Contacts of the helix formed by residues 56 - 74 (chain D) in PDB entry 3F5O
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 HIS 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.5 32.0 - + + +
22C GLU* 2.9 41.4 + - - -
62C THR* 4.0 9.3 - - + +
65C ASP* 3.7 6.8 + - - -
66C ASN* 3.1 24.6 + - - -
48D HIS 3.0 20.0 + - - +
50D ASN* 3.8 10.3 - - - +
54D THR 3.2 3.8 + - - -
55D LEU* 1.3 72.6 - - - +
57D GLY* 1.3 62.3 + - - +
58D GLY* 2.8 34.6 + - - -
59D LEU* 3.0 19.2 + - - +
60D THR* 3.0 11.3 + - - -
151D CL 3.7 13.4 - - + +
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Residues in contact with GLY 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP* 3.6 11.7 - - - -
83C SER* 5.2 0.9 - - - -
86C MET* 5.1 0.4 - - - -
150C COA 4.1 8.0 - - - +
55D LEU 3.4 3.0 + - - -
56D HIS* 1.3 75.6 - - - +
58D GLY* 1.3 56.7 + - - +
60D THR* 3.4 3.1 + - - -
61D ALA* 3.0 18.5 + - - +
90D TYR* 2.8 42.3 + - - -
151D CL 3.2 10.8 - - - +
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Residues in contact with GLY 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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21C PHE* 3.8 1.8 - - - -
58C GLY 3.9 0.3 - - - +
61C ALA 4.8 1.1 - - - -
62C THR* 3.3 30.0 + - - -
65C ASP* 3.4 6.4 + - - -
86C MET* 5.2 0.4 - - - -
56D HIS* 2.8 16.1 - - - -
57D GLY* 1.3 74.1 - - - +
59D LEU* 1.3 60.4 + - - +
61D ALA* 3.4 9.1 - - - +
62D THR* 2.8 30.0 + - - -
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.6 37.5 - - + -
24D VAL* 4.1 11.4 - - + +
25D LEU* 3.5 27.1 - - + -
42D MET* 4.3 2.9 - - + -
48D HIS* 3.3 55.4 - - + +
55D LEU* 3.7 13.5 - - + -
56D HIS 3.0 9.4 + - - +
58D GLY* 1.3 75.8 - - - +
60D THR* 1.3 59.1 + - - +
62D THR* 3.0 4.8 + - - -
63D LEU* 2.8 34.3 + - + +
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Residues in contact with THR 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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150C COA 5.9 0.2 - - - -
55D LEU* 3.3 28.4 + - - +
56D HIS 3.0 6.8 + - - -
57D GLY* 3.5 9.5 - - - -
58D GLY 3.4 0.2 - - - -
59D LEU* 1.3 74.3 - - - +
61D ALA* 1.3 58.0 + - - +
63D LEU* 3.2 12.6 + - - +
64D VAL* 2.9 29.6 + - + +
88D ILE* 4.0 7.0 - - + -
90D TYR* 3.7 24.6 - - + -
120D LEU* 3.8 14.8 - - + -
129D ILE* 5.3 1.9 - - - +
130D ALA* 3.8 23.8 - - + -
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLY* 4.8 0.9 - - - -
61C ALA* 3.4 30.7 - - + -
86C MET* 4.3 1.3 - - + -
57D GLY 3.0 15.3 + - - +
58D GLY* 3.4 10.3 - - - +
59D LEU 3.1 0.2 - - - -
60D THR* 1.3 77.5 - - - +
62D THR* 1.3 56.9 + - - +
64D VAL* 3.3 3.3 + - - +
65D ASP* 2.9 29.1 + - - +
86D MET* 3.8 6.1 - - + +
88D ILE* 3.8 28.5 - - + -
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Residues in contact with THR 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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21C PHE* 4.5 0.5 - - - -
56C HIS* 4.1 14.6 - - + +
58C GLY* 3.3 20.4 - - - -
21D PHE* 3.5 18.5 - - + +
22D GLU* 6.5 0.4 - - - -
24D VAL* 3.9 23.6 - - + -
25D LEU* 4.2 11.7 - - + -
58D GLY 2.8 15.9 + - - -
59D LEU* 3.0 14.9 + - - -
61D ALA* 1.3 75.2 - - - +
63D LEU* 1.3 54.4 + - - +
65D ASP* 3.3 2.8 + - - +
66D ASN* 2.8 37.5 + - - +
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Residues in contact with LEU 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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25D LEU* 3.7 33.2 - - + -
28D ILE* 3.9 16.6 - - + -
42D MET* 4.2 14.4 - - + -
55D LEU* 4.7 2.9 - - + -
59D LEU* 2.8 23.9 + - + +
60D THR* 3.4 10.8 - - - +
62D THR* 1.3 69.2 - - - +
64D VAL* 1.3 66.7 + - - +
67D ILE* 2.9 36.5 + - + +
100D ILE* 4.1 16.6 - - + -
102D ILE* 4.0 23.1 - - + -
120D LEU* 4.0 25.4 - - + -
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Residues in contact with VAL 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 THR* 2.9 23.0 + - + +
61D ALA* 3.6 7.9 - - - +
63D LEU* 1.3 74.4 - - - +
65D ASP* 1.3 56.1 + - - +
68D SER* 2.7 36.2 + - - -
86D MET* 3.7 24.7 - - + -
88D ILE* 4.4 13.5 - - + -
118D VAL* 3.6 26.3 - - + +
120D LEU* 4.0 21.8 - - + -
132D GLY* 4.3 21.1 - - - +
134D HIS* 4.5 7.6 - - + -
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Residues in contact with ASP 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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56C HIS* 3.8 9.5 + - - -
57C GLY* 3.5 11.4 + - - -
58C GLY 3.3 23.3 + - - +
90C TYR* 4.9 0.5 + - - -
151C CL 4.2 1.0 - - - +
61D ALA 2.9 17.1 + - - +
62D THR* 3.4 8.1 - - - +
64D VAL* 1.3 76.4 - - - +
66D ASN* 1.3 63.0 + - - +
68D SER* 3.1 3.5 + - - -
69D THR* 2.8 36.2 + - - -
83D SER* 3.7 9.3 + - - -
86D MET* 4.0 10.6 - - + +
134D HIS* 3.2 25.8 - - - -
136D LYS* 4.7 1.2 + - - -
149D UOC 5.1 2.3 - - - +
150D COA 5.9 0.4 - - - -
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Residues in contact with ASN 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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56C HIS* 3.1 34.4 + - - -
15D MET* 3.3 19.1 - - - +
22D GLU* 3.0 19.9 + - - +
25D LEU* 3.6 22.6 - - + +
62D THR* 2.8 22.8 + - - +
65D ASP* 1.3 77.4 + - - +
67D ILE* 1.3 59.1 + - - +
69D THR* 3.1 7.4 + - - -
70D MET* 2.9 37.7 + - + +
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Residues in contact with ILE 67 (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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25D LEU* 4.1 9.6 - - + -
28D ILE* 3.6 20.0 - - + -
38D VAL* 3.8 23.9 - - + +
40D CYS* 4.0 8.3 - - + -
63D LEU* 2.9 28.8 + - + +
66D ASN* 1.3 73.0 - - - +
68D SER* 1.3 65.7 + - - +
70D MET* 3.3 30.4 + - + +
71D ALA* 3.0 17.8 + - - +
102D ILE* 3.7 38.4 - - + +
104D ALA* 3.5 18.4 - - + +
118D VAL* 5.1 0.7 - - + -
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Residues in contact with SER 68 (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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64D VAL 2.7 25.5 + - - -
65D ASP 3.1 2.4 + - - -
67D ILE* 1.3 77.7 - - - +
69D THR* 1.3 61.4 + - - +
71D ALA* 3.1 5.0 + - - +
72D LEU* 3.1 25.1 + - - +
104D ALA* 3.8 10.6 - - - +
116D THR* 3.1 36.1 + - - -
118D VAL* 3.7 9.6 - - - +
134D HIS* 2.7 25.0 + - - -
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Residues in contact with THR 69 (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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65D ASP* 2.8 27.4 + - - -
66D ASN* 3.1 9.6 + - - -
68D SER* 1.3 75.7 + - - +
70D MET* 1.3 56.5 + - - +
72D LEU* 3.1 11.4 + - - +
73D LEU* 3.0 31.7 + - + +
80D PRO* 3.9 22.4 - - + +
136D LYS* 2.8 37.0 + - - +
149D UOC 4.3 15.5 - - + -
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Residues in contact with MET 70 (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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8D LEU* 4.0 28.4 - - + +
11D VAL* 5.9 2.0 - - + -
12D ILE* 4.1 21.5 - - + -
15D MET* 4.0 31.4 - - + -
28D ILE* 4.0 10.8 - - + -
38D VAL* 3.8 6.7 - - + -
40D CYS* 4.5 6.1 - - - -
66D ASN* 2.9 20.2 + - + +
67D ILE* 3.4 40.2 - - + +
69D THR* 1.3 75.8 - - + +
71D ALA* 1.3 61.5 + - - +
73D LEU* 3.1 25.7 + - + +
74D CYS* 3.2 17.5 + - - -
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Residues in contact with ALA 71 (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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36D GLY* 3.7 18.0 - - - +
38D VAL* 3.6 18.1 - - + +
67D ILE 3.0 12.0 + - - +
68D SER* 3.1 10.0 + - - +
70D MET* 1.3 75.0 - - - +
72D LEU* 1.3 61.7 + - - +
74D CYS* 3.2 15.4 + - - +
75D THR* 3.5 13.2 - - - +
104D ALA* 4.1 17.9 - - + +
105D HIS 4.8 0.4 - - - -
106D VAL* 3.8 15.7 - - + +
116D THR* 4.9 0.2 - - - +
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Residues in contact with LEU 72 (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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68D SER 3.1 16.0 + - - +
69D THR* 3.1 8.5 + - - +
71D ALA* 1.3 73.0 - - - +
73D LEU* 1.3 62.1 + - - +
74D CYS 3.0 1.3 - - - -
75D THR* 2.7 32.0 + - + +
78D GLY* 3.6 7.3 - - - -
79D ALA 3.7 17.1 - - - +
80D PRO* 3.8 10.1 - - + +
106D VAL* 3.8 24.7 - - + -
109D GLN* 4.8 5.4 - - - +
114D ALA* 3.5 32.8 - - + -
115D PHE 5.5 0.7 - - - +
116D THR* 5.4 8.3 - - - -
136D LYS* 3.7 35.2 - - + -
138D LEU* 4.9 3.6 - - + -
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Residues in contact with LEU 73 (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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4D MET* 5.2 1.2 - - - +
8D LEU* 4.7 13.7 - - + -
11D VAL* 5.4 8.1 - - + -
69D THR* 3.0 22.9 + - + +
70D MET* 3.1 20.4 + - + +
72D LEU* 1.3 75.6 - - - +
74D CYS* 1.3 59.3 + - - +
75D THR 3.3 6.2 + - - +
78D GLY* 3.6 28.6 - - - +
80D PRO* 4.0 24.0 - - + -
149D UOC 4.3 31.4 - - + -
10E GLU* 5.0 6.5 - - + -
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Residues in contact with CYS 74 (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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4D MET* 3.7 39.9 - - - +
8D LEU* 3.9 26.5 - - - -
33D ALA* 4.1 5.4 - - - -
34D ALA 3.5 16.2 - - - +
35D PRO* 3.0 10.2 - - - +
36D GLY 2.9 18.7 + - - -
38D VAL* 4.1 3.6 - - - -
70D MET 3.2 15.4 + - - +
71D ALA* 3.2 13.8 + - - +
72D LEU 3.0 1.4 - - - -
73D LEU* 1.3 77.3 - - - +
75D THR* 1.3 57.2 + - - +
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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
------------------------------------------------------------
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