* 2.8 31.1 + - - +
420B GLY* 4.0 3.7 - - - -
449B LEU 4.6 0.3 - - - +
450B THR* 3.1 42.3 + - - +
452B GLN* 3.3 28.9 + - - +
453B GLU* 3.0 38.4 + - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.7 4.0 - - - +
24B GLY* 3.6 20.6 - - - +
48B ASN* 3.3 33.8 - - + +
50B ASN 2.9 16.2 + - - +
51B GLU* 3.4 11.2 - - - +
53B ASN* 1.3 76.8 - - - +
55B ALA* 1.3 52.3 + - - +
57B ALA* 3.2 2.4 + - - +
58B ALA* 2.8 34.5 + - - +
70B ILE* 3.8 6.3 - - + -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU 3.0 13.4 + - - +
52B LEU 3.1 8.0 + - - +
54B ALA* 1.3 74.1 - - - +
56B TYR* 1.3 66.2 + - - +
58B ALA* 3.2 5.9 + - - +
59B ASP* 3.0 23.2 + - - +
70B ILE* 3.5 16.7 - - + +
81B ALA* 3.7 24.9 - - + +
84B GLY* 3.7 15.6 - - - -
85B ILE* 4.2 7.8 - - + +
88B SER* 4.7 2.4 + - - -
95B VAL* 5.2 1.7 - - - +
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 4.5 0.5 + - - -
52B LEU* 3.0 43.5 + - + +
53B ASN* 3.5 11.0 - - - +
55B ALA* 1.3 76.4 - - - +
57B ALA* 1.3 57.4 + - - +
59B ASP* 3.3 9.0 + - + +
60B GLY 3.0 22.9 + - - -
83B ASN* 3.0 14.7 + - - -
84B GLY* 3.9 18.4 - - - -
409B GLN* 5.3 2.0 - - - -
414B SER* 2.8 25.9 + - - -
415B ILE 4.2 5.0 + - - -
416B GLY 3.7 5.8 - - - -
417B PHE* 3.5 54.7 - + + +
420B GLY* 3.8 6.3 - - - -
421B ALA* 3.6 7.8 - - - -
450B THR* 3.6 27.8 - - + -
600B TPP 4.8 1.2 - - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.7 24.0 - - + -
53B ASN 2.8 17.0 + - - +
54B ALA* 3.5 7.0 - - - +
55B ALA 3.1 0.2 - - - -
56B TYR* 1.3 74.2 - - - +
58B ALA* 1.3 60.4 + - - +
60B GLY 3.2 1.2 + - - -
61B TYR* 2.8 26.5 + - - +
420B GLY* 3.1 22.4 + - - +
423B LEU* 3.9 14.6 - - + -
424B GLY* 3.2 10.4 - - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.7 22.8 - - + -
54B ALA 2.8 19.2 + - - +
55B ALA 3.2 5.4 + - - +
57B ALA* 1.3 72.2 - - - +
59B ASP* 1.3 57.5 + - - +
61B TYR 3.4 0.2 + - - -
62B ALA* 2.9 19.9 + - - +
68B SER* 2.7 32.3 + - - +
70B ILE* 4.1 15.0 - - + +
95B VAL* 3.9 15.9 - - + -
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA 3.0 10.0 + - - +
56B TYR* 3.3 11.0 - - + +
57B ALA 3.2 0.2 - - - -
58B ALA* 1.3 72.6 - - - +
60B GLY* 1.3 66.3 + - - +
62B ALA 3.2 1.7 + - - -
63B ARG* 2.7 55.0 + - - +
84B GLY 4.6 1.8 - - - +
87B GLY 4.2 3.5 - - - +
88B SER* 2.7 38.4 + - - +
93B VAL* 3.6 12.2 - - - +
95B VAL* 3.9 10.2 - - - +
409B GLN* 4.6 1.0 + - - -
417B PHE* 3.5 19.0 - - + -
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR 3.0 11.3 + - - -
57B ALA 3.2 2.9 + - - -
59B ASP* 1.3 78.8 + - - +
61B TYR* 1.3 63.1 + - - +
63B ARG* 3.3 18.1 + - - +
64B ILE* 3.3 19.1 + - - +
407B ILE* 4.6 4.0 - - - +
421B ALA* 3.7 28.0 - - - +
425B ALA* 3.8 6.7 - - - +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.2 15.0 - - + -
20B ASN 2.8 23.7 + - - -
21B THR* 3.8 13.2 - - - -
23B PHE* 3.5 24.9 - + + -
57B ALA 2.8 17.0 + - - +
58B ALA 3.6 2.7 - - - +
60B GLY* 1.3 76.2 - - - +
62B ALA* 1.3 53.4 + - - +
64B ILE* 3.1 3.1 + - - +
65B LYS* 2.8 56.7 + - + +
67B MET 3.4 22.0 - - - -
68B SER* 3.9 7.4 - - - -
424B GLY 3.5 23.1 - - - +
427B PHE* 3.9 1.6 - - + -
428B ALA* 3.7 16.8 - - + -
431B GLU* 2.6 37.9 + - - -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ALA 2.9 18.3 + - - +
59B ASP 3.2 0.2 + - - -
61B TYR* 1.3 76.4 - - - +
63B ARG* 1.3 59.6 + - - +
66B GLY* 2.8 30.9 + - - +
67B MET* 3.6 17.0 - - - -
68B SER* 3.5 11.9 - - - +
93B VAL* 3.5 23.6 - - + -
94B GLY 3.5 16.4 - - - +
95B VAL* 4.4 0.2 - - + -
160B GLN* 5.0 1.2 - - - +
224B ARG* 4.5 3.0 + - - -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASP* 2.7 38.7 + - - +
60B GLY* 3.6 8.5 - - - +
61B TYR 3.2 0.2 - - - -
62B ALA* 1.3 76.6 - - - +
64B ILE* 1.3 60.0 + - - +
66B GLY* 4.6 1.2 + - - -
91B GLU* 2.9 43.2 + - - +
93B VAL* 3.8 15.9 - - + +
224B ARG* 3.5 33.9 + - - +
247B MET 5.9 0.8 + - - -
405B TYR* 3.1 36.9 + - + +
406B GLY 5.4 1.2 + - - -
407B ILE* 4.0 41.9 - - + +
408B SER 4.6 8.1 + - - +
409B GLN* 4.2 11.1 - - - +
417B PHE* 4.1 4.6 - - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLY 3.3 12.1 + - - +
61B TYR 3.1 2.1 + - - +
63B ARG* 1.3 80.3 - - - +
65B LYS* 1.3 59.6 + - - +
66B GLY 3.6 0.4 - - - -
383B VAL* 4.0 24.5 - - + -
405B TYR* 3.4 44.1 - - + -
407B ILE* 4.2 3.6 - - + -
425B ALA* 3.9 19.3 - - + +
428B ALA* 3.7 22.7 - - + -
429B ALA* 4.3 8.5 - - - +
432B ILE* 3.7 24.7 - - + +
436B LYS* 5.2 4.0 - - - -
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL 5.2 1.0 - - - +
18B ASN* 2.9 70.0 + - - +
20B ASN* 3.0 15.0 + - - -
61B TYR* 2.8 38.6 + - + +
64B ILE* 1.3 72.6 - - - +
66B GLY* 1.3 56.4 + - - +
67B MET 3.7 2.8 + - - +
428B ALA* 4.0 19.3 - - + +
431B GLU* 2.8 40.1 + - - +
432B ILE* 4.2 16.2 - - + -
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA 2.8 16.2 + - - +
63B ARG 4.6 1.3 + - - -
64B ILE 3.6 1.0 - - - -
65B LYS* 1.3 78.1 - - - +
67B MET* 1.3 57.2 + - - +
157B TYR* 3.8 15.9 - - - -
160B GLN* 2.8 36.1 + - - +
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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