Contacts of the helix formed by residues 89 - 102 (chain D) in PDB entry 1QSW
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 ILE 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D PHE* 3.9 10.7 - - + -
8D LEU* 3.7 25.1 - - + -
11D THR* 3.7 32.1 - - + -
12D LEU* 4.1 16.2 - - + -
15D LEU* 4.2 3.6 - - + -
40D THR* 3.6 31.9 - - + -
56D ILE* 4.3 18.4 - - + -
86D GLN 4.2 1.8 - - - +
87D ASP 3.5 4.4 + - - +
88D ASN* 1.3 73.0 + - - +
90D ALA* 1.3 64.3 + - - +
91D ASP 3.3 2.9 - - - -
92D ALA* 3.2 14.0 + - + +
93D VAL* 3.0 29.0 + - + +
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Residues in contact with ALA 90 (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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15D LEU* 4.1 28.1 - - + +
88D ASN* 3.1 16.7 + - - +
89D ILE* 1.3 75.4 - - - +
91D ASP* 1.3 65.3 + - - +
93D VAL* 3.3 3.2 + - - +
94D ALA* 3.0 23.1 + - - +
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Residues in contact with ASP 91 (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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79D LEU* 3.8 25.9 - - + +
83D ALA* 4.3 5.1 - - + +
86D GLN* 3.1 31.5 + - - +
88D ASN* 4.6 2.3 + - - +
89D ILE 3.3 0.8 - - - -
90D ALA* 1.3 79.0 - - - +
92D ALA* 1.3 57.5 + - - +
94D ALA* 3.1 9.7 + - - +
95D CYS* 3.0 28.6 + - - +
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Residues in contact with ALA 92 (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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55D GLY* 6.3 0.2 - - - -
56D ILE* 4.7 7.6 - - + +
57D PHE* 4.4 12.8 - - + -
59D ILE* 3.6 6.5 - - + +
83D ALA 4.8 2.3 + - - +
84D LEU* 3.7 38.0 - - + +
89D ILE* 3.2 21.0 + - + +
91D ASP* 1.3 78.4 - - - +
93D VAL* 1.3 51.3 + - - +
95D CYS 3.4 0.9 + - - -
96D ALA* 2.8 35.5 + - - +
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Residues in contact with VAL 93 (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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12D LEU* 4.0 22.4 - - + -
15D LEU* 3.8 31.4 - - + +
17D MET* 3.8 16.8 - - + +
57D PHE* 4.0 15.9 - - + -
89D ILE* 3.0 24.4 + - + +
90D ALA* 3.6 4.7 - - - +
92D ALA* 1.3 72.5 - - - +
94D ALA* 1.3 69.1 + - - +
96D ALA* 3.3 2.6 + - - +
97D LYS* 3.1 46.5 + - - +
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Residues in contact with ALA 94 (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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79D LEU* 6.2 0.2 - - + -
90D ALA 3.0 13.8 + - - +
91D ASP* 3.1 13.0 + - - +
93D VAL* 1.3 82.3 - - - +
95D CYS* 1.3 59.8 + - - +
97D LYS* 3.4 11.5 + - - +
98D ARG* 3.3 19.1 + - - +
101D ARG* 5.2 0.9 + - - -
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Residues in contact with CYS 95 (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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59D ILE* 4.0 28.7 - - - -
63D TYR* 4.4 1.6 - - - -
77D CYS* 2.0 53.2 - - + -
79D LEU* 4.4 5.6 - - + -
84D LEU* 4.2 15.0 - - + -
91D ASP 3.0 15.3 + - - +
92D ALA 3.7 4.5 - - - +
94D ALA* 1.3 74.5 - - - +
96D ALA* 1.3 65.5 + - - +
98D ARG* 3.0 14.1 + - - +
99D VAL* 3.1 16.7 + - - +
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Residues in contact with ALA 96 (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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17D MET* 4.3 9.9 - - + -
28D TRP* 4.3 10.3 - - + -
57D PHE* 3.8 27.1 - - + -
59D ILE* 3.8 10.0 - - + +
92D ALA 2.8 20.5 + - - +
93D VAL 3.3 4.9 + - - +
95D CYS* 1.3 72.8 - - - +
97D LYS* 1.3 61.5 + - - +
99D VAL* 3.3 8.3 + - - +
100D VAL* 3.0 29.7 + - - +
109D TRP* 4.6 3.9 - - + -
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Residues in contact with LYS 97 (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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15D LEU 2.9 26.3 + - - -
16D GLY* 4.0 12.9 + - - -
17D MET* 3.6 29.6 - - - -
20D TYR* 3.5 36.5 - - + +
28D TRP* 5.1 1.1 - - - -
93D VAL* 3.1 25.4 + - - +
94D ALA* 3.6 11.8 - - - +
96D ALA* 1.3 76.2 - - - +
98D ARG* 1.3 61.4 + - - +
100D VAL* 3.3 21.9 - - - +
101D ARG* 3.3 22.3 + - - +
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Residues in contact with ARG 98 (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* 2.8 69.9 + - - +
76D ALA 3.3 19.8 + - - -
77D CYS* 3.8 13.2 - - - +
78D HIS* 3.1 37.0 + - - +
94D ALA 3.3 9.3 + - - +
95D CYS* 3.0 11.9 + - - +
97D LYS* 1.3 77.6 - - - +
99D VAL* 1.3 55.9 + - - +
101D ARG* 2.8 60.0 + - - +
102D ASP* 3.3 8.5 - - - +
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Residues in contact with VAL 99 (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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59D ILE* 4.3 16.6 - - + -
63D TYR* 3.8 52.2 + - + +
95D CYS* 3.1 20.1 + - - +
96D ALA* 3.5 9.0 - - - +
98D ARG* 1.3 74.4 - - - +
100D VAL* 1.3 58.1 + - - +
102D ASP* 3.0 26.7 + - - +
105D GLY 4.6 3.6 + - - +
108D ALA* 4.9 11.9 - - + +
109D TRP* 3.7 29.4 - - + -
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Residues in contact with VAL 100 (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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20D TYR* 4.0 14.1 - - + -
21D ARG* 4.4 12.0 + - + +
23D ILE* 3.8 18.4 - - + -
28D TRP* 3.6 29.2 - - + -
96D ALA 3.0 14.5 + - - +
97D LYS* 3.3 21.3 - - - +
99D VAL* 1.3 75.4 - - - +
101D ARG* 1.3 55.9 + - - +
102D ASP 3.2 4.7 - - - +
105D GLY* 3.2 22.4 - - - -
106D ILE* 3.8 17.5 - - + +
109D TRP* 3.7 23.3 - - + -
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Residues in contact with ARG 101 (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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20D TYR* 2.9 30.2 + - + +
21D ARG* 3.9 36.2 + - - +
75D ASN* 4.1 10.3 - - - +
94D ALA 5.2 0.8 + - - -
97D LYS* 3.3 29.1 + - - +
98D ARG* 2.8 58.0 + - - +
100D VAL* 1.3 73.4 - - - +
102D ASP* 1.3 68.3 + - - +
103D PRO* 3.8 0.5 - - - +
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Residues in contact with ASP 102 (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 ARG* 5.2 1.0 + - - -
63D TYR* 2.7 31.3 + - - +
73D ALA 4.9 0.5 - - - +
74D VAL* 3.6 7.8 - - - +
75D ASN* 3.2 40.2 + - - +
98D ARG 3.3 13.0 - - - +
99D VAL 3.0 12.2 + - - +
100D VAL 3.3 3.6 - - - +
101D ARG* 1.3 83.0 - - - +
103D PRO* 1.3 77.3 - - + +
104D GLN 3.1 5.8 + - - +
105D GLY* 3.3 10.8 + - - -
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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