Contacts of the helix formed by residues 66 - 80 (chain D) in PDB entry 4U2M
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D VAL* 3.5 6.1 - - - +
31D ASP* 6.0 0.4 - - - -
64D ILE* 3.4 2.4 - - - +
65D SER* 1.3 86.2 - - - +
67D ALA* 1.3 69.7 + - - +
68D ALA* 3.5 8.1 + - - +
69D GLY* 2.7 25.4 + - - -
70D LEU* 3.3 22.5 + - - +
91D ASP* 2.8 38.8 + - + +
94D ALA* 6.0 1.6 - - + -
95D VAL* 3.9 10.9 - - + +
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Residues in contact with ALA 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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30D VAL* 3.5 28.3 - - - +
31D ASP* 4.7 8.2 - - + +
33D VAL* 4.2 13.5 - - + -
35D PHE* 3.6 23.2 - - + -
66D ASN* 1.3 74.9 - - - +
68D ALA* 1.3 61.3 + - - +
70D LEU* 3.2 0.9 + - - +
71D GLY* 2.9 25.5 + - - -
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Residues in contact with ALA 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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66D ASN* 3.5 11.5 - - - +
67D ALA* 1.3 75.6 - - - +
69D GLY* 1.3 66.1 + - - +
71D GLY* 4.0 1.2 - - - +
72D GLN* 3.1 26.7 + - - +
88D ASN* 5.2 10.4 + - + -
91D ASP* 4.2 14.1 - - + +
92D VAL* 4.6 1.2 - - - +
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ASN* 2.7 22.6 + - - -
68D ALA* 1.3 73.5 - - - +
70D LEU* 1.3 57.0 + - - +
72D GLN* 3.3 2.8 + - - +
73D VAL* 3.0 30.7 + - - +
91D ASP* 3.5 25.5 - - - +
92D VAL* 3.8 8.5 - - - +
95D VAL* 3.9 8.3 - - - -
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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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28D PHE* 4.0 16.6 - - + -
30D VAL* 3.7 28.0 - - + -
35D PHE* 3.7 17.9 - - + -
49D PHE* 5.9 2.0 - - + -
64D ILE* 3.7 31.0 - - + -
66D ASN 3.3 18.3 + - - +
67D ALA* 3.2 5.1 + - - +
68D ALA 3.2 0.4 - - - -
69D GLY* 1.3 74.3 - - - +
71D GLY* 1.3 61.0 + - - +
73D VAL* 3.1 5.8 + - + +
74D LEU* 2.8 46.6 + - + +
95D VAL* 3.8 14.5 - - + +
99D LEU* 4.8 7.9 - - + -
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Residues in contact with GLY 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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18D ARG* 5.1 1.7 + - - -
35D PHE* 3.9 21.7 - - - -
67D ALA 2.9 15.5 + - - -
68D ALA* 4.0 1.6 - - - -
70D LEU* 1.3 76.0 - - - +
72D GLN* 1.3 56.9 + - - +
74D LEU* 3.5 4.3 + - - +
75D GLU* 2.9 31.9 + - - +
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Residues in contact with GLN 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 ALA 3.1 17.2 + - - +
71D GLY* 1.3 78.3 - - - +
73D VAL* 1.3 56.1 + - - +
75D GLU* 3.3 15.4 + - - +
76D PHE* 3.0 27.0 + - - +
81D LYS 4.3 2.9 - - - +
82D LEU* 4.0 11.8 - - + +
83D SER* 3.1 44.4 + - - +
88D ASN* 3.6 24.6 - - - +
92D VAL* 3.7 17.9 - - + -
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Residues in contact with VAL 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 GLY 3.0 19.7 + - - +
70D LEU* 3.1 11.9 + - + +
72D GLN* 1.3 76.4 - - - +
74D LEU* 1.3 63.5 + - + +
76D PHE* 3.3 4.6 + - - +
77D MET* 3.0 28.2 + - + +
82D LEU* 5.1 0.7 - - - -
92D VAL* 4.5 14.6 - - + +
95D VAL* 3.7 20.9 - - + -
96D ALA* 4.7 4.0 - - - +
99D LEU* 4.2 13.2 - - + -
101D MET* 3.9 28.9 - - + -
104D ILE* 4.1 20.0 - - + -
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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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18D ARG* 4.0 16.4 - - - +
28D PHE* 4.6 12.8 - - + -
35D PHE* 3.7 38.6 - - + -
36D LYS 4.7 9.2 - - - +
37D ALA* 4.6 6.7 - - + -
42D LEU* 4.0 28.5 - - + -
49D PHE* 6.0 1.6 - - + -
70D LEU* 2.8 37.8 + - + +
71D GLY* 3.8 3.6 - - - +
73D VAL* 1.3 73.8 - - + +
75D GLU* 1.3 63.8 + - - +
77D MET* 3.1 11.7 + - + -
78D TYR* 3.0 33.6 + - + -
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Residues in contact with GLU 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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15D ASN* 5.0 1.6 + - - -
18D ARG* 3.0 29.8 + - - +
19D GLN* 5.8 0.9 + - - -
71D GLY 2.9 18.2 + - - +
72D GLN* 3.5 22.9 - - - +
74D LEU* 1.3 76.4 - - - +
76D PHE* 1.3 53.2 + - - +
78D TYR 3.4 0.2 + - - -
79D THR* 2.7 59.7 + - - +
81D LYS* 4.6 4.7 - - + +
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Residues in contact with PHE 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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45D CYS* 5.6 1.8 - - + -
72D GLN 3.0 13.6 + - - +
73D VAL* 3.5 8.5 - - - +
74D LEU 3.2 0.2 - - - -
75D GLU* 1.3 74.7 - - - +
77D MET* 1.3 71.6 + - + +
80D ALA* 2.8 29.4 + - - -
81D LYS 3.3 18.5 + - - +
82D LEU* 4.0 12.8 - - + -
101D MET* 3.9 20.0 - - + -
103D ASP* 4.8 14.6 - - + -
104D ILE* 3.6 24.9 - - + -
134D PHE* 3.4 45.3 - + + -
137D HIS* 3.5 30.8 + + - -
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Residues in contact with MET 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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11D LEU* 3.5 10.2 - - - +
41D VAL* 4.8 2.8 - - + +
42D LEU* 3.7 26.9 - - - +
45D CYS* 3.6 36.4 - - + -
46D SER* 4.2 5.6 - - - -
49D PHE* 4.1 22.2 - - + -
73D VAL* 3.0 22.8 + - + +
74D LEU* 3.1 18.8 + - + +
76D PHE* 1.3 84.8 - - + +
78D TYR* 1.3 66.7 + - + +
101D MET* 3.6 31.9 - - + -
137D HIS* 2.8 24.6 + - - -
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Residues in contact with TYR 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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11D LEU* 3.4 21.8 - - - +
12D GLU* 5.2 0.5 - - - -
14D LEU* 3.5 35.7 - - + -
15D ASN* 3.5 39.1 - - - +
18D ARG* 3.6 31.9 - - + +
37D ALA* 3.6 4.8 - - + +
38D HIS* 2.7 48.7 + - - +
41D VAL* 3.7 23.5 - - + +
42D LEU* 4.3 14.6 - - + -
74D LEU* 3.0 26.9 + - + +
75D GLU 4.2 0.2 - - - +
77D MET* 1.3 80.0 - - + +
79D THR* 1.3 58.8 + - - +
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Residues in contact with THR 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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8D GLN* 5.2 5.4 + - - +
11D LEU* 3.9 8.9 - - - +
15D ASN* 3.7 21.1 - - - +
75D GLU* 2.7 46.1 + - - +
78D TYR* 1.3 84.2 - - + +
80D ALA* 1.3 65.2 + - - +
81D LYS* 3.0 42.5 + - - +
133D GLN* 5.6 0.2 - - - +
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Residues in contact with ALA 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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8D GLN* 5.5 4.3 - - - +
11D LEU* 4.4 5.8 - - + -
76D PHE* 2.8 22.8 + - - -
79D THR* 1.3 79.0 - - - +
81D LYS* 1.3 59.9 + - - +
132D ILE 3.5 1.4 - - - +
133D GLN* 3.5 6.4 - - + -
134D PHE* 2.9 49.7 + - - +
137D HIS* 3.7 22.6 - - + -
138D ALA 5.0 1.6 - - - +
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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
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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