Contacts of the helix formed by residues 45 - 66 (chain D) in PDB entry 3EVK
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 LYS 45 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ASN* 3.7 38.1 - - + +
41D LEU* 2.9 35.4 + - + +
44D GLN* 1.3 105.1 - - + +
46D HIS* 1.3 59.5 + - - +
47D HIS 3.6 0.4 - - - -
48D GLN* 3.6 1.8 + - - +
49D GLY* 3.0 25.8 + - - -
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Residues in contact with HIS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B GLU* 4.1 5.4 + - - -
183B TYR* 2.8 37.9 + + - -
188B ASN* 3.6 21.9 - - + +
41D LEU* 3.0 19.6 + - + -
42D HIS* 3.2 22.0 - - + +
45D LYS* 1.3 76.3 - - - +
47D HIS* 1.3 65.7 + - - +
49D GLY* 3.4 9.4 + - - -
50D TYR* 3.1 30.6 + - + -
180D HIS* 3.6 41.3 + + + +
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Residues in contact with HIS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.6 10.9 - - + +
21D PRO* 3.7 17.2 - - + +
42D HIS 2.8 15.8 + - - +
43D HIS* 3.4 17.5 + - - +
46D HIS* 1.3 70.2 - - - +
48D GLN* 1.3 66.2 + - - +
50D TYR* 3.1 18.2 + + - +
51D VAL* 3.3 7.3 + - + +
86D GLY 4.5 0.2 - - - -
87D HIS* 3.0 42.3 + - - -
90D HIS* 3.4 24.8 - + + +
91D SER* 3.6 17.7 - - - -
94D TRP* 3.0 28.2 + - + -
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Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.4 32.8 - - + +
43D HIS 3.3 4.9 + - - +
44D GLN* 3.0 28.6 - - - +
45D LYS* 3.7 3.6 - - - +
46D HIS 3.3 0.2 - - - -
47D HIS* 1.3 78.4 - - - +
49D GLY* 1.3 62.6 + - - +
51D VAL* 3.1 14.3 + - - +
52D ASN* 2.7 60.2 + - - +
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Residues in contact with GLY 49 (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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45D LYS 3.0 18.1 + - - -
46D HIS 3.8 3.1 - - - -
47D HIS 3.3 0.6 - - - -
48D GLN* 1.3 75.5 - - - +
50D TYR* 1.3 59.2 + - - +
52D ASN* 3.4 8.7 + - - +
53D GLY* 2.8 26.3 + - - -
83D HIS* 4.0 4.8 + - - -
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Residues in contact with TYR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS* 3.1 29.8 + - + -
47D HIS* 3.1 13.4 + - - +
49D GLY* 1.3 75.0 - - - +
51D VAL* 1.3 59.8 + - - +
54D ALA* 2.9 30.8 + - - +
82D PHE* 3.8 15.7 - + - -
83D HIS* 3.4 39.3 - + - +
86D GLY* 3.9 12.3 - - - -
87D HIS* 3.8 9.4 - - - +
90D HIS* 3.4 30.5 - + - -
161D HIS* 3.0 31.1 + + - -
178D TRP* 4.2 6.6 - - - -
180D HIS* 3.7 20.4 - - - -
301D MN 4.4 0.9 - - - -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D TYR* 3.3 34.5 - - + +
19D THR* 3.8 7.4 - - - -
20D LEU* 3.9 26.7 - - + +
47D HIS* 3.5 13.2 - - + +
48D GLN* 3.1 12.7 + - - +
50D TYR* 1.3 75.2 - - - +
52D ASN* 1.3 68.7 + - - +
54D ALA* 3.3 5.7 + - - +
55D ASN* 3.0 29.0 + - - +
87D HIS* 3.7 27.4 - - - +
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Residues in contact with ASN 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLN* 2.7 41.8 + - - +
49D GLY* 3.7 9.6 - - - +
51D VAL* 1.3 77.8 - - - +
53D GLY* 1.3 58.5 + - - +
55D ASN* 3.4 6.7 + - - +
56D ALA* 2.9 31.0 + - - +
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Residues in contact with GLY 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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49D GLY 2.8 17.5 + - - -
51D VAL 3.3 0.2 - - - -
52D ASN* 1.3 69.5 - - - +
54D ALA* 1.3 64.6 + - - +
56D ALA* 3.4 6.5 + - - +
57D ALA* 3.1 22.7 + - - +
79D ASP* 5.5 0.5 - - - +
83D HIS* 3.6 34.1 + - - -
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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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18D TYR* 4.4 20.4 - - + -
50D TYR 2.9 18.3 + - - +
51D VAL* 3.6 6.1 - - - +
53D GLY* 1.3 76.6 - - - +
55D ASN* 1.3 58.3 + - - +
57D ALA* 3.2 5.8 + - - +
58D LEU* 3.0 31.9 + - - +
80D LEU* 4.1 11.9 - - + +
83D HIS* 3.4 12.9 - - + +
84D LEU* 4.2 16.2 - - + +
87D HIS* 5.4 1.3 - - + -
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Residues in contact with ASN 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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17D ARG* 3.4 35.9 + - - +
18D TYR* 2.8 54.0 + - - +
51D VAL* 3.0 23.9 + - - +
52D ASN* 3.9 6.9 + - - +
54D ALA* 1.3 75.5 - - - +
56D ALA* 1.3 57.3 + - - +
58D LEU* 3.3 3.9 + - - +
59D GLU* 3.0 29.1 + - - +
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Residues in contact with ALA 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 ASN 2.9 18.4 + - - +
53D GLY* 3.6 9.0 - - - +
55D ASN* 1.3 78.1 - - - +
57D ALA* 1.3 60.6 + - - +
59D GLU* 3.4 7.9 + - - +
60D LYS* 3.3 35.3 + - - +
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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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53D GLY 3.1 13.6 + - - +
54D ALA 3.5 8.3 - - - +
56D ALA* 1.3 73.4 - - - +
58D LEU* 1.3 64.9 + - - +
60D LYS* 3.2 10.0 + - - +
61D LEU* 3.0 27.5 + - - +
76D VAL* 3.5 15.9 - - + +
79D ASP* 4.5 6.3 - - + -
80D LEU* 3.9 35.4 - - + +
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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
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152A GLN* 4.4 7.9 - - - +
154A LEU* 3.8 28.9 - - + -
15D THR* 4.1 15.0 - - + +
16D LYS 3.4 25.1 - - - +
17D ARG* 3.9 15.0 - - - +
18D TYR* 3.6 22.9 - - + -
54D ALA 3.0 19.2 + - - +
55D ASN* 3.3 14.6 + - - +
57D ALA* 1.3 75.3 - - - +
59D GLU* 1.3 52.9 + - - +
61D LEU* 3.3 12.6 + - + +
62D GLU* 2.7 37.0 + - - +
65D ARG* 5.4 0.4 - - - +
80D LEU* 3.9 13.2 - - + -
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Residues in contact with GLU 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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17D ARG* 3.0 33.6 + - - +
55D ASN 3.0 12.9 + - - +
56D ALA* 3.5 12.8 - - - +
57D ALA 3.2 0.2 - - - -
58D LEU* 1.3 76.2 - - - +
60D LYS* 1.3 57.6 + - + +
62D GLU* 3.3 9.8 + - - +
63D LYS* 2.8 53.0 + - - +
66D LYS* 5.9 0.5 + - - -
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Residues in contact with LYS 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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72C ASP* 4.8 8.9 + - - +
56D ALA* 3.3 23.5 + - - +
57D ALA* 3.2 9.4 + - - +
59D GLU* 1.3 76.7 - - + +
61D LEU* 1.3 58.4 + - - +
63D LYS* 3.7 8.0 + - - +
64D PHE* 3.0 27.9 + - - +
69D ALA* 5.8 0.3 - - - +
70D GLN 5.1 2.3 - - - +
71D ILE* 3.6 7.7 - - + +
76D VAL* 3.8 31.2 - - + +
79D ASP* 4.3 15.6 + - - -
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Residues in contact with LEU 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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128A GLU* 4.0 10.5 - - - +
154A LEU* 5.5 0.4 - - + -
57D ALA 3.0 24.3 + - - +
58D LEU* 3.6 15.0 - - + +
60D LYS* 1.3 75.0 - - - +
62D GLU* 1.3 54.7 + - - +
64D PHE* 3.2 4.6 + - + +
65D ARG* 2.8 59.9 + - + +
71D ILE* 3.7 21.5 - - + -
73D ILE* 3.8 13.5 - - + -
76D VAL* 3.7 9.6 - - + -
77D LEU* 3.8 31.9 - - + -
80D LEU* 4.1 17.9 - - + -
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Residues in contact with GLU 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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13D VAL* 3.8 18.7 - - + +
14D THR* 4.6 0.9 - - - -
15D THR* 2.6 40.5 + - + +
17D ARG* 2.8 17.5 + - - -
58D LEU 2.7 20.1 + - - +
59D GLU* 3.3 10.7 + - - +
61D LEU* 1.3 68.8 - - - +
63D LYS* 1.3 65.2 + - - +
65D ARG* 3.2 11.3 + - - +
66D LYS* 3.1 60.5 + - - +
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Residues in contact with LYS 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 GLU* 2.8 39.7 + - - +
60D LYS* 3.7 8.5 - - - +
62D GLU* 1.3 75.5 - - - +
64D PHE* 1.3 59.1 + - - +
66D LYS* 3.5 4.2 + - - -
68D GLU* 3.1 66.3 + - + +
69D ALA* 3.4 27.7 + - + -
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Residues in contact with PHE 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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124A LYS* 3.3 37.5 + - + -
127A GLU* 4.3 21.1 - - + -
128A GLU* 3.8 40.2 - - + -
131A GLN* 5.6 7.2 - - + -
60D LYS 3.0 19.2 + - - +
61D LEU* 3.4 7.4 - - - +
62D GLU 3.2 0.2 - - - -
63D LYS* 1.3 76.4 - - - +
65D ARG* 1.3 55.6 + - - +
67D GLY* 2.8 23.3 + - - -
69D ALA* 3.6 21.9 - - - +
70D GLN* 4.5 8.7 - - - +
71D ILE* 3.5 45.3 - - + -
73D ILE* 4.8 2.5 - - + -
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Residues in contact with ARG 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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118A PHE* 2.7 45.3 + - - +
119A PHE* 3.6 32.4 - - + +
120A GLY* 5.5 0.3 - - - -
124A LYS* 3.4 30.8 - - + +
128A GLU* 3.3 31.7 + - - +
152A GLN* 5.5 1.0 + - - -
153A LEU 4.4 9.3 + - - -
154A LEU* 4.5 14.6 - - - +
155A ILE 5.1 1.0 - - - +
13D VAL* 3.7 26.3 - - + +
14D THR 3.7 1.8 + - - -
15D THR* 3.4 25.5 - - - +
58D LEU* 5.4 0.2 - - - +
61D LEU* 2.8 45.7 + - - +
62D GLU* 3.2 6.5 + - - +
64D PHE* 1.3 73.8 - - + +
66D LYS* 1.3 58.9 + - - +
67D GLY 3.2 0.4 - - - -
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Residues in contact with LYS 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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124A LYS* 4.9 0.2 - - - -
13D VAL* 3.9 29.4 + - + +
59D GLU* 5.9 0.4 + - - -
62D GLU* 3.1 48.8 + - - +
63D LYS* 3.8 6.5 - - - +
64D PHE 3.1 0.6 - - - -
65D ARG* 1.3 76.0 - - - +
67D GLY* 1.3 62.6 + - - +
68D GLU* 3.3 24.1 + - + +
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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