Contacts of the helix formed by residues 90 - 102 (chain D) in PDB entry 3AZG
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 THR 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLY* 4.7 2.5 - - - -
47C ALA* 4.0 5.2 - - - -
86D ARG* 3.8 21.9 + - - +
88D THR* 3.9 14.6 - - + +
89D ILE* 1.3 77.0 - - - +
91D SER* 1.3 59.5 + - - +
92D ARG* 3.3 17.4 + - - +
93D GLU* 2.6 43.6 + - - +
94D ILE* 3.2 10.6 + - - +
201D CL 3.5 18.8 - - + -
258J T 5.3 1.8 - - - +
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Residues in contact with SER 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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46C GLY* 3.9 21.1 - - - -
47C ALA* 3.9 9.5 - - - +
50C TYR* 3.8 23.7 - - - -
90D THR* 1.3 74.7 - - - +
92D ARG* 1.3 59.8 + - - +
94D ILE* 3.7 6.4 - - - +
95D GLN* 2.9 29.6 + - - +
118D VAL* 4.4 11.5 - - - +
201D CL 3.3 9.9 - - - +
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Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU 3.4 15.4 + - - -
75B HIS* 2.8 57.1 + - + +
77B LYS* 3.6 31.3 - - - +
86D ARG* 5.8 2.8 - - - +
90D THR* 2.9 13.5 + - - +
91D SER* 1.3 84.0 + - - +
93D GLU* 1.3 65.6 + - - +
95D GLN* 3.5 9.3 + - + +
96D THR* 3.1 27.6 + - - +
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Residues in contact with GLU 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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75B HIS* 3.3 30.1 + - + +
77D ALA* 4.0 24.0 - - + +
80D LEU* 4.4 5.2 - - + +
81D ALA* 4.3 8.9 - - + +
86D ARG* 3.2 24.0 + - - -
88D THR 3.6 9.8 - - - +
89D ILE* 4.0 19.1 - - + -
90D THR* 2.6 52.8 + - - +
92D ARG* 1.3 73.2 + - - +
94D ILE* 1.3 68.0 + - - +
95D GLN 3.0 1.7 + - - -
96D THR* 3.2 2.5 + - - -
97D ALA* 2.9 25.1 + - - +
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Residues in contact with ILE 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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34C LEU* 4.8 5.2 - - + -
47C ALA* 3.8 29.2 - - + +
50C TYR* 3.7 23.3 - - + -
51C LEU* 4.1 27.4 - - + +
54C VAL* 5.3 0.2 - - + -
73D ILE* 3.9 23.8 - - + -
74D ALA* 5.4 2.7 - - - -
77D ALA* 4.2 6.5 - - + -
89D ILE* 4.0 17.5 - - + -
90D THR 3.2 11.8 + - - +
91D SER* 3.3 6.7 + - - +
93D GLU* 1.3 76.1 - - - +
95D GLN* 1.3 57.1 + - - +
97D ALA* 3.7 6.0 - - - +
98D VAL* 3.0 30.4 + - + +
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 2.5 41.8 + - + +
91D SER 2.9 17.9 + - - +
92D ARG* 3.7 9.8 - - + +
93D GLU 3.0 0.4 - - - -
94D ILE* 1.3 76.4 - - - +
96D THR* 1.3 66.4 + - - +
98D VAL* 3.2 5.2 + - - +
99D ARG* 3.2 35.9 + - - +
111D VAL* 3.6 19.0 - - + +
115D THR* 3.4 16.4 + - - -
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Residues in contact with THR 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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71B THR* 3.5 27.6 - - + +
72B TYR* 5.6 0.2 - - - -
75B HIS* 2.7 42.9 - - + +
80D LEU* 3.5 22.4 - - + -
92D ARG* 3.1 10.8 + - - +
93D GLU 3.9 0.7 - - - -
95D GLN* 1.3 74.2 - - - +
97D ALA* 1.3 65.9 + - - +
99D ARG* 3.1 9.2 + - - +
100D LEU* 3.1 24.2 + - + +
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Residues in contact with ALA 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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73D ILE* 3.6 33.7 - - + +
76D GLU* 3.8 26.5 - - + +
77D ALA* 3.9 4.9 - - - +
80D LEU* 4.0 1.5 - - + +
93D GLU 2.9 17.0 + - - +
94D ILE 3.7 4.9 - - - +
96D THR* 1.3 76.1 - - - +
98D VAL* 1.3 57.5 + - - +
100D LEU* 3.3 1.1 + - - -
101D LEU* 2.9 35.7 + - - +
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Residues in contact with VAL 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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50C TYR* 4.6 2.5 - - + -
54C VAL* 3.9 24.0 - - + -
73D ILE* 3.7 24.0 - - + -
94D ILE* 3.0 25.5 + - + +
95D GLN* 3.5 10.1 - - - +
96D THR 3.1 0.2 - - - -
97D ALA* 1.3 77.4 - - - +
99D ARG* 1.3 57.2 + - - +
102D LEU* 2.9 51.2 + - + +
107D ALA* 4.3 4.6 - - - +
110D ALA* 4.0 14.6 - - + -
111D VAL* 4.3 16.6 - - + +
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Residues in contact with ARG 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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67B ARG* 6.2 0.2 - - - -
68B ASP* 5.5 0.3 - - - +
71B THR* 4.7 15.9 - - + +
95D GLN* 3.2 27.5 + - - +
96D THR* 3.1 11.9 + - - +
98D VAL* 1.3 75.9 - - - +
100D LEU* 1.3 62.2 + - - +
102D LEU 3.6 11.1 - - - +
107D ALA* 4.5 17.3 - - + +
108D LYS* 5.1 8.7 - - - +
111D VAL* 3.7 41.0 - - + +
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Residues in contact with LEU 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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68B ASP* 3.6 38.1 - - - +
71B THR* 3.9 26.2 - - + +
72B TYR* 3.9 15.0 - - + +
92B ARG* 3.3 30.5 + - - +
76D GLU* 3.3 31.0 - - + +
80D LEU* 4.0 11.7 - - + -
96D THR* 3.1 20.0 + - + +
97D ALA 3.6 6.3 - - - +
99D ARG* 1.3 79.1 - - - +
101D LEU* 1.3 67.7 + - + +
102D LEU 4.8 0.7 - - - +
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Residues in contact with LEU 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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92B ARG* 3.4 23.1 - - - +
96C LEU* 4.0 11.9 - - + +
72D ARG* 4.0 42.0 - - + +
73D ILE* 4.3 14.6 - - + -
76D GLU* 3.7 29.6 - - + +
97D ALA* 2.9 23.1 + - + +
98D VAL 4.1 1.3 - - - +
100D LEU* 1.3 77.4 - - + +
102D LEU* 1.3 67.4 + - + +
103D PRO* 3.9 5.5 - - - +
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Residues in contact with LEU 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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54C VAL* 4.6 2.9 - - + -
58C LEU* 4.1 28.0 - - + -
96C LEU* 3.5 35.9 - - + -
69D ILE* 5.2 5.6 - - + -
73D ILE* 5.3 3.6 - - + -
98D VAL* 2.9 28.7 + - + +
99D ARG 3.6 11.6 - - - +
100D LEU 4.8 0.7 - - - +
101D LEU* 1.3 78.8 - - + +
103D PRO* 1.3 70.5 - - + +
106D LEU* 3.9 9.9 - - + +
107D ALA* 3.6 21.7 - - - +
110D ALA* 3.8 29.6 - - + -
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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