Contacts of the helix formed by residues 49 - 62 (chain D) in PDB entry 6WNX
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 MET 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ILE 3.3 0.8 + - - -
46D SER 3.3 21.1 + - - +
47D GLU* 3.1 17.4 - - - +
48D GLY* 1.3 80.0 - - - +
50D LEU* 1.3 58.7 + - - +
51D TRP 3.3 3.3 + - - -
52D LYS* 3.5 28.5 + - + +
53D LYS* 3.1 29.6 + - - +
87D PRO 4.3 8.3 - - - +
88D PRO* 4.1 4.7 - - + -
89D ASN* 3.5 43.3 - - + +
92D TYR* 4.7 2.9 - - - -
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Residues in contact with LEU 50 (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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20D GLU* 3.4 38.4 - - + +
23D LEU* 3.7 16.4 - - + +
24D SER* 3.7 23.1 - - - +
31D LEU* 4.3 11.1 - - + +
44D VAL 3.8 7.6 - - - +
45D ILE* 3.2 37.3 + - + +
48D GLY* 3.5 26.2 - - - +
49D MET* 1.3 74.4 - - - +
51D TRP* 1.3 56.4 + - - +
53D LYS* 3.5 9.5 - - + +
54D LEU* 2.8 33.4 + - - +
89D ASN* 3.7 0.6 + - - -
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Residues in contact with TRP 51 (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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28D ALA* 4.3 10.5 - - + -
31D LEU* 3.5 30.7 - - + +
32D CYS* 4.0 24.5 - - - -
35D GLU* 3.2 27.0 + - - -
45D ILE* 4.4 7.2 - - + +
49D MET 3.3 0.6 - - - -
50D LEU* 1.3 73.4 - - - +
52D LYS* 1.3 65.7 + - - +
54D LEU* 3.2 10.4 + - + +
55D ILE* 3.0 28.2 + - - +
89D ASN* 3.7 26.6 + - - +
92D TYR* 3.6 24.5 - - + +
93D ARG* 3.5 32.9 - - + +
96D TYR* 3.8 45.1 - + + -
139E ASN* 5.9 1.3 - - + -
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Residues in contact with LYS 52 (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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49D MET* 3.5 27.4 + - + +
51D TRP* 1.3 77.4 - - - +
53D LYS* 1.3 58.4 + - + +
55D ILE* 3.3 4.3 + - - +
56D GLU* 2.9 59.1 + - - +
77D TYR 3.5 20.9 - - - -
78D LEU* 4.3 4.8 - - + +
79D PHE 3.1 24.8 + - - +
80D LYS 4.8 4.0 - - - -
87D PRO* 5.7 1.6 - - - +
89D ASN* 4.6 0.4 + - - -
92D TYR* 3.6 45.9 - - + +
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Residues in contact with LYS 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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20D GLU* 3.4 34.9 + - + -
21D ASN* 5.6 5.4 - - - +
24D SER* 4.6 17.0 + - - +
48D GLY 3.4 13.6 + - - +
49D MET* 3.1 19.4 + - + +
50D LEU* 3.5 23.6 - - + +
51D TRP 3.2 0.4 - - - -
52D LYS* 1.3 75.4 - - + +
54D LEU* 1.3 57.1 + - - +
56D GLU* 3.4 18.3 + - - +
57D ARG* 3.0 26.7 + - - +
60D ARG* 5.7 0.9 + - - -
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Residues in contact with LEU 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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24D SER* 5.0 6.5 - - - +
26D LEU 4.0 7.0 - - - +
27D ASP* 5.2 0.7 - - - -
28D ALA* 4.3 15.5 - - - +
31D LEU* 4.1 11.9 - - + -
50D LEU 2.8 18.3 + - - +
51D TRP* 3.2 22.4 + - + +
53D LYS* 1.3 72.8 - - - +
55D ILE* 1.3 54.1 - - - +
57D ARG* 2.8 39.9 + - - +
58D MET* 2.7 47.5 + - + +
96D TYR* 3.5 34.1 - - + +
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Residues in contact with ILE 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 TRP* 3.0 22.5 + - + +
52D LYS 3.6 4.0 - - - +
54D LEU* 1.3 75.4 - - - +
56D GLU* 1.3 57.2 + - - +
58D MET* 3.2 10.0 + - - +
59D VAL* 2.9 28.3 + - + +
65D TRP* 4.3 8.1 - - + -
74D TRP* 3.8 30.3 - - + -
78D LEU* 3.8 17.0 - - + -
92D TYR* 4.0 23.6 - - + +
95D LEU* 3.9 24.9 - - + -
96D TYR* 4.1 23.3 - - + +
99D ILE* 4.3 7.0 - - + -
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Residues in contact with GLU 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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52D LYS* 2.9 36.0 + - - +
53D LYS* 3.5 24.8 - - - +
55D ILE* 1.3 75.3 - - - +
57D ARG* 1.3 57.0 + - - +
59D VAL* 3.1 7.0 + - - +
60D ARG* 2.9 38.3 + - - +
78D LEU* 3.8 9.1 - - + -
79D PHE* 2.7 66.3 + - + -
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Residues in contact with ARG 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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24D SER* 2.9 29.2 + - - +
25D TYR* 3.2 33.7 + - - +
26D LEU 3.0 28.7 + - - -
27D ASP* 4.3 2.8 - - - +
53D LYS 3.0 12.4 + - - +
54D LEU* 2.8 27.6 + - - +
56D GLU* 1.3 69.1 - - - +
58D MET* 1.3 81.2 + - + +
60D ARG* 3.4 24.7 - - - +
61D THR* 3.0 42.2 + - + +
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Residues in contact with MET 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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54D LEU* 2.7 32.6 + - + +
55D ILE 3.4 8.1 - - - +
57D ARG* 1.3 111.4 - - + +
59D VAL* 1.3 55.4 + - - +
61D THR* 4.0 9.4 - - - +
62D ASP* 2.7 40.2 + - - +
65D TRP* 3.4 50.3 - - + -
96D TYR* 4.7 5.4 - - - +
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Residues in contact with VAL 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 ILE 2.9 17.4 + - - +
56D GLU* 3.1 9.6 + - - +
58D MET* 1.3 76.2 - - - +
60D ARG* 1.3 63.0 + - - +
61D THR 3.3 0.7 + - - -
62D ASP 3.5 10.0 + - - +
65D TRP* 3.9 28.0 - - + +
66D LYS* 3.7 35.4 - - + +
69D SER* 4.1 11.0 - - - +
74D TRP* 4.1 5.8 - - + -
78D LEU* 4.0 20.2 - - + -
79D PHE* 4.4 19.1 - - + -
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Residues in contact with ARG 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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53D LYS 5.7 0.8 + - - -
56D GLU* 2.9 18.9 + - - +
57D ARG* 3.4 36.0 - - - +
58D MET 3.3 0.4 - - - -
59D VAL* 1.3 78.4 - - - +
61D THR* 1.3 70.7 + - + +
66D LYS* 5.9 1.2 - - - +
79D PHE* 5.4 13.1 - - + -
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Residues in contact with THR 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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57D ARG* 3.0 27.6 + - + +
58D MET* 3.5 13.7 + - + +
59D VAL 4.3 0.2 - - - -
60D ARG* 1.3 94.3 - - + +
62D ASP* 1.3 64.3 + - - +
63D PRO* 3.4 13.0 - - - +
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Residues in contact with ASP 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 MET* 2.7 26.0 + - - +
59D VAL 3.5 3.9 - - - +
61D THR* 1.3 73.5 + - - +
63D PRO* 1.3 72.8 - - - +
64D LEU* 3.1 33.1 + - - +
65D TRP* 3.0 31.9 + - + -
66D LYS 3.1 9.0 + - - -
389D GLU* 4.3 7.2 - - - +
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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