Contacts of the helix formed by residues 67 - 73 (chain A) in PDB entry 1QQJ
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 LEU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.7 38.8 - - + +
20A GLY* 4.2 2.0 - - - +
21A VAL* 4.5 3.1 - - + -
32A ILE* 3.7 36.8 - - + -
66A THR* 1.3 71.1 - - - +
68A ASN* 1.3 64.8 + - - +
69A ASN 3.3 2.2 - - - -
70A PHE* 3.1 25.5 + - + -
71A MET* 2.9 41.1 + - + +
118A PRO* 2.9 40.4 + - + +
226A PHE* 4.9 2.0 - - + -
263A VAL* 4.3 7.0 - - + -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 3.1 16.4 + - - +
67A LEU* 1.3 76.3 - - - +
69A ASN* 1.3 65.5 + - - +
71A MET* 3.3 11.0 + - - +
72A GLY* 2.9 24.4 + - - -
119A ALA* 3.3 7.5 - - - +
120A THR* 2.8 53.5 + - - +
342A PRO* 3.3 30.9 + - + +
343A GLY* 4.0 2.4 - - - -
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS* 5.1 6.1 + - - -
61A VAL* 3.9 20.6 - - + +
64A GLU* 3.7 33.8 + - + -
66A THR* 4.6 2.4 + - - +
67A LEU 3.3 0.4 - - - -
68A ASN* 1.3 81.9 - - - +
70A PHE* 1.3 61.4 + - - +
72A GLY* 3.2 10.6 + - - +
73A LEU* 3.3 19.4 + - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.6 32.5 - + - -
32A ILE* 5.5 0.4 - - + -
55A LEU* 4.6 2.5 - - + -
61A VAL* 3.9 26.0 + - + +
62A PHE* 3.8 32.8 - + + -
67A LEU* 3.1 26.9 + - + +
69A ASN* 1.3 75.0 - - - +
71A MET* 1.3 63.3 + - - +
73A LEU* 3.2 18.8 + - + +
77A ALA 4.2 7.2 - - - -
78A TRP* 3.0 35.5 + + - -
81A ALA* 3.7 25.1 - - + -
226A PHE* 3.7 26.0 - + - -
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 2.9 46.9 + - + +
68A ASN* 3.4 7.4 - - - +
70A PHE* 1.3 71.7 - - - +
72A GLY* 1.3 61.0 + - - +
73A LEU 3.2 1.0 + - - -
74A GLY 3.5 0.5 + - - -
78A TRP* 3.1 31.6 + - - +
118A PRO 5.2 0.2 - - - -
119A ALA* 4.1 9.0 - - + -
205A PHE* 3.6 37.9 - - + -
206A VAL 3.8 12.3 - - - +
207A GLY* 3.3 7.8 - - - -
226A PHE* 3.8 36.6 - - + -
263A VAL* 4.7 1.3 - - + -
342A PRO* 4.5 2.2 - - + -
343A GLY* 3.8 26.2 - - - -
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN 2.9 14.9 + - - -
69A ASN* 3.2 6.4 + - - -
71A MET* 1.3 74.5 - - - +
73A LEU* 1.3 62.7 + - - +
74A GLY 3.3 0.8 + - - -
208A PRO* 3.8 18.9 - - - +
342A PRO* 3.8 22.8 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 4.9 0.7 - - - +
55A LEU* 3.8 27.8 - - + -
58A HIS* 3.9 42.0 - - + +
61A VAL* 4.0 20.9 - - + -
69A ASN 3.3 15.6 + - - +
70A PHE* 3.5 10.8 - - + +
71A MET 3.2 1.6 + - - -
72A GLY* 1.3 78.6 - - - +
74A GLY* 1.3 60.2 + - - +
76A ALA* 6.1 0.2 - - - +
77A ALA* 3.5 18.6 + - + +
208A PRO* 4.4 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