Contacts of the helix formed by residues 69 - 84 (chain D) in PDB entry 3OQN
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 ASP 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D TYR* 3.4 19.7 - - + +
30D ASP* 3.5 30.7 + - - +
31D ALA* 3.2 24.9 + - - +
67D GLY 2.6 6.9 + - - -
68D ALA* 1.3 84.0 - - - +
70D GLU* 1.3 56.3 + - - +
71D ASN* 2.8 16.6 + - - +
72D ASP* 3.4 16.6 + - + +
73D ALA* 3.1 18.2 + - - +
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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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2D ALA* 3.4 32.8 + - + +
31D ALA* 4.0 9.0 - - - -
65D ALA* 4.0 6.0 - - + +
66D SER* 3.4 23.9 - - - +
67D GLY* 3.0 37.3 + - - +
69D ASP* 1.3 76.8 + - - +
71D ASN* 1.3 74.9 + - - +
73D ALA* 3.9 4.6 - - - +
74D LEU* 3.3 20.4 + - - +
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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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2D ALA* 5.0 6.2 - - - +
68D ALA 5.6 1.6 + - - -
69D ASP* 2.8 4.2 + - - +
70D GLU* 1.3 88.9 - - - +
72D ASP* 1.3 74.7 + - - +
73D ALA 2.9 2.2 + - - -
74D LEU* 3.0 12.6 + - - +
75D ASN* 2.9 21.3 + - - +
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Residues in contact with ASP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 4.0 15.9 + - + +
69D ASP* 3.4 18.9 + - + +
71D ASN* 1.3 80.0 + - - +
73D ALA* 1.3 56.4 + - - +
75D ASN* 3.3 10.5 + - - +
76D ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 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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29D TYR* 3.7 35.9 - - + -
31D ALA* 4.6 0.9 - - + -
33D VAL* 4.4 16.2 - - + -
65D ALA* 5.2 1.8 - - + -
69D ASP* 3.1 18.9 + - - +
70D GLU* 3.9 9.6 - - - +
71D ASN 2.9 0.6 + - - -
72D ASP* 1.3 74.4 - - - +
74D LEU* 1.3 60.5 + - - +
75D ASN 3.0 1.7 + - - -
76D ALA* 3.1 3.6 + - - +
77D LEU* 2.9 34.9 + - - +
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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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2D ALA* 3.6 25.8 - - + +
3D GLN 3.5 26.0 - - - +
4D LYS* 4.5 9.2 - - + -
6D PHE* 5.2 2.5 - - + -
63D ILE* 3.8 36.8 - - + +
64D SER 4.9 1.6 - - - +
65D ALA* 4.9 2.6 - - + +
70D GLU 3.3 13.8 + - - +
71D ASN* 3.0 5.8 + - - +
73D ALA* 1.3 78.1 - - - +
75D ASN* 1.3 60.5 + - - +
77D LEU* 3.8 7.7 - - + +
78D GLU* 3.0 44.0 + - + +
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ASN* 2.9 27.5 + - - +
72D ASP* 3.3 13.5 - - - +
73D ALA 3.0 0.8 - - - -
74D LEU* 1.3 75.5 - - - +
76D ALA* 1.3 66.8 + - - +
78D GLU* 2.9 29.4 + - - +
79D GLU* 3.0 12.0 + - - +
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Residues in contact with ALA 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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25D THR* 3.9 11.5 - - + +
28D LYS* 6.1 0.2 - - + -
29D TYR* 3.0 36.6 - - + +
72D ASP 2.9 10.4 + - - +
73D ALA 3.5 3.8 - - - +
75D ASN* 1.3 76.0 - - - +
77D LEU* 1.3 63.9 + - - +
79D GLU* 2.8 27.2 + - - +
80D THR* 3.2 8.0 + - - +
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Residues in contact with LEU 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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6D PHE* 5.5 0.4 - - + -
22D LEU* 3.4 35.1 - - + +
25D THR* 4.0 6.7 - - + -
26D ALA* 4.1 10.5 - - + +
29D TYR* 5.9 0.9 - - + -
33D VAL* 3.4 35.0 - - + -
44D LEU* 3.6 16.6 - - + -
63D ILE* 3.6 24.7 - - + -
64D SER 4.8 1.8 - - - +
73D ALA 2.9 22.8 + - - +
74D LEU* 3.8 10.5 - - + +
76D ALA* 1.3 76.7 - - - +
78D GLU* 1.3 56.2 + - - +
80D THR* 3.2 5.2 + - - -
81D MET* 2.9 35.5 + - - +
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Residues in contact with GLU 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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4D LYS* 3.1 28.1 - - - +
6D PHE* 3.7 23.5 - - + -
74D LEU* 3.0 30.5 + - + +
75D ASN* 2.9 23.0 + - - +
77D LEU* 1.3 75.1 - - - +
79D GLU* 1.3 72.2 + - - +
81D MET* 2.8 17.0 + - - +
82D LYS* 3.0 15.9 + - + +
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Residues in contact with GLU 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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75D ASN 3.0 8.5 + - - +
76D ALA* 2.8 16.6 + - - +
78D GLU* 1.3 77.9 - - - +
80D THR* 1.3 62.2 + - + +
82D LYS* 2.9 34.0 + - - +
83D SER* 2.3 51.1 + - - +
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Residues in contact with THR 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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21D VAL* 3.8 24.5 - - + -
22D LEU* 4.3 8.8 - - - +
25D THR* 3.3 30.1 + - + +
76D ALA 3.2 7.6 + - - +
77D LEU* 3.2 15.9 + - - -
79D GLU* 1.3 85.0 - - + +
81D MET* 1.3 63.2 + - - +
83D SER* 2.8 22.3 + - - +
84D GLU* 3.0 17.7 + - - +
86D LEU* 4.9 0.6 - - - +
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Residues in contact with MET 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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6D PHE* 4.0 21.8 - - + -
14D ILE* 4.9 1.6 - - + -
22D LEU* 3.2 39.5 - - + -
61D ILE* 4.6 12.3 - - - -
63D ILE* 4.0 21.3 - - + -
77D LEU 2.9 26.7 + - - +
78D GLU* 2.8 15.3 + - - +
80D THR* 1.3 72.6 + - - +
82D LYS* 1.3 53.7 + - + +
86D LEU* 2.6 93.9 + - + +
87D GLY 3.7 1.6 - - - +
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Residues in contact with LYS 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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78D GLU 3.0 11.2 + - - +
79D GLU* 2.9 55.9 + - - +
81D MET* 1.3 75.1 - - + +
83D SER* 1.3 66.1 + - - +
84D GLU 3.4 1.8 - - - -
85D GLY* 3.7 9.9 + - - +
87D GLY 4.5 8.7 - - - +
88D GLU* 5.6 7.4 - - + +
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLU* 2.3 49.4 + - - +
80D THR* 2.8 10.6 + - - +
82D LYS* 1.3 82.2 - - - +
84D GLU* 1.3 74.5 + - - +
85D GLY 3.3 1.6 + - - -
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Residues in contact with GLU 84 (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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10D ALA* 4.8 2.3 - - - +
18D PRO* 3.6 41.1 - - + +
21D VAL* 4.0 30.7 - - + +
80D THR* 3.0 8.5 + - - +
83D SER* 1.3 93.1 - - - +
85D GLY* 1.3 66.0 + - - +
86D LEU* 3.2 18.6 + - + +
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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