Contacts of the helix formed by residues 64 - 83 (chain D) in PDB entry 4QYL
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 ASN 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D PHE* 3.4 14.7 - - - -
62D TYR* 3.5 1.1 - - - +
63D LEU* 1.3 84.8 + - - +
65D PHE* 1.3 63.0 + - - +
66D ASP* 3.2 12.4 + - - +
67D ASP* 2.9 65.9 + - - +
68D PHE* 3.6 4.9 + - - +
116D ILE 4.6 0.7 - - - -
117D ASP 3.2 16.8 - - - +
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Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PHE* 3.8 7.3 - + + -
11D LEU* 4.7 3.1 - - + -
12D LEU* 4.0 24.5 - - + -
15D THR* 4.4 6.1 - - + -
64D ASN* 1.3 69.9 - - - +
66D ASP* 1.3 66.4 + - - +
68D PHE* 3.1 9.6 + + - +
69D GLU* 2.9 35.4 + - + +
104D LEU* 3.9 24.5 - - + -
107D ALA* 3.7 28.3 - - + -
108D ARG* 3.6 51.6 - - + +
111D ALA* 4.1 14.1 - - + -
117D ASP* 2.7 28.3 + - + +
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Residues in contact with ASP 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ASN* 3.2 10.2 + - - +
65D PHE* 1.3 79.4 - - - +
67D ASP* 1.3 52.8 + - - +
69D GLU* 3.3 3.1 + - - +
70D GLU* 2.9 36.5 + - - +
108D ARG* 2.8 36.3 + - - +
117D ASP 4.3 2.6 + - - -
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Residues in contact with ASP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ARG 4.4 4.0 - - - +
62D TYR* 3.6 26.5 - - + -
63D LEU* 3.1 22.7 + - - +
64D ASN* 2.9 45.0 + - - +
65D PHE 3.2 0.2 - - - -
66D ASP* 1.3 72.9 - - - +
68D PHE* 1.3 65.7 + - - +
70D GLU* 3.5 13.0 + - - +
71D ASP* 3.4 17.5 + - - +
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Residues in contact with PHE 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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12D LEU* 3.8 40.6 - - + -
15D THR* 3.9 21.3 - - + -
16D LEU* 4.0 26.5 - - + -
19D LEU* 4.0 20.6 - - + -
53D MET* 3.5 32.6 - - + +
57D LEU* 4.6 4.3 - - + -
62D TYR* 3.7 32.5 - + + -
64D ASN 3.6 4.2 + - - +
65D PHE* 3.1 13.4 + + - +
67D ASP* 1.3 79.4 - - - +
69D GLU* 1.3 71.2 + - - +
71D ASP* 3.2 10.0 + - - +
72D PHE* 3.2 9.8 + - + +
104D LEU* 4.2 8.5 - - + -
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Residues in contact with GLU 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 PHE* 2.9 27.7 + - + +
66D ASP* 3.7 4.0 - - - +
68D PHE* 1.3 84.1 - - - +
70D GLU* 1.3 57.0 + - - +
72D PHE* 3.2 6.5 + - - +
73D ASN* 2.9 43.2 + - - +
104D LEU* 4.0 33.2 - - + +
108D ARG* 2.8 37.0 + - - +
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Residues in contact with GLU 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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46D LYS* 5.0 6.9 + - - -
66D ASP 2.9 18.5 + - - +
67D ASP* 3.7 11.5 - - - +
69D GLU* 1.3 74.4 - - - +
71D ASP* 1.3 65.6 + - - +
73D ASN* 3.4 12.2 + - - +
74D LEU* 3.0 32.6 + - + +
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Residues in contact with ASP 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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46D LYS* 3.6 21.8 + - - -
48D MET* 3.5 31.0 - - + +
53D MET* 4.0 7.0 - - + -
56D ASN* 3.5 10.9 + - - -
62D TYR* 2.5 40.6 + - - +
67D ASP 3.4 4.5 + - - +
68D PHE 3.2 8.1 + - - +
69D GLU 3.2 0.6 - - - -
70D GLU* 1.3 82.7 - - - +
72D PHE* 1.3 63.4 + - - +
74D LEU* 3.0 21.4 + - - +
75D ILE* 3.1 10.6 + - - +
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Residues in contact with PHE 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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19D LEU* 3.9 27.8 - - + -
50D PHE* 4.2 15.0 - + - -
53D MET* 3.8 15.4 - - + -
68D PHE* 3.2 10.7 + - + +
69D GLU* 3.2 10.8 + - - +
71D ASP* 1.3 74.6 - - - +
73D ASN* 1.3 74.9 + - - +
75D ILE* 3.1 17.6 + - + +
76D VAL* 3.3 23.3 + - + +
96D LEU* 3.6 52.0 - - + -
97D ARG* 4.7 6.7 - - + -
100D GLY* 3.9 13.5 - - - -
101D GLY 4.9 0.7 - - - -
104D LEU* 3.4 30.1 - - + -
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Residues in contact with ASN 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 GLU* 2.9 39.0 + - - +
70D GLU* 3.5 10.3 - - - +
72D PHE* 1.3 92.5 - - - +
74D LEU* 1.3 55.7 + - - +
76D VAL* 3.4 6.5 + - - +
77D SER* 2.8 31.6 + - - -
104D LEU* 4.7 1.6 - - - +
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Residues in contact with LEU 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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46D LYS* 3.7 45.1 - - + +
48D MET* 3.9 11.0 - - + -
70D GLU* 3.0 21.1 + - + +
71D ASP* 3.0 25.1 + - - +
73D ASN* 1.3 72.6 - - - +
75D ILE* 1.3 68.7 + - - +
77D SER* 3.6 9.6 - - - +
78D ASN* 2.8 49.4 + - - +
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Residues in contact with ILE 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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28D PHE* 3.5 37.2 - - + -
48D MET* 3.7 28.7 - - + +
49D ASP 3.6 25.4 - - - +
50D PHE* 3.8 19.5 - - + +
53D MET* 3.7 22.4 - - - -
71D ASP 3.1 9.6 + - - +
72D PHE* 3.1 10.9 + - + +
74D LEU* 1.3 78.2 - - - +
76D VAL* 1.3 64.9 + - + +
78D ASN* 4.2 2.1 - - - +
79D CYS* 3.4 18.7 + - - +
96D LEU* 4.2 10.3 - - + -
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 5.6 0.4 - - - -
72D PHE* 3.3 35.1 + - + +
73D ASN* 3.7 8.7 - - - +
74D LEU 3.1 0.2 - - - -
75D ILE* 1.3 82.8 - - - +
77D SER* 1.3 65.1 + - - +
79D CYS* 3.1 4.3 + - - +
80D LEU* 3.0 45.0 + - + +
93D ALA* 3.9 13.6 - - - +
96D LEU* 4.1 11.7 - - + -
97D ARG* 3.7 42.8 - - + +
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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 ASN* 2.8 23.3 + - - -
74D LEU* 3.6 17.8 - - - +
76D VAL* 1.3 77.5 - - - +
78D ASN* 1.3 65.1 + - - +
80D LEU* 3.3 8.7 + - - +
81D LYS* 3.0 25.6 + - - +
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Residues in contact with ASN 78 (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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40D TYR* 3.6 16.3 + - - +
44D ILE* 3.5 28.5 - - + +
45D LYS 5.3 0.5 + - - -
46D LYS 2.8 27.1 + - - +
47D PRO* 3.5 15.0 - - - +
48D MET 3.5 9.1 + - - +
74D LEU* 2.8 40.3 + - - +
75D ILE* 4.2 2.9 - - - +
77D SER* 1.3 75.6 + - - +
79D CYS* 1.3 59.1 + - - +
81D LYS* 3.3 2.3 + - - +
82D TYR* 2.9 32.4 + - - +
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Residues in contact with CYS 79 (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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28D PHE* 3.7 21.5 - - + -
40D TYR* 4.8 1.3 + - - -
75D ILE 3.4 11.3 + - - +
76D VAL 3.1 10.3 + - - +
78D ASN* 1.3 79.2 - - - +
80D LEU* 1.3 63.6 + - - +
82D TYR* 5.0 0.4 - - - -
83D ASN* 3.0 51.5 + - - +
89D PHE* 3.2 32.5 - - - -
90D TYR* 4.6 0.5 - - - -
93D ALA* 3.7 10.1 - - + -
5H ALY 3.8 11.2 - - + +
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Residues in contact with LEU 80 (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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76D VAL* 3.0 34.7 + - + +
77D SER* 3.9 7.9 - - - +
79D CYS* 1.3 76.8 - - - +
81D LYS* 1.3 62.7 + - - +
83D ASN 3.5 6.8 - - - +
90D TYR* 3.5 56.7 - - + +
93D ALA* 3.7 21.8 - - + -
94D VAL* 3.8 9.2 - - + -
97D ARG* 3.4 31.4 - - - +
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Residues in contact with LYS 81 (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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43D HIS* 2.8 37.3 + - + +
44D ILE* 3.9 12.6 - - + +
45D LYS* 5.2 3.8 - - - +
77D SER 3.0 17.6 + - - +
78D ASN* 3.7 5.2 - - - +
80D LEU* 1.3 78.1 - - - +
82D TYR* 1.3 64.0 + - - +
83D ASN 4.4 1.0 - - - +
1H SER* 3.9 15.6 + - - -
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Residues in contact with TYR 82 (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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37D VAL* 3.2 15.6 - - + +
39D ASP* 2.6 28.5 + - - -
40D TYR* 3.7 38.6 - + + -
43D HIS* 4.0 19.3 - - + -
44D ILE* 4.2 5.4 - - + -
78D ASN 2.9 17.8 + - - +
81D LYS* 1.3 78.5 - - - +
83D ASN* 1.3 77.5 + - - +
1H SER* 3.3 6.1 - - - -
2H GLY* 3.1 44.2 + - - +
3H ARG* 4.0 0.3 - - - +
4H GLY* 3.1 38.7 + - - -
5H ALY 4.0 17.0 - - + -
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Residues in contact with ASN 83 (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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79D CYS* 3.0 35.6 + - - +
80D LEU 3.5 6.6 - - - +
81D LYS 4.4 0.3 - - - +
82D TYR* 1.3 93.2 - - - +
84D ALA* 1.3 62.9 - - - +
85D LYS 3.7 0.2 + - - -
87D THR* 3.5 17.6 - - + +
89D PHE* 3.8 15.3 - - - +
90D TYR* 3.4 20.7 - - + +
1H SER* 3.7 4.9 + - - -
4H GLY* 5.1 2.7 - - - -
5H ALY 2.8 48.8 + - - +
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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