Contacts of the helix formed by residues 59 - 77 (chain D) in PDB entry 1PY1
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 GLN 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU* 3.7 28.4 - - + +
14C ILE* 4.5 1.8 - - - +
15C ASN* 2.9 43.8 + - - +
50C LEU* 4.2 16.8 - - + +
53C HIS* 6.0 0.8 + - - -
54C LYS* 4.1 9.5 - - - +
20D PRO* 3.7 14.7 - - + +
57D SER* 3.0 11.5 + - - +
58D PRO* 1.3 77.1 - - + +
60D GLU* 1.3 64.9 + - - +
61D TRP* 3.5 2.5 - - + +
62D GLU* 2.9 36.0 + - + +
63D ALA 3.3 5.2 + - - -
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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
----------------------------------------------------------
57D SER 5.0 0.7 - - - -
58D PRO 3.4 7.0 + - - +
59D GLN* 1.3 69.8 - - - +
61D TRP* 1.3 60.5 + - - +
62D GLU 2.9 0.9 + - - -
63D ALA* 3.0 6.8 + - - +
64D ILE* 2.8 57.8 + - + +
108D SER* 3.0 37.5 + - - +
110D LYS* 3.5 26.5 + - - +
111D VAL* 3.8 4.0 - - + -
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Residues in contact with TRP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASN 3.8 2.2 + - - -
20D PRO* 3.0 37.3 + - + -
22D ASN 2.9 26.4 + - - -
23D LYS 4.9 2.2 - - - -
24D GLU* 4.4 12.8 - - - -
25D LEU* 3.8 20.0 - - + -
59D GLN* 3.5 1.7 - - + -
60D GLU* 1.3 78.9 + - - +
62D GLU* 1.3 59.9 + - - +
64D ILE* 4.1 23.6 - - + -
65D GLN* 3.1 61.2 + - + +
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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
----------------------------------------------------------
53C HIS* 4.5 6.6 + - - -
54C LYS* 4.8 8.6 + - - -
18D THR* 3.5 24.6 + - - +
20D PRO* 3.9 23.1 - - + +
54D LYS* 3.4 40.0 + - + +
57D SER* 2.7 31.5 + - - +
59D GLN* 2.9 28.0 + - + +
61D TRP* 1.3 79.0 - - - +
63D ALA* 1.3 59.0 + - - +
66D ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS 3.3 12.9 + - - +
55D ILE* 3.2 28.1 - - - +
57D SER 4.1 14.4 - - - +
59D GLN 3.3 1.4 + - - +
60D GLU* 3.0 6.1 + - - +
62D GLU* 1.3 76.6 - - - +
64D ILE* 1.3 61.8 + - - +
66D ALA* 3.1 4.0 + - - +
67D LEU* 2.8 33.6 + - - +
111D VAL* 4.1 18.4 - - + -
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Residues in contact with ILE 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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25D LEU* 6.4 0.2 - - + -
60D GLU* 2.8 43.9 + - + +
61D TRP* 4.3 22.4 - - + +
63D ALA* 1.3 73.0 - - - +
65D GLN* 1.3 67.9 + - - +
67D LEU* 2.9 11.9 + - + +
68D THR* 2.9 26.7 + - - +
110D LYS* 3.5 33.2 - - + -
111D VAL* 3.8 17.3 - - + -
114D LYS* 5.7 7.1 - - + +
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Residues in contact with GLN 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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17D ALA 2.9 23.1 + - - +
18D THR* 3.5 20.1 - - - +
19D ASN 3.1 21.3 - - - +
22D ASN* 3.2 17.6 - - - +
24D GLU 4.3 3.8 + - - -
25D LEU* 3.9 18.5 - - + +
26D ASP 4.4 0.6 - - - +
30D ILE* 5.3 1.6 - - + +
61D TRP* 3.1 61.7 + - + +
62D GLU 4.0 0.7 - - - +
64D ILE* 1.3 80.9 - - - +
66D ALA* 1.3 56.9 - - - +
68D THR* 2.9 11.7 + - - -
69D VAL* 2.8 29.3 + - - +
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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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18D THR* 3.5 13.6 - - + +
51D LEU* 3.5 11.3 - - + +
54D LYS* 3.6 28.9 - - + -
55D ILE* 3.8 15.1 - - + +
62D GLU 3.0 17.1 + - - +
63D ALA 3.1 9.4 + - - +
65D GLN* 1.3 77.4 - - - +
67D LEU* 1.3 57.4 + - - +
69D VAL* 3.3 7.1 + - - +
70D LEU* 3.0 22.5 + - - +
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE* 3.6 33.9 - - + -
63D ALA 2.8 17.4 + - - +
64D ILE* 2.9 11.2 + - - +
66D ALA* 1.3 73.8 - - - +
68D THR* 1.3 57.4 + - - +
70D LEU* 2.8 18.5 + - + +
71D GLU* 2.6 36.5 + - - +
94D LEU* 4.8 0.4 - - + -
111D VAL* 3.7 23.6 - - + +
114D LYS* 3.6 32.3 - - + -
115D ILE* 3.5 30.3 - - + -
118D LEU* 4.2 8.6 - - + +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 4.0 30.0 - - + +
27D TRP* 4.3 17.3 - - + -
30D ILE* 4.3 10.1 - - + -
64D ILE* 2.9 20.2 + - - +
65D GLN* 2.9 12.3 + - - -
67D LEU* 1.3 75.9 - - - +
69D VAL* 1.3 58.0 + - - +
71D GLU* 3.7 15.3 + - - +
72D THR* 2.9 30.9 + - - +
114D LYS* 5.1 4.9 + - - +
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 4.0 3.6 - - + -
17D ALA* 4.0 17.0 - - + +
18D THR* 4.3 8.5 - - + -
30D ILE* 3.9 35.0 - - + -
33D PHE* 3.8 28.5 - - + -
34D CYS* 4.0 1.7 - - - -
51D LEU* 3.5 21.1 - - + -
65D GLN 2.8 15.3 + - - +
66D ALA* 3.4 9.4 - - - +
67D LEU 3.1 0.4 - - - -
68D THR* 1.3 76.5 - - - +
70D LEU* 1.3 57.6 + - - +
72D THR* 4.6 0.2 - - - -
73D CYS* 3.1 30.1 + - - -
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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
----------------------------------------------------------
51D LEU* 4.5 12.1 - - + -
55D ILE* 3.9 22.7 - - + -
66D ALA 3.0 12.7 + - - +
67D LEU* 2.8 19.2 + - + +
69D VAL* 1.3 76.7 - - - +
71D GLU* 1.3 65.9 + - - +
73D CYS* 3.5 1.8 + - - +
74D MET* 3.1 35.3 + - + +
81D PHE* 4.0 23.8 - - + -
85D VAL* 4.0 14.4 - - + -
90D PHE* 3.9 16.2 - - + -
94D LEU* 4.7 5.2 - - + -
118D LEU* 4.3 4.7 - - + -
122D TRP* 3.8 26.9 - - + -
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Residues in contact with GLU 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 LEU 2.6 18.4 + - - +
68D THR* 3.7 12.3 + - - +
70D LEU* 1.3 76.5 - - - +
72D THR* 1.3 66.2 + - - +
74D MET* 3.2 11.8 + - - +
75D LYS* 3.3 46.2 + - + +
114D LYS* 2.5 35.4 + - - -
118D LEU* 3.5 26.6 - - + +
122D TRP* 5.3 1.3 - - - +
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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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27D TRP* 3.3 33.5 - - + -
30D ILE* 4.2 6.5 - - + -
31D ASN* 3.9 19.5 - - - +
34D CYS* 3.9 15.0 - - - -
68D THR* 2.9 21.0 + - - +
69D VAL 4.2 2.0 - - - -
71D GLU* 1.3 79.7 - - - +
73D CYS* 1.3 62.6 + - - +
75D LYS* 3.3 10.2 + - - +
76D SER* 3.1 26.8 + - - +
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Residues in contact with CYS 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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33D PHE* 3.8 12.3 - - - -
34D CYS* 2.0 59.2 - - + -
37D LEU* 3.7 12.1 - - + -
51D LEU* 5.5 0.2 - - - -
69D VAL* 3.1 24.2 + - - +
71D GLU 3.4 0.2 - - - -
72D THR* 1.3 77.2 - - - +
74D MET* 1.3 63.3 + - - +
76D SER 4.5 0.2 - - - +
77D CYS* 3.0 29.9 + - - +
81D PHE* 3.4 25.2 - - + -
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Residues in contact with MET 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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70D LEU* 3.1 19.2 + - + +
71D GLU 3.2 8.9 + - - +
73D CYS* 1.3 76.9 - - - +
75D LYS* 1.3 64.8 + - + +
77D CYS 3.7 0.9 - - - +
81D PHE* 3.7 12.3 - - + -
82D HIS* 2.5 43.0 + - + +
85D VAL* 3.5 38.4 - - + -
122D TRP* 3.5 47.1 - - + +
126D LEU* 3.7 29.0 - - + +
132D ILE* 4.6 6.5 - - + -
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Residues in contact with LYS 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 GLU* 3.4 42.7 + - + +
72D THR* 3.3 9.6 + - - +
73D CYS 3.2 0.4 - - - -
74D MET* 1.3 82.6 - - + +
76D SER* 1.3 62.6 + - - +
77D CYS 3.9 2.8 - - - +
82D HIS* 5.2 0.5 + - - -
121D SER* 6.1 0.7 - - - -
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Residues in contact with SER 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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31D ASN* 4.7 5.7 + - - -
34D CYS* 4.8 7.4 - - - +
72D THR* 3.1 24.6 + - - +
73D CYS* 4.2 3.1 - - - -
75D LYS* 1.3 75.1 - - - +
77D CYS* 1.3 71.9 + - - +
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Residues in contact with CYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D CYS* 3.6 39.0 - - - -
37D LEU* 4.1 17.5 - - + -
38D ASN* 4.8 8.7 - - + +
73D CYS* 3.0 24.1 + - - +
74D MET 3.7 1.9 - - - +
75D LYS 3.9 3.3 - - - +
76D SER* 1.3 82.0 - - - +
78D GLY* 1.3 61.5 + - - +
80D ARG* 5.7 1.8 - - + -
81D PHE* 3.8 18.8 - - + +
82D HIS* 3.6 17.6 + - - -
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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