Contacts of the helix formed by residues 41 - 64 (chain D) in PDB entry 3H90
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 ALA 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D ILE* 5.5 0.6 - - + +
40D LEU* 1.3 75.3 - - - +
42D ALA* 1.3 55.4 + - - +
43D LEU* 2.9 17.5 + - - -
44D VAL* 3.1 28.5 + - + +
45D ASP* 3.8 2.6 + - - +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 4.2 14.2 + - - -
40D LEU* 3.4 14.5 - - + +
41D ALA* 1.3 74.7 - - - +
43D LEU* 1.3 57.7 - - - +
44D VAL 3.5 0.2 - - - -
45D ASP* 3.7 24.6 - - + +
46D SER* 4.0 4.3 + - - -
121D THR* 6.0 3.1 - - + -
160D MET* 4.7 19.3 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 4.0 14.5 - - + +
31D TRP* 3.8 46.9 - - + +
40D LEU 3.3 25.3 + - - +
41D ALA* 2.9 4.2 - - - -
42D ALA* 1.3 77.0 - - - +
44D VAL* 1.3 74.9 + - + +
45D ASP 3.3 0.4 - - - -
46D SER* 3.6 8.7 + - - -
47D LEU* 3.2 29.8 + - + +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ALA* 3.1 21.5 + - + +
43D LEU* 1.3 90.8 - - + +
45D ASP* 1.3 55.5 + - - +
47D LEU* 3.4 17.9 - - + +
48D VAL* 2.7 46.3 + - + +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 5.1 6.3 + - - -
41D ALA 3.8 2.8 + - - +
42D ALA* 3.7 24.6 - - + +
44D VAL* 1.3 78.7 - - - +
46D SER* 1.3 57.6 + - - +
48D VAL* 3.5 7.4 - - - +
49D ASP* 2.8 25.1 + - - +
153D HIS* 4.0 6.1 - - - -
157D ASP* 3.8 10.4 - - - +
160D MET* 5.3 5.9 - - - +
293D ZN 2.7 29.7 - - - -
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Residues in contact with SER 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 3.4 39.9 - - - +
27D LYS* 4.0 21.9 + - - -
28D ILE* 3.5 26.9 + - - +
42D ALA 4.0 2.1 + - - -
43D LEU* 3.6 8.7 + - - -
44D VAL 3.2 0.2 - - - -
45D ASP* 1.3 77.1 - - - +
47D LEU* 1.3 62.9 + - - +
48D VAL 3.3 0.2 - - - -
49D ASP* 3.6 2.6 - - - +
50D ILE* 3.0 26.5 + - - +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 4.0 22.0 - - + -
43D LEU* 3.2 20.7 + - + +
44D VAL* 3.0 23.2 + - + +
46D SER* 1.3 73.6 + - - +
48D VAL* 1.3 66.9 + - + +
50D ILE* 3.0 30.8 - - + +
51D GLY* 3.6 2.4 + - - -
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D VAL* 2.7 28.7 + - + +
45D ASP* 3.5 11.0 - - - +
47D LEU* 1.3 76.7 - - + +
49D ASP* 1.3 59.7 + - - +
51D GLY* 2.9 5.9 + - - -
52D ALA* 2.7 43.8 + - + +
89D PHE* 6.6 0.2 - - + -
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D SER 5.6 0.2 - - - -
24D LEU* 3.0 33.0 - - + +
45D ASP* 2.8 16.8 + - - +
46D SER 3.6 2.2 - - - +
47D LEU 3.3 0.4 - - - -
48D VAL* 1.3 81.2 - - - +
50D ILE* 1.3 55.6 + - - +
52D ALA* 4.0 8.0 - - - +
53D SER* 2.7 37.9 + - - -
153D HIS* 2.8 22.2 + - - -
154D TYR* 3.1 12.4 - - - +
157D ASP* 3.0 1.6 - - - +
293D ZN 2.1 34.5 - - - -
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Residues in contact with ILE 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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21D SER 5.7 0.7 - - - -
22D LEU* 4.4 16.3 - - + +
24D LEU* 4.5 8.0 + - - +
25D LEU* 3.5 52.3 - - + +
28D ILE* 4.7 7.9 - - + -
46D SER 3.0 13.5 + - - +
47D LEU* 3.0 35.0 - - + +
49D ASP* 1.3 74.7 - - - +
51D GLY* 1.3 63.3 + - - +
53D SER* 5.2 0.7 - - - -
54D LEU* 3.0 33.6 + - + +
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Residues in contact with GLY 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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47D LEU 3.6 2.2 + - - -
48D VAL 2.9 6.2 + - - -
50D ILE* 1.3 82.9 - - - +
52D ALA* 1.3 62.7 + - - +
54D LEU* 3.2 11.3 + - - +
55D THR* 2.8 30.2 + - - -
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Residues in contact with ALA 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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48D VAL* 2.7 31.2 + - + +
49D ASP* 3.8 9.9 - - - +
51D GLY* 1.3 74.0 - - - +
53D SER* 1.3 62.4 + - - +
55D THR* 3.3 8.6 + - - -
56D ASN* 3.2 18.5 + - - +
86D GLN* 6.1 0.2 - - - -
150D ASP* 5.4 2.0 - - - +
153D HIS* 6.5 0.9 - - + -
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Residues in contact with SER 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ALA* 4.3 3.8 - - - +
21D SER* 3.6 18.6 - - - -
22D LEU* 3.7 11.7 - - - +
49D ASP* 2.7 20.9 + - - -
52D ALA* 1.3 72.9 - - - +
54D LEU* 1.3 58.4 + - - +
56D ASN* 3.4 10.5 + - - +
57D LEU* 3.1 24.4 + - - +
150D ASP* 3.4 20.7 + - - +
154D TYR* 2.4 28.5 + - - -
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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
----------------------------------------------------------
22D LEU* 3.7 27.5 - - + +
50D ILE* 3.0 26.0 + - + +
51D GLY* 3.4 9.4 - - - +
53D SER* 1.3 74.7 - - - +
55D THR* 1.3 65.4 + - - +
57D LEU* 3.1 18.8 + - + +
58D LEU* 3.0 32.7 + - + +
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Residues in contact with THR 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 GLY 2.8 17.6 + - - -
52D ALA* 3.3 9.5 + - - -
54D LEU* 1.3 74.1 - - - +
56D ASN* 1.3 59.4 + - - +
58D LEU* 2.8 23.3 + - + +
59D VAL* 2.8 37.9 + - + +
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Residues in contact with ASN 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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18D ALA* 5.1 4.4 - - + +
52D ALA 3.2 9.4 + - - +
53D SER* 3.4 13.2 - - - +
55D THR* 1.3 78.8 - - - +
57D LEU* 1.3 55.7 + - - +
59D VAL* 3.8 4.6 - - - +
60D VAL* 2.9 43.5 + - - +
82D ALA* 4.4 10.5 - - - +
86D GLN* 3.0 31.9 + - - +
146D ALA* 3.3 14.7 + - - +
147D VAL* 4.9 2.0 - - - +
150D ASP* 3.2 27.3 + - - +
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA* 4.2 9.4 - - - +
18D ALA* 3.5 28.7 - - + +
19D MET* 4.3 20.4 - - + +
22D LEU* 4.5 8.7 - - + -
53D SER 3.1 11.3 + - - +
54D LEU* 3.1 28.4 + - + +
56D ASN* 1.3 72.1 - - - +
58D LEU* 1.3 63.0 + - + +
60D VAL* 3.3 11.5 - - + +
61D ARG* 3.0 67.6 + - - +
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LEU* 3.0 29.8 + - + +
55D THR* 2.8 21.2 + - + +
57D LEU* 1.3 78.0 - - + +
59D VAL* 1.3 59.3 + - + +
61D ARG* 3.4 7.6 + - - +
62D TYR* 3.0 24.4 + - - +
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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 THR* 2.8 29.7 + - + +
56D ASN* 4.0 5.2 - - - +
58D LEU* 1.3 75.5 - - + +
60D VAL* 1.3 59.8 + - + +
61D ARG 3.1 1.6 - - - -
62D TYR* 3.2 8.5 + - + +
63D SER* 2.8 25.8 + - - -
78D ALA* 3.5 33.8 - - + +
79D GLU* 5.4 0.9 - - - -
82D ALA* 3.8 19.3 - - + -
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Residues in contact with VAL 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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14D ILE* 3.6 26.5 - - + +
15D ALA* 4.6 7.9 - - + -
18D ALA* 4.2 15.5 - - + -
56D ASN* 2.9 40.4 + - - +
57D LEU* 3.3 20.9 - - + +
59D VAL* 1.3 72.7 - - + +
61D ARG* 1.3 65.4 + - + +
63D SER* 3.3 10.1 - - - -
64D LEU* 3.0 31.6 + - + +
79D GLU* 5.1 1.1 - - + -
146D ALA* 3.8 22.7 - - + -
147D VAL* 5.3 3.6 - - + -
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Residues in contact with ARG 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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15D ALA* 5.1 13.7 - - + +
19D MET* 3.4 34.4 - - - +
57D LEU* 3.0 41.6 + - - +
58D LEU* 3.5 8.1 - - - +
60D VAL* 1.3 78.3 - - + +
62D TYR* 1.3 64.9 + - - +
64D LEU* 3.5 15.1 + - + +
65D GLN* 3.7 12.7 + - - +
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Residues in contact with TYR 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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203B GLN* 4.5 7.5 + - - -
206B LEU* 4.3 18.8 - - + +
6D ZN 3.8 0.5 - - - -
58D LEU 3.0 13.7 + - - +
59D VAL* 3.3 12.8 - - + +
61D ARG* 1.3 73.2 - - - +
63D SER* 1.3 66.3 + - - +
64D LEU 3.0 1.2 + - - -
65D GLN* 3.1 47.7 + - - +
71D HIS* 3.2 30.1 + - - -
75D HIS* 3.3 31.0 + + + +
78D ALA* 4.0 15.9 - - + -
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Residues in contact with SER 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 5.3 0.2 - - - +
59D VAL 2.8 16.0 + - - -
60D VAL* 3.3 17.2 + - - +
62D TYR* 1.3 74.8 - - - +
64D LEU* 1.3 67.3 + - - +
65D GLN 3.5 2.6 + - - +
75D HIS* 3.4 34.8 + - - +
76D GLY* 3.8 7.3 + - - -
78D ALA* 4.3 5.1 - - - +
79D GLU* 3.3 34.8 + - - +
241D PRO* 5.1 1.7 - - - +
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Residues in contact with LEU 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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11D ARG* 4.3 37.5 - - + +
12D ALA* 5.9 0.2 - - - -
14D ILE* 4.0 22.0 - - + -
15D ALA* 4.8 12.6 - - + -
60D VAL* 3.0 24.9 + - + +
61D ARG* 3.5 9.2 + - + +
62D TYR 3.1 1.2 - - - -
63D SER* 1.3 85.9 - - - +
65D GLN* 1.3 67.7 + - - +
66D PRO* 3.4 5.2 - - - +
241D PRO* 4.8 7.4 - - + -
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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
------------------------------------------------------------
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