Contacts of the helix formed by residues 50 - 66 (chain D) in PDB entry 2VK8
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ASN* 5.1 7.3 - - - +
52C LEU* 6.0 7.4 - - + +
449C LEU* 3.0 41.6 + - + +
25D LEU* 3.3 12.3 - - - +
48D ASN* 3.8 1.6 - - - +
49D ALA* 1.3 78.1 - - - +
51D GLU* 1.3 60.6 + - - +
52D LEU* 3.4 8.0 + - - +
53D ASN* 2.8 36.3 + - - +
54D ALA* 3.0 26.0 + - - +
80D SER* 6.4 0.2 - - - -
449D LEU 5.2 0.8 + - - -
452D GLN* 3.5 19.8 + - - +
453D GLU* 3.7 2.0 + - - -
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C LEU* 3.8 9.9 - - - +
1564C TPP 2.6 43.7 + - - +
25D LEU* 3.5 27.3 - - + +
50D ASN* 1.3 71.9 - - - +
52D LEU* 1.3 66.4 + - - +
54D ALA* 3.3 8.0 + - - +
55D ALA* 3.0 23.0 + - - +
70D ILE* 3.9 2.6 - - - +
72D THR* 3.9 17.7 - - + -
73D THR* 5.1 0.5 - - - +
77D GLY* 3.6 39.1 - - - +
80D SER* 3.7 12.6 + - - -
81D ALA* 4.0 4.8 - - - +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASN* 6.0 7.6 - - + +
52C LEU* 6.0 9.4 - - + -
80C SER* 4.0 21.1 - - - +
50D ASN* 3.4 8.5 + - - +
51D GLU* 1.3 77.8 - - - +
53D ASN* 1.3 67.3 + - - +
55D ALA* 3.1 3.1 + - - +
56D TYR* 3.0 53.1 + - + +
80D SER* 3.5 24.2 + - - +
81D ALA* 4.3 1.6 - - - +
83D ASN* 3.8 10.5 - - + -
84D GLY 3.5 28.3 - - - +
449D LEU* 5.7 2.5 - - + +
450D THR* 5.1 4.3 - - + -
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ASN* 4.7 1.6 - - - -
50D ASN* 2.8 26.6 + - - +
52D LEU* 1.3 77.8 - - - +
54D ALA* 1.3 57.0 + - - +
56D TYR* 3.3 9.8 + - - +
57D ALA* 2.8 30.4 + - - +
420D GLY* 3.9 4.3 - - - -
449D LEU 4.6 0.2 - - - +
450D THR* 3.1 41.8 + - - +
452D GLN* 3.3 29.3 + - - +
453D GLU* 2.9 36.4 + - + +
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.6 4.5 - - - +
24D GLY* 3.5 23.1 - - - +
48D ASN* 3.3 30.9 - - + +
50D ASN 3.0 16.0 + - - +
51D GLU* 3.4 10.8 - - - +
52D LEU 3.2 0.4 - - - -
53D ASN* 1.3 77.4 - - - +
55D ALA* 1.3 56.1 - - - +
57D ALA* 3.3 2.6 + - - +
58D ALA* 2.8 28.2 + - - +
70D ILE* 3.7 6.7 - - + -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU 3.0 12.3 + - - +
52D LEU 3.1 8.0 + - - +
54D ALA* 1.3 72.8 - - - +
56D TYR* 1.3 66.1 + - - +
58D ALA* 3.3 5.9 + - - +
59D ASP* 3.0 23.0 + - - +
70D ILE* 3.5 16.5 - - + +
81D ALA* 3.6 24.9 - - + +
84D GLY* 3.7 15.2 - - - -
85D ILE* 4.2 8.0 - - + +
88D SER* 4.8 2.6 + - - -
95D VAL* 5.2 1.4 - - - +
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Residues in contact with TYR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER* 4.6 0.3 + - - -
52D LEU* 3.0 44.9 + - + +
53D ASN* 3.5 11.0 - - - +
55D ALA* 1.3 76.0 - - - +
57D ALA* 1.3 58.7 + - - +
59D ASP* 3.2 8.8 + - + +
60D GLY 3.0 23.0 + - - -
83D ASN* 3.0 15.8 + - - -
84D GLY* 4.0 17.7 - - - -
409D GLN* 5.3 2.2 - - - -
412D TRP* 5.8 0.2 - - - -
414D SER* 2.8 26.7 + - - -
415D ILE 4.1 4.3 + - - -
416D GLY 3.8 5.8 - - - -
417D PHE* 3.5 56.7 - + + +
420D GLY* 3.9 6.7 - - - -
421D ALA* 3.5 8.1 - - - +
450D THR* 3.7 18.8 - - + -
1564D TPP 4.9 0.9 - - - +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.7 25.1 - - + -
53D ASN 2.8 17.4 + - - +
54D ALA* 3.5 6.7 - - - +
56D TYR* 1.3 74.5 - - - +
58D ALA* 1.3 60.0 + - - +
60D GLY 3.2 0.9 + - - -
61D TYR* 2.8 27.0 + - - +
420D GLY 3.1 21.5 + - - +
421D ALA* 4.3 0.2 - - - +
423D LEU* 3.9 14.4 - - + -
424D GLY* 3.2 10.2 - - - +
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.7 21.5 - - + -
54D ALA 2.8 20.2 + - - +
55D ALA 3.3 5.8 + - - +
57D ALA* 1.3 73.1 - - - +
59D ASP* 1.3 56.9 + - - +
62D ALA* 2.9 18.9 + - - +
68D SER* 2.7 32.6 + - - +
69D CYS 4.5 1.3 - - - +
70D ILE* 4.2 13.0 - - + -
95D VAL* 4.0 15.9 - - + -
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Residues in contact with ASP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA 3.0 13.5 + - - +
56D TYR* 3.3 10.5 - - - +
57D ALA 3.1 0.2 - - - -
58D ALA* 1.3 76.5 - - - +
60D GLY* 1.3 64.3 + - - +
62D ALA* 3.2 3.8 + - - +
63D ARG* 2.7 55.2 + - - +
84D GLY 4.6 1.8 - - - +
87D GLY 4.2 2.9 - - - +
88D SER* 2.7 36.6 + - - +
93D VAL* 3.6 15.2 - - - +
95D VAL* 4.1 3.3 - - - +
409D GLN* 4.6 1.2 + - - -
417D PHE* 3.5 19.9 - - + -
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR 3.0 13.1 + - - -
57D ALA 3.7 2.2 - - - -
59D ASP* 1.3 77.8 + - - +
61D TYR* 1.3 62.7 + - - +
63D ARG* 3.3 9.8 + - - +
64D ILE* 3.3 27.5 + - - +
407D ILE* 4.6 4.4 - - - +
421D ALA* 3.8 26.4 - - - +
425D ALA 3.8 6.5 - - - -
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Residues in contact with TYR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN 3.8 0.2 + - - -
19D VAL* 4.3 11.7 - - + -
20D ASN 2.9 20.1 + - - -
21D THR* 3.8 18.8 - - - -
23D PHE* 3.6 25.1 - + + -
57D ALA 2.8 17.0 + - - +
58D ALA 3.6 3.1 - - - +
60D GLY* 1.3 75.3 - - - +
62D ALA* 1.3 53.1 + - - +
64D ILE* 3.2 1.9 + - - -
65D LYS* 2.7 57.4 + - + +
67D MET 3.4 21.5 - - - -
68D SER* 3.7 8.1 - - - -
424D GLY 3.5 22.9 - - - +
427D PHE* 4.0 1.3 - - + -
428D ALA* 3.7 17.1 - - + +
431D GLU* 2.5 37.9 + - - -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ALA 2.9 19.1 + - - +
61D TYR* 1.3 75.8 - - - +
63D ARG* 1.3 59.2 + - - +
66D GLY* 2.9 30.6 + - - +
67D MET* 3.7 16.4 - - - +
68D SER* 3.4 12.3 - - - +
93D VAL* 3.5 23.6 - - + -
94D GLY 3.5 15.9 - - - +
160D GLN* 5.1 0.7 - - - +
224D ARG* 4.5 3.1 + - - -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASP* 2.7 40.2 + - - +
60D GLY* 3.6 7.6 - - - +
61D TYR 3.2 0.2 - - - -
62D ALA* 1.3 78.1 - - - +
64D ILE* 1.3 60.2 + - - +
66D GLY* 4.7 0.7 + - - -
91D GLU* 2.9 41.0 + - - +
93D VAL* 3.8 11.8 - - + +
224D ARG* 3.5 35.4 + - - +
405D TYR* 3.1 36.1 + - + +
407D ILE* 4.0 42.8 - - + +
408D SER 4.7 6.1 + - - +
409D GLN* 4.2 11.3 - - - +
417D PHE* 4.1 5.6 - - - -
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLY 3.3 14.1 + - - +
61D TYR 3.2 1.4 + - - -
63D ARG* 1.3 76.7 - - - +
65D LYS* 1.3 62.0 + - - +
383D VAL* 3.9 26.5 - - + -
405D TYR* 3.5 41.3 - - + -
407D ILE* 4.2 4.0 - - + -
425D ALA* 3.8 19.1 - - + +
428D ALA* 3.6 23.1 - - + -
429D ALA* 4.2 10.3 - - + +
432D ILE* 3.8 25.5 - - + +
436D LYS* 5.1 4.3 - - - +
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN* 2.9 58.0 + - - +
20D ASN* 2.9 22.4 + - - -
61D TYR* 2.7 38.8 + - + +
64D ILE* 1.3 75.5 - - - +
66D GLY* 1.3 55.2 + - - +
67D MET 3.8 2.2 - - - +
428D ALA* 3.9 20.0 - - + +
431D GLU* 2.8 40.2 + - - +
432D ILE* 4.3 15.7 - - + -
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Residues in contact with GLY 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ALA 2.9 14.7 + - - +
63D ARG 4.7 0.6 - - - -
64D ILE 3.7 0.6 - - - -
65D LYS* 1.3 78.4 - - - +
67D MET* 1.3 60.8 + - - +
157D TYR* 3.8 16.9 - - - -
160D GLN* 3.0 33.6 + - - +
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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