Contacts of the helix formed by residues 58 - 77 (chain D) in PDB entry 2E52
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 THR 58 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLN 6.1 1.1 - - - +
20D PHE* 4.2 10.1 - - + -
57D SER* 1.3 72.1 - - - +
59D GLN* 1.3 59.9 + - + +
61D LYS* 3.1 8.1 + - - +
62D LEU* 2.8 42.4 + - + +
10F G 3.6 20.9 + - - -
11F G 2.7 28.7 + - - +
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Residues in contact with GLN 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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12D ILE* 4.0 24.3 - - + +
13D GLU* 4.0 30.4 - - - +
16D THR* 4.4 15.2 - - + +
52D ALA 4.9 2.4 - - - +
53D ILE* 3.7 29.4 - - + +
54D LYS 5.1 1.6 + - - -
57D SER* 3.2 10.1 + - - +
58D THR* 1.3 79.9 - - + +
60D GLU* 1.3 55.2 + - - +
62D LEU* 3.7 5.9 - - + +
63D PHE* 2.8 29.3 + - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 4.1 13.8 - - + +
53D ILE* 3.3 10.5 - - + +
54D LYS 3.8 5.2 - - - +
55D PRO* 3.4 4.2 - - - +
56D SER* 2.7 27.7 + - - -
57D SER* 3.1 22.4 + - - +
59D GLN* 1.3 75.3 - - - +
61D LYS* 1.3 59.4 + - + +
63D PHE* 3.2 5.1 + - - +
64D SER* 2.9 28.9 + - - -
113D ARG* 2.8 36.7 + - - -
5H A 4.4 10.5 - - + +
6H G 3.3 35.4 + - - +
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Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 3.9 16.6 - - + -
56D SER* 2.9 31.7 + - - +
57D SER 3.2 4.8 + - - +
58D THR* 3.1 8.8 + - - +
60D GLU* 1.3 77.0 + - + +
62D LEU* 1.4 57.5 + - - +
64D SER* 3.1 8.5 + - - -
65D LYS* 2.9 29.1 + - - +
88D ARG* 4.0 20.8 + - - +
9F T 2.8 30.0 + - - -
10F G 3.5 25.4 + - - -
11F G 4.2 16.4 - - - +
4H A 4.1 17.9 - - - -
5H A 4.2 14.2 + - + +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 4.3 26.5 - - + +
15D LEU* 4.5 18.8 - - + +
16D THR* 6.3 0.2 - - - -
20D PHE* 3.5 25.5 - - + -
23D ALA* 3.6 34.3 - - + -
24D THR* 4.5 2.9 - - - +
27D LEU* 3.7 23.5 - - + +
58D THR* 2.8 30.1 + - + +
59D GLN* 3.7 9.0 - - + +
61D LYS* 1.4 74.8 - - - +
63D PHE* 1.3 59.5 + - - +
65D LYS* 3.3 3.9 + - + +
66D ALA* 2.8 29.1 + - - +
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 4.1 12.3 - - + -
8D LEU* 4.3 2.2 - - + -
9D LEU* 3.7 28.5 - - + -
12D ILE* 3.8 14.4 - - + +
45D SER 4.3 2.0 - - - -
46D ILE* 3.3 50.1 - - + +
48D ILE 3.4 23.8 - - - -
49D LEU* 3.5 24.7 - - + -
50D PRO* 3.7 16.8 - - + -
53D ILE* 3.9 9.0 - - + -
59D GLN 2.8 21.3 + - - +
60D GLU 3.6 4.5 - - - +
62D LEU* 1.3 72.7 - - - +
64D SER* 1.3 62.5 + - - +
66D ALA* 3.3 6.6 - - - +
67D GLY* 3.1 15.8 + - - -
111D SER* 4.4 3.8 - - - -
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Residues in contact with SER 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 5.8 1.6 - - - -
60D GLU 2.9 18.0 + - - -
61D LYS* 3.1 15.4 + - - -
63D PHE* 1.3 76.9 - - - +
65D LYS* 1.3 59.9 + - - +
67D GLY* 3.0 16.7 + - - +
68D ASP* 3.1 19.4 + - - +
88D ARG* 5.0 0.3 + - - -
109D ALA* 5.0 3.6 - - - +
111D SER* 5.2 4.9 - - - -
5H A 3.2 39.4 + - - -
6H G 3.8 11.2 - - - -
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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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20D PHE* 4.3 10.5 - - + -
24D THR* 3.8 42.6 - - + +
27D LEU* 4.6 4.3 - - + -
61D LYS 2.9 19.1 + - - +
62D LEU* 3.3 9.4 + - - +
64D SER* 1.3 72.3 + - - +
66D ALA* 1.3 66.4 + - - +
68D ASP* 3.1 24.6 + - + +
69D ILE* 3.0 34.4 + - + +
84D PRO* 4.3 10.5 - - + +
85D LEU 2.9 29.9 + - - -
86D GLU* 4.4 8.0 + - - +
88D ARG* 4.4 18.5 - - - +
12F C 5.6 2.5 - - - -
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Residues in contact with ALA 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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8D LEU* 4.0 28.7 - - + -
27D LEU* 4.2 5.7 - - + +
31D ILE* 4.1 12.1 - - + -
46D ILE* 4.1 11.4 - - + -
62D LEU 2.8 13.9 + - - +
63D PHE* 3.3 13.0 - - - +
65D LYS* 1.3 76.0 - - - +
67D GLY* 1.3 55.4 + - - +
69D ILE* 3.7 5.6 - - - +
70D VAL* 2.8 34.5 + - - +
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 3.6 25.7 - - - +
63D PHE 3.1 9.0 + - - -
64D SER* 3.0 10.8 + - - -
66D ALA* 1.3 72.9 - - - +
68D ASP* 1.3 58.6 + - - +
70D VAL* 3.8 0.7 - - - +
71D LEU* 2.8 30.7 + - - +
109D ALA* 3.8 9.4 - - - -
111D SER* 5.7 1.6 - - - -
169D TRP* 3.5 8.8 - - - -
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D SER* 3.1 15.0 + - - +
65D LYS* 3.1 25.1 + - + +
67D GLY* 1.3 75.5 - - - +
69D ILE* 1.3 58.5 + - - +
71D LEU 3.3 0.5 + - - -
72D ALA* 2.9 26.0 + - - +
84D PRO* 4.1 14.3 - - + +
88D ARG* 5.5 3.3 + - - -
93D ASP* 3.2 32.5 - - - +
94D VAL* 3.2 24.9 - - + +
109D ALA* 3.2 20.7 - - - +
5H A 5.7 2.8 - - - +
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Residues in contact with ILE 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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24D THR* 4.0 4.9 - - + +
27D LEU* 3.6 29.2 - - + -
28D ILE* 3.7 28.7 - - + -
31D ILE* 3.7 22.9 - - + -
32D TYR* 3.6 23.5 - - + -
65D LYS* 3.0 35.2 + - + +
66D ALA* 3.3 6.5 + - - +
68D ASP* 1.3 72.3 - - - +
70D VAL* 1.3 62.2 + - - +
72D ALA* 3.3 3.1 + - - +
73D LYS* 2.9 27.4 + - - +
84D PRO* 4.0 18.2 - - + -
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE* 3.8 27.6 - - + -
39D VAL* 4.7 4.3 - - + +
42D LEU* 3.8 27.4 - - + -
43D VAL* 3.6 39.9 - - + +
46D ILE* 4.1 15.7 - - + -
66D ALA 2.8 22.3 + - - +
67D GLY* 3.8 5.2 - - - +
69D ILE* 1.3 76.4 - - - +
71D LEU* 1.3 58.5 + - - +
73D LYS* 3.6 2.2 - - - +
74D ALA* 2.8 28.4 + - - +
169D TRP* 4.4 2.9 - - + -
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Residues in contact with LEU 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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67D GLY 2.8 19.1 + - - +
68D ASP* 3.6 5.4 - - - +
70D VAL* 1.3 76.4 - - - +
72D ALA* 1.3 61.7 + - - +
74D ALA* 3.2 3.3 + - - +
75D PHE* 2.9 49.3 + - + -
94D VAL* 4.1 10.1 - - + -
107D ALA* 4.0 16.8 - - + -
108D ASP 3.8 22.4 - - - +
109D ALA* 3.9 13.7 - - + -
142D THR* 3.9 19.7 - - - +
167D PHE* 5.9 0.4 - - + -
169D TRP* 4.1 8.5 - - + -
172D LEU* 3.6 26.2 - - + -
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Residues in contact with ALA 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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32D TYR* 3.7 17.3 - - - +
68D ASP 2.9 17.5 + - - +
69D ILE 3.7 3.8 - - - +
71D LEU* 1.3 76.6 - - - +
73D LYS* 1.3 62.1 + - - +
75D PHE* 3.2 4.2 + - - +
76D GLN* 3.0 28.5 + - - +
82D SER* 3.4 22.2 - - - +
83D LYS* 3.8 22.0 - - - +
84D PRO* 3.8 2.5 - - + -
94D VAL* 4.2 3.3 - - + +
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Residues in contact with LYS 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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31D ILE* 4.1 10.8 - - + +
32D TYR* 3.0 50.2 + - + +
34D LEU 4.1 15.3 + - - -
39D VAL* 3.9 26.5 - - + -
69D ILE 2.9 17.4 + - - +
70D VAL* 3.6 4.3 - - - +
72D ALA* 1.3 75.9 - - - +
74D ALA* 1.3 61.4 + - - +
76D GLN* 3.2 27.4 + - - +
77D LEU* 3.0 40.2 + - + +
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Residues in contact with ALA 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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39D VAL* 4.7 2.4 - - + +
43D VAL* 4.2 5.8 - - + -
70D VAL 2.8 20.9 + - - +
71D LEU 3.6 4.9 - - - +
73D LYS* 1.3 73.3 - - - +
75D PHE* 1.3 63.3 + - - +
77D LEU* 3.1 8.0 + - - +
78D LEU* 3.0 25.3 + - - +
172D LEU* 3.7 29.6 - - + -
176D LEU* 3.8 24.7 - - + +
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Residues in contact with PHE 75 (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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71D LEU* 2.9 48.3 + - + -
72D ALA 3.5 6.7 - - - +
74D ALA* 1.3 75.2 - - - +
76D GLN* 1.3 62.9 + - - +
78D LEU* 3.1 26.5 + - + +
79D ASN 3.4 0.2 + - - -
80D LEU* 3.0 30.8 + - + +
82D SER* 3.5 25.1 - - - -
94D VAL* 3.9 6.5 - - + -
96D ALA* 4.0 11.9 - - + -
105D LEU* 3.8 23.1 - - + -
107D ALA* 3.9 18.2 - - + -
140D VAL* 4.8 6.7 - - + -
142D THR* 5.1 0.2 - - - -
167D PHE* 5.5 1.8 - + - -
172D LEU* 5.5 3.6 - - + -
192D TRP* 3.7 31.2 - + - -
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Residues in contact with GLN 76 (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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32D TYR* 3.4 31.2 + - - -
72D ALA 3.0 16.5 + - - +
73D LYS* 3.4 31.5 + - + +
75D PHE* 1.3 75.5 - - - +
77D LEU* 1.3 59.1 + - + +
79D ASN* 2.9 22.5 + - - +
80D LEU 3.3 15.9 + - - +
81D ASN* 5.1 0.7 - - - +
82D SER 2.9 33.2 + - - +
99D LYS* 5.0 2.4 + - - -
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Residues in contact with LEU 77 (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 ARG* 4.1 42.7 + - + +
39D VAL* 3.8 37.5 - - + -
73D LYS* 3.0 35.6 + - + +
74D ALA* 3.1 7.8 + - - +
76D GLN* 1.3 72.3 - - + +
78D LEU* 1.3 58.6 + - - +
79D ASN 3.1 6.0 + - - -
176D LEU* 3.6 19.9 - - + +
180D LEU 4.5 2.6 - - - +
181D GLU* 3.9 19.5 - - - +
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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