Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 1QI9
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A PRO* 3.0 32.1 + - + +
60A HIS* 4.4 1.5 - - - +
61A ASP 6.0 0.4 - - - +
65A GLN 3.7 0.6 + - - -
66A VAL* 1.3 75.9 - - - +
68A ALA* 1.3 65.3 + - - +
69A ASP* 3.4 13.4 + - - +
70A ALA* 2.9 34.5 + - + +
71A PHE* 2.9 20.4 + - - +
90A PRO* 5.6 0.5 - - - +
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Residues in contact with ALA 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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50A LEU* 5.3 6.5 - - + -
66A VAL* 3.4 7.1 + - - +
67A ASP* 1.3 74.3 + - - +
69A ASP* 1.3 68.2 + - - +
71A PHE* 3.2 7.4 + - - +
72A ALA* 3.1 22.0 + - - +
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.4 11.5 + - - +
68A ALA* 1.3 80.6 - - - +
70A ALA* 1.3 64.0 + - - +
72A ALA* 3.3 9.0 + - - +
73A ALA* 3.0 21.6 + - - +
90A PRO* 5.4 1.1 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.4 14.9 - - + +
59A PRO* 3.6 31.4 - - + -
67A ASP* 2.9 22.2 + - + +
68A ALA 3.3 0.2 - - - -
69A ASP* 1.3 77.9 - - - +
71A PHE* 1.3 57.3 + - - +
73A ALA* 3.1 4.3 + - - +
74A LEU* 2.9 22.9 + - - +
90A PRO* 3.8 26.9 - - + +
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Residues in contact with PHE 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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50A LEU* 3.7 29.4 - - + -
53A LYS* 3.9 22.7 - - + -
54A PHE 3.5 23.6 - - - -
55A HIS* 4.0 29.6 - + + -
58A LEU* 3.6 6.0 - - - +
66A VAL* 4.0 11.7 - - + -
67A ASP 2.9 15.8 + - - +
68A ALA 3.2 4.5 + - - +
70A ALA* 1.3 75.4 - - - +
72A ALA* 1.3 56.5 + - - +
74A LEU* 3.0 14.1 + - + +
75A GLU* 3.0 60.1 + - + +
346A ARG* 4.8 12.6 - - - -
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Residues in contact with ALA 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 ALA 3.1 11.3 + - - +
69A ASP* 3.6 10.8 - - - +
70A ALA 3.3 0.2 - - - -
71A PHE* 1.3 76.6 - - - +
73A ALA* 1.3 62.6 + - - +
75A GLU* 3.4 18.1 + - - +
76A ASP* 3.1 26.4 + - - +
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Residues in contact with ALA 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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69A ASP 3.0 13.5 + - - +
70A ALA 3.1 8.2 + - - +
72A ALA* 1.3 76.1 - - - +
74A LEU* 1.3 63.0 + - - +
76A ASP* 3.0 22.9 - - + +
77A CYS* 3.1 10.2 + - - +
85A ILE* 5.1 1.4 - - - +
88A ASP* 4.4 7.4 - - + +
89A VAL* 3.7 11.0 - - - +
90A PRO* 3.9 20.0 - - + -
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Residues in contact with LEU 74 (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 PHE* 3.7 33.2 - - + +
55A HIS* 4.5 1.8 - - - -
58A LEU* 4.2 21.1 - - + -
70A ALA 2.9 12.4 + - - +
71A PHE* 3.0 18.3 + - + +
73A ALA* 1.3 77.9 - - - +
75A GLU* 1.3 57.3 + - + +
77A CYS* 3.2 7.3 + - - +
78A ILE* 2.8 48.6 + - + +
89A VAL* 4.0 16.7 - - + +
102A LEU* 4.2 24.5 - - + -
342A TRP* 4.0 20.4 - - + -
346A ARG* 6.2 0.4 - - - -
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Residues in contact with GLU 75 (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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71A PHE* 3.0 44.6 + - + +
72A ALA* 3.7 20.4 - - - +
73A ALA 3.3 0.2 - - - -
74A LEU* 1.3 75.3 - - + +
76A ASP* 1.3 62.4 + - - +
78A ILE* 3.3 9.5 + - + +
79A LEU* 3.1 25.6 + - - +
346A ARG* 4.7 16.7 + - - +
10B ASP* 4.3 14.5 - - - +
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Residues in contact with ASP 76 (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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72A ALA 3.1 15.7 + - - +
73A ALA* 3.0 17.0 - - - +
75A GLU* 1.3 75.2 - - - +
77A CYS* 1.3 62.9 + - - +
79A LEU* 4.6 2.7 - - - -
80A ASN* 2.9 44.9 + - - +
85A ILE* 3.7 22.6 - - + +
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Residues in contact with CYS 77 (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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73A ALA 3.1 1.2 + - - +
74A LEU* 3.4 14.4 - - - +
76A ASP* 1.3 83.8 - - - +
78A ILE* 1.4 63.6 + - - +
79A LEU 3.4 0.3 + - - -
80A ASN* 3.7 5.8 + - - +
81A GLY 3.9 7.4 + - - -
82A ASP 4.9 0.3 + - - -
85A ILE* 3.9 8.7 - - - +
86A CYS* 2.0 63.2 - - - -
89A VAL* 3.6 26.9 - - + -
102A LEU* 4.8 2.0 - - - -
105A PRO* 3.7 22.3 - - - +
106A THR* 4.7 2.3 - - - +
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Residues in contact with ILE 78 (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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74A LEU* 2.8 42.4 + - + +
75A GLU* 3.7 7.6 - - + +
77A CYS* 1.4 77.7 - - - +
79A LEU* 1.3 62.6 + - - +
81A GLY 4.4 0.2 + - - -
105A PRO* 4.8 4.0 - - + +
106A THR* 5.8 0.5 - - - -
109A PHE* 3.3 8.1 - - - -
342A TRP* 3.3 59.9 - - + +
343A GLN* 2.9 45.7 + - + +
346A ARG* 3.8 20.0 - - + -
10B ASP* 4.0 11.2 - - + +
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Residues in contact with LEU 79 (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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75A GLU 3.1 17.5 + - - +
76A ASP* 3.7 5.8 - - - +
77A CYS 3.3 0.2 - - - -
78A ILE* 1.3 79.9 - - - +
80A ASN* 1.3 79.4 + - - +
81A GLY 3.6 0.2 - - - -
109A PHE* 3.6 7.4 - - - -
10B ASP* 3.8 37.2 - - + +
11B ASP 3.8 5.2 - - - +
12B PRO* 3.5 33.6 - - + +
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Residues in contact with ASN 80 (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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76A ASP* 2.9 39.4 + - - +
77A CYS 3.7 1.5 + - - +
78A ILE 3.5 0.4 - - - -
79A LEU* 1.3 99.0 - - - +
81A GLY* 1.3 63.9 + - - +
82A ASP* 3.0 7.3 + - + +
85A ILE* 3.8 24.6 - - + +
109A PHE* 4.8 0.4 - - - -
12B PRO* 5.3 6.4 - - - +
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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