Contacts of the helix formed by residues 63 - 75 (chain D) in PDB entry 3IKH
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 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D GLY 3.3 0.7 - - - +
62D ASN* 1.3 83.0 - - - +
64D SER* 1.3 65.9 + - - +
65D ASN* 3.9 12.4 + - - +
66D GLY* 2.7 19.4 + - - -
67D ALA* 3.2 17.3 + - - +
70D ARG* 4.8 1.7 + - - -
89D HIS* 3.3 23.3 - - + +
90D SER* 2.7 50.1 + - - +
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Residues in contact with SER 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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64B SER* 4.0 21.8 + - - -
63D ASP* 1.3 74.4 - - - +
65D ASN* 1.3 69.9 + - - +
67D ALA* 3.2 8.5 + - - +
68D TRP* 2.9 23.3 + - - +
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Residues in contact with ASN 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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31B LYS* 5.9 2.6 - - - +
64B SER* 4.1 24.8 + - - -
11D VAL* 3.8 28.0 - - + +
63D ASP* 3.2 14.7 + - - +
64D SER* 1.3 83.0 + - - +
66D GLY* 1.3 52.7 + - - +
68D TRP* 3.1 15.9 + - - +
69D ILE* 2.7 40.4 + - - +
90D SER* 4.0 9.8 + - - -
92D THR* 3.9 21.8 - - - +
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Residues in contact with GLY 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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60D THR* 4.6 1.1 - - - -
61D GLY 3.7 11.9 - - - -
63D ASP* 2.7 18.9 + - - -
65D ASN* 1.3 73.6 - - - +
67D ALA* 1.3 55.3 + - - +
69D ILE* 3.2 6.3 + - - +
70D ARG* 2.9 43.5 + - - +
90D SER* 3.1 18.5 + - - -
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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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63D ASP 3.2 12.6 + - - +
64D SER* 3.6 11.4 - - - +
66D GLY* 1.3 74.8 - - - +
68D TRP* 1.3 63.0 + - - +
70D ARG* 3.6 20.4 + - - +
71D GLN* 3.1 24.9 + - - +
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Residues in contact with TRP 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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11D VAL* 3.7 39.9 - - + -
34D GLN* 3.8 39.9 - - + -
35D ASP* 4.1 8.7 - - - -
36D ILE* 3.8 16.2 - - + -
64D SER 2.9 13.0 + - - +
65D ASN* 3.4 14.8 - - - +
67D ALA* 1.3 77.8 - - - +
69D ILE* 1.3 61.7 + - - +
71D GLN* 3.4 5.4 + - + +
72D GLN* 3.0 56.2 + - + +
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Residues in contact with ILE 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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9D ILE* 3.2 40.6 - - + +
10D THR* 4.0 21.8 - - - +
11D VAL* 3.8 25.6 - - + -
36D ILE* 3.9 17.3 - - + -
60D THR* 4.1 14.1 - - + -
65D ASN 2.7 24.4 + - - +
66D GLY* 3.5 5.4 - - - +
68D TRP* 1.3 72.5 - - - +
70D ARG* 1.3 63.5 + - - +
72D GLN* 3.1 4.2 + - - +
73D ILE* 3.0 28.6 + - + +
80D LEU* 5.0 0.2 - - + -
90D SER* 4.2 20.4 - - - -
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Residues in contact with ARG 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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60D THR* 2.8 46.8 + - + +
61D GLY 2.9 22.2 + - - -
62D ASN* 5.3 1.4 - - - +
63D ASP 4.8 2.0 + - - -
66D GLY 2.9 23.3 + - - +
67D ALA* 3.7 24.5 - - - +
69D ILE* 1.3 73.6 - - - +
71D GLN* 1.3 57.5 + - - +
73D ILE* 3.5 1.9 + - - +
74D LYS* 3.1 29.2 + - - +
80D LEU* 4.3 15.0 - - + +
82D PRO 6.1 0.7 - - - -
83D ASP 4.7 15.0 - - - -
84D GLY 5.4 0.7 - - - -
85D HIS* 3.5 27.8 + - - +
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Residues in contact with GLN 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 ALA 3.1 18.2 + - - +
68D TRP* 3.6 7.0 - - + +
70D ARG* 1.3 75.0 - - - +
72D GLN* 1.3 74.6 + - - +
74D LYS* 3.0 40.5 + - - +
75D ASN* 3.0 46.8 + - - +
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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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36D ILE* 3.6 25.5 - - + +
68D TRP* 3.0 45.0 + - + +
69D ILE 3.1 6.5 + - - +
71D GLN* 1.3 83.8 - - - +
73D ILE* 1.3 62.8 + - - +
75D ASN* 3.2 26.7 + - - +
76D GLU* 3.4 15.4 + - - +
271D LEU* 4.4 15.3 - - + +
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Residues in contact with ILE 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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9D ILE* 3.7 32.1 - - + -
36D ILE* 4.5 8.3 - - + -
41D ALA* 5.0 0.7 - - + -
45D ILE* 3.9 29.4 - - + -
56D LEU* 5.1 0.7 - - + -
69D ILE 3.0 16.9 + - - +
70D ARG 3.8 4.3 - - - +
72D GLN* 1.3 74.1 - - - +
74D LYS* 1.3 66.8 + - - +
75D ASN 3.1 0.2 - - - -
76D GLU* 3.1 11.1 + - + +
78D LEU* 3.1 51.3 + - + +
80D LEU* 3.7 27.1 - - + -
271D LEU* 5.7 1.1 - - + -
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Residues in contact with LYS 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 ARG 3.1 17.8 + - - +
71D GLN* 3.0 40.8 + - - +
73D ILE* 1.3 77.0 - - - +
75D ASN* 1.3 59.7 + - - +
77D PRO* 3.3 21.9 - - - +
78D LEU 5.0 2.9 - - - -
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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
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71D GLN* 3.0 37.4 + - - +
72D GLN* 3.5 23.8 + - - +
73D ILE 3.1 0.6 - - - -
74D LYS* 1.3 81.5 - - - +
76D GLU* 1.3 63.7 + - - +
77D PRO* 3.7 0.8 - - - +
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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