Contacts of the helix formed by residues 56 - 77 (chain D) in PDB entry 4P5K
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 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D VAL* 4.0 20.7 - - + +
39D LYS 3.7 22.9 - - - +
40D GLU* 4.0 2.0 - - - -
41D THR* 3.5 28.9 - - - +
54D PHE* 3.0 6.4 + - - -
55D GLU* 1.3 76.9 + - - +
57D GLN* 1.3 58.5 + - - +
58D GLY 2.8 7.4 + - - -
59D GLY* 3.0 14.6 + - - -
60D LEU* 3.6 8.8 + - + +
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Residues in contact with GLN 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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55D GLU* 2.9 19.2 + - + +
56D ALA* 1.3 72.7 - - - +
58D GLY* 1.3 56.3 + - - +
59D GLY 3.5 0.4 - - - -
60D LEU* 3.8 26.9 - - + +
61D ALA* 3.2 24.1 + - - +
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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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22D PHE* 4.9 0.4 - - - -
54D PHE* 4.7 7.0 - - - -
55D GLU* 3.2 9.3 + - - +
56D ALA 2.8 4.2 + - - -
57D GLN* 1.3 76.3 - - - +
59D GLY* 1.3 57.4 + - - -
61D ALA* 3.5 8.0 - - - +
62D ASN* 3.0 32.2 + - - +
-21E THR* 5.2 6.5 - - - +
-19E LEU* 4.7 4.9 - - - +
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Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 3.6 37.2 - - - -
34D VAL* 4.5 1.8 - - - -
36D LEU* 5.3 1.1 - - - -
54D PHE* 4.2 6.5 - - - -
56D ALA 3.0 8.5 + - - -
58D GLY* 1.3 72.3 - - - +
60D LEU* 1.3 55.6 + - - +
62D ASN* 2.9 2.9 + - - +
63D ILE* 2.7 43.4 + - - +
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Residues in contact with LEU 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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34D VAL* 4.4 8.9 - - + +
36D LEU* 3.8 28.7 - - + +
39D LYS* 3.9 40.2 - - + +
56D ALA* 3.6 9.9 + - + +
57D GLN* 3.8 33.9 - - + +
59D GLY* 1.3 74.6 - - - +
61D ALA* 1.3 63.3 + - - +
63D ILE* 3.3 7.1 + - + +
64D ALA* 3.0 23.7 + - - +
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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
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57D GLN 3.2 13.3 + - - +
58D GLY* 3.5 11.4 - - - +
59D GLY 3.1 0.4 - - - -
60D LEU* 1.3 78.1 - - - +
62D ASN* 1.3 59.6 + - - +
64D ALA* 3.0 9.9 + - - +
65D ILE* 2.9 33.3 + - + +
-19E LEU* 3.9 20.0 - - + -
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Residues in contact with ASN 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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11D ALA* 5.9 0.2 - - + -
22D PHE* 3.9 19.5 - - + -
58D GLY 3.0 15.9 + - - +
59D GLY 2.9 5.3 + - - +
61D ALA* 1.3 74.7 - - - +
63D ILE* 1.3 60.1 + - - +
65D ILE* 3.4 9.3 + - - +
66D LEU* 2.8 33.7 + - - +
-21E THR* 3.7 16.6 - - - +
-20E GLN 2.7 24.6 + - - -
-19E LEU* 3.3 9.5 - - - +
-18E PHE* 3.1 37.4 + - + -
13E GLN* 4.0 6.3 + - - -
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Residues in contact with ILE 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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11D ALA* 4.3 7.2 - - + -
12D PHE 3.7 11.9 - - - +
13D VAL* 3.6 10.8 - - + +
19D THR* 5.5 3.4 - - + -
20D GLY* 4.8 2.5 - - - -
21D GLU 3.3 37.9 - - - +
22D PHE* 3.8 12.6 - - + -
36D LEU* 4.1 24.9 - - + -
59D GLY 2.7 22.3 + - - +
60D LEU* 3.7 7.2 - - + +
62D ASN* 1.3 71.3 - - - +
64D ALA* 1.3 55.8 + - - +
66D LEU* 3.4 1.5 + - + -
67D ASN* 2.8 54.8 + - - +
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Residues in contact with ALA 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 LEU 3.0 14.5 + - - +
61D ALA* 3.3 11.7 - - - +
63D ILE* 1.3 75.9 - - - +
65D ILE* 1.3 65.2 + - + +
67D ASN* 3.4 9.4 + - - +
68D ASN* 3.1 30.2 + - - +
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Residues in contact with ILE 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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61D ALA* 2.9 15.7 + - + +
62D ASN* 3.6 22.7 - - - +
63D ILE 3.3 0.2 - - - -
64D ALA* 1.3 75.7 - - + +
66D LEU* 1.3 60.1 + - - +
68D ASN* 2.8 27.3 + - - +
69D ASN* 2.9 13.2 + - - +
-19E LEU* 4.0 20.0 - - + -
-18E PHE* 3.4 33.9 - - + +
-17E HIS 3.6 26.7 - - - +
-16E THR* 4.1 16.2 - - + -
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Residues in contact with LEU 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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11D ALA* 3.7 43.1 - - + +
12D PHE* 4.2 8.1 - - - +
13D VAL* 3.8 12.6 - - + -
62D ASN 2.8 23.8 + - - +
63D ILE* 3.7 5.4 - - + +
65D ILE* 1.3 72.0 - - - +
67D ASN* 1.3 53.1 + - - +
69D ASN* 3.3 10.5 + - - +
70D LEU* 2.8 33.5 + - - +
-18E PHE* 4.0 34.1 - - + -
9E PHE* 3.5 34.9 - - + +
11E GLY 4.4 4.5 - - - +
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Residues in contact with ASN 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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13D VAL* 2.7 29.9 - - - +
14D GLN 5.4 0.3 - - - +
19D THR* 5.3 7.8 - - - +
63D ILE* 2.8 45.3 + - - +
64D ALA* 3.5 9.2 - - - +
66D LEU* 1.3 73.1 - - - +
68D ASN* 1.3 69.9 + - - +
70D LEU* 3.3 9.6 + - - +
71D ASN* 3.3 27.9 + - - +
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Residues in contact with ASN 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 ALA* 3.1 17.2 + - - +
65D ILE* 2.8 17.5 + - - +
67D ASN* 1.3 72.0 - - - +
69D ASN* 1.3 66.8 + - - +
71D ASN* 3.2 13.9 + - - +
72D THR* 3.0 24.6 + - - +
-16E THR* 4.5 17.5 - - + +
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Residues in contact with ASN 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 ILE* 2.9 13.6 + - - +
66D LEU* 3.6 13.4 - - - +
68D ASN* 1.3 77.2 - - - +
70D LEU* 1.3 57.7 + - - +
72D THR* 3.1 8.3 + - - -
73D LEU* 2.8 33.2 + - - +
-17E HIS 2.9 17.4 - - - +
-16E THR* 3.4 10.1 - - - +
-15E ILE* 2.9 39.9 + - + +
9E PHE* 3.6 34.9 - - + -
28E TYR* 4.0 8.5 - - - -
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Residues in contact with LEU 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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13D VAL* 3.5 28.9 - - + +
14D GLN* 4.1 14.1 - - - +
15D THR* 4.7 8.1 - - + -
66D LEU 2.8 15.0 + - - +
67D ASN* 3.3 14.4 - - - +
68D ASN 3.1 0.4 - - - -
69D ASN* 1.3 75.4 - - - +
71D ASN* 1.3 61.2 + - - +
73D LEU* 3.1 4.0 + - - +
74D ILE* 2.9 45.0 + - + +
7E TYR* 3.8 6.1 - - + +
8E LEU* 3.6 19.5 - - - +
9E PHE* 3.6 33.7 - - + +
30E TYR* 4.9 4.0 - - + -
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Residues in contact with ASN 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 ASN* 3.3 15.7 + - - +
68D ASN* 3.2 14.3 + - - +
70D LEU* 1.3 77.6 - - - +
72D THR* 1.3 63.1 + - - +
73D LEU 3.2 0.5 + - - -
74D ILE* 3.3 17.4 + - - +
75D GLN* 2.7 44.9 + - - +
-12E GLY* 5.6 0.2 - - - -
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Residues in contact with THR 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 ASN* 3.0 15.8 + - - +
69D ASN* 3.3 10.8 - - - -
71D ASN* 1.3 76.0 - - - +
73D LEU* 1.3 61.4 + - + +
75D GLN* 3.4 4.5 + - - +
76D ARG* 3.2 33.4 + - + +
-15E ILE* 3.6 41.4 + - + +
-14E THR 4.0 5.2 - - - +
-13E GLY* 4.0 1.6 - - - +
-12E GLY* 3.4 34.8 + - - +
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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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69D ASN 2.8 21.2 + - - +
70D LEU 3.9 1.8 - - - +
72D THR* 1.3 85.8 - - + +
74D ILE* 1.3 56.8 + - - +
75D GLN 3.0 1.3 - - - -
76D ARG* 4.2 13.5 - - + +
77D SER* 2.7 38.3 + - - -
-15E ILE* 4.2 15.5 - - + -
9E PHE* 3.9 15.3 - - + -
30E TYR* 3.6 28.7 - - + -
35E PHE* 3.5 36.6 - - + -
51E LEU* 3.6 24.2 - - + -
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Residues in contact with ILE 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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15D THR* 4.6 7.4 - - + -
70D LEU* 2.9 36.1 + - + +
71D ASN* 3.3 19.7 + - - +
73D LEU* 1.3 75.5 - - - +
75D GLN* 1.3 66.6 + - - +
77D SER* 3.3 4.7 + - - -
79D HIS* 2.9 69.9 + - + +
7E TYR* 3.7 42.6 - - + -
30E TYR* 4.2 4.9 - - + +
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Residues in contact with GLN 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 ASN* 2.7 42.4 + - - +
72D THR* 3.7 8.5 - - - +
74D ILE* 1.3 86.5 - - - +
76D ARG* 1.3 67.0 + - + +
78D ASN* 3.3 18.7 + - - +
79D HIS* 4.3 15.3 + - - -
-12E GLY* 4.5 14.6 - - - -
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Residues in contact with ARG 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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72D THR* 3.2 22.3 + - + +
73D LEU* 3.3 13.8 + - + +
75D GLN* 1.3 73.5 - - + +
77D SER* 1.3 59.0 + - - +
78D ASN* 2.9 20.3 + - - +
-15E ILE* 3.4 17.9 - - - +
-14E THR 3.4 22.6 + - - -
-13E GLY* 4.9 12.8 - - - -
35E PHE* 4.0 10.5 - - - -
51E LEU* 3.3 37.1 + - + +
54E PRO* 4.3 16.7 - - - +
55E ASP* 2.8 30.1 + - - -
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Residues in contact with SER 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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73D LEU* 2.7 23.1 + - - +
74D ILE 3.3 5.4 + - - -
76D ARG* 1.3 75.1 - - - +
78D ASN* 1.3 65.4 + - - +
80D THR* 2.7 36.9 + - - -
30E TYR* 2.9 39.8 + - - -
51E LEU* 4.9 11.1 - - - +
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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
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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