Contacts of the helix formed by residues 67 - 76 (chain D) in PDB entry 3QIR
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 PHE 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C SER* 4.0 18.6 - - - -
51D LYS* 5.2 4.0 - - + -
52D THR 3.7 14.4 - - - -
53D PRO* 3.2 21.1 + - + +
55D ASP* 3.1 37.5 + - + -
56D SER 4.5 4.5 - - - -
57D PHE* 3.6 33.9 - + + -
66D THR* 1.3 73.1 - - - +
68D LEU* 1.3 61.9 + - - +
70D TYR* 3.2 4.8 + - - -
71D TYR* 3.0 48.9 + + + -
79D VAL* 5.4 0.4 - - - -
86D LEU* 3.6 31.0 - - + -
107D LEU* 4.0 23.6 - - + -
109D LEU* 4.7 7.2 - - + -
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Residues in contact with LEU 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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53D PRO* 3.3 29.0 + - + +
54D LYS* 4.3 15.3 - - + -
66D THR* 3.2 8.3 - - + +
67D PHE* 1.3 76.4 - - - +
69D GLU* 1.3 60.5 + - - +
71D TYR* 3.6 2.3 + - - +
72D SER* 3.2 23.9 + - - -
77D ILE 4.6 1.4 - - - +
79D VAL* 3.7 34.2 + - + +
82D GLU* 3.8 40.4 - - + +
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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 ILE* 4.0 17.9 - - + -
66D THR* 3.2 16.3 + - - +
68D LEU* 1.3 74.7 - - - +
70D TYR* 1.4 56.5 + - - +
72D SER* 3.9 5.1 - - - -
73D LYS* 2.8 38.7 + - + +
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Residues in contact with TYR 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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59C MET* 3.4 41.0 - - + +
60C SER* 3.7 14.6 - - - -
61C ASP* 2.5 36.1 + - - -
63C LYS* 3.6 12.3 - - - +
57D PHE* 3.5 25.4 - + + -
59D MET* 5.5 0.4 - - - -
65D ILE* 4.0 10.9 - - + +
66D THR 3.1 14.2 + - - +
67D PHE 3.2 8.3 + - - +
69D GLU* 1.4 75.6 - - - +
71D TYR* 1.3 79.3 + + - +
73D LYS* 5.0 0.4 - - - -
74D ASN* 2.9 61.0 + - - +
75D TYR* 3.9 12.0 + + - -
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Residues in contact with TYR 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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60C SER* 4.6 2.0 + - - -
61C ASP* 3.3 26.7 - - - +
37D TYR* 3.4 23.1 + + - -
67D PHE* 3.0 39.5 + + + +
68D LEU 4.3 0.2 - - - +
70D TYR* 1.3 89.4 - + - +
72D SER* 1.4 60.3 + - - +
75D TYR* 3.0 44.1 + + - +
76D GLY 3.2 5.9 + - - -
77D ILE* 3.3 21.1 + - + +
79D VAL* 4.1 12.8 - - + -
107D LEU 3.7 10.4 + - - -
108D LEU* 4.5 0.5 - - - -
109D LEU* 3.7 41.1 + - + +
112D LEU* 3.6 22.0 - - + -
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Residues in contact with SER 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 LEU 3.2 18.4 + - - -
69D GLU* 3.9 5.6 - - - -
71D TYR* 1.4 75.0 - - - +
73D LYS* 1.4 58.0 + - - +
76D GLY* 3.1 24.1 + - - -
77D ILE 3.2 17.5 + - - +
78D THR* 5.3 6.1 - - - -
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Residues in contact with LYS 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* 2.8 22.9 + - + +
70D TYR* 4.3 1.8 - - - +
72D SER* 1.4 73.6 - - - +
74D ASN* 1.3 65.7 + - - +
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Residues in contact with ASN 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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59C MET* 5.0 5.7 - - - +
63C LYS* 3.3 33.8 + - - +
70D TYR* 2.9 58.3 + - - +
73D LYS* 1.3 85.7 - - - +
75D TYR* 1.3 79.0 + - + +
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Residues in contact with TYR 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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61C ASP* 2.8 33.3 + - - -
63C LYS* 3.5 32.3 - - + +
37D TYR* 3.5 31.5 - + + -
38D ASN* 4.2 9.6 + - + -
70D TYR* 4.0 6.5 - + - -
71D TYR* 3.0 37.9 + + - +
74D ASN* 1.3 93.4 - - + +
76D GLY* 1.3 63.8 + - - +
77D ILE* 3.5 22.2 + - + +
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Residues in contact with GLY 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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72D SER* 3.1 20.9 + - - -
73D LYS 4.8 0.2 - - - -
74D ASN 3.9 0.4 - - - -
75D TYR* 1.3 78.1 - - - +
77D ILE* 1.4 59.8 + - - +
78D THR* 4.0 4.7 + - - -
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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