Contacts of the helix formed by residues 16 - 30 (chain A) in PDB entry 6B0Z
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLY* 1.3 73.1 - - - +
17A GLU* 1.3 67.2 + - - +
18A MET 3.5 0.2 + - - -
19A THR* 2.9 23.2 + - - -
20A ARG* 3.1 10.0 + - - +
44A LEU 3.9 1.0 - - - +
45A GLY* 3.3 5.6 - - - -
46A ILE* 2.8 30.4 + - - +
49A ARG* 2.8 17.0 + - - -
73A CYS* 4.3 0.6 - - - -
74A ALA 3.0 6.5 + - - -
75A THR* 3.6 3.1 - - - -
76A ILE* 2.8 55.2 + - + +
311A THR* 3.6 6.3 - - + -
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Residues in contact with GLU 17 (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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16A ASP* 1.3 72.1 - - + +
18A MET* 1.3 65.1 + - - +
20A ARG* 3.2 19.5 + - - +
21A ILE* 3.4 11.1 + - - +
76A ILE* 3.6 18.4 - - + +
82A ARG* 2.8 32.0 + - - -
85A GLU* 4.7 0.7 - - - +
86A PHE* 5.0 2.5 - - + -
311A THR* 2.6 31.3 + - - +
313A THR* 2.8 25.5 + - - +
316A TYR* 3.3 39.5 - - + -
317A ARG* 3.6 10.4 + - - -
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Residues in contact with MET 18 (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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17A GLU* 1.3 79.5 - - - +
19A THR* 1.3 61.8 + - - +
21A ILE* 3.2 27.9 + - + +
22A ILE* 3.1 31.4 + - + +
311A THR 3.2 15.3 + - - +
312A VAL* 3.5 13.7 - - + +
315A HIS* 4.0 13.0 - - + +
316A TYR* 3.4 24.9 - - + -
319A TYR* 4.0 18.6 - - + -
325A THR* 4.3 15.5 - - - +
327A THR* 3.7 30.5 - - + +
394A THR* 5.0 4.0 - - + -
395A PHE* 4.9 4.9 - - + -
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Residues in contact with THR 19 (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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16A ASP 2.9 16.1 + - - -
18A MET* 1.3 72.8 - - - +
20A ARG* 1.3 53.7 + - - +
22A ILE* 3.6 10.8 - - + +
23A TRP* 2.7 37.7 + - - +
73A CYS* 3.6 12.2 - - - -
74A ALA* 3.4 17.5 + - + +
309A HIS* 3.6 21.3 - - + -
310A GLY 3.3 24.0 - - - +
311A THR* 3.3 14.8 + - - -
312A VAL* 4.4 4.0 - - + -
327A THR* 6.0 0.2 - - + -
332A SER* 4.5 8.4 + - - +
501A NDP 5.8 0.2 - - - +
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Residues in contact with ARG 20 (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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14A GLN* 3.4 27.5 + - + -
15A GLY 2.4 42.0 + - - +
16A ASP* 3.1 21.1 + - - +
17A GLU 3.2 12.1 + - - +
19A THR* 1.3 77.0 + - - +
21A ILE* 1.3 68.9 + - + +
23A TRP* 3.3 4.0 + - - +
24A GLU* 3.1 37.1 + - + +
43A ASP* 3.2 29.7 + - - -
45A GLY* 3.8 6.3 - - - -
73A CYS* 3.8 8.7 - - - -
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Residues in contact with ILE 21 (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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17A GLU 3.6 14.6 - - - +
18A MET* 3.2 25.7 + - + +
20A ARG* 1.3 84.6 - - + +
22A ILE* 1.3 62.6 + - + +
24A GLU* 3.5 5.6 + - + +
25A LEU* 3.1 24.6 + - + +
316A TYR* 4.5 6.7 - - + -
319A TYR* 4.4 33.4 - - + +
395A PHE* 4.4 21.3 - - + -
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Residues in contact with ILE 22 (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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18A MET* 3.1 21.0 + - + +
19A THR* 3.8 11.4 - - + +
21A ILE* 1.3 74.7 - - + +
23A TRP* 1.3 61.8 + - - +
25A LEU* 3.2 10.9 + - + +
26A ILE* 2.8 42.7 + - + +
327A THR* 3.6 40.6 - - + +
328A ASN 4.7 4.7 - - - +
329A PRO* 3.7 26.7 - - + -
332A SER* 4.3 9.9 - - - +
394A THR* 3.9 22.7 - - + -
398A MET* 5.1 2.0 - - - -
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Residues in contact with TRP 23 (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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12A GLU* 2.8 32.2 + - + +
13A MET 4.1 3.0 + - - -
14A GLN* 4.6 5.8 - - + -
19A THR* 2.7 23.0 + - - +
20A ARG* 3.5 6.3 - - + +
22A ILE* 1.3 73.6 - - - +
24A GLU* 1.3 75.5 + - - +
26A ILE* 3.2 9.3 + - + +
27A LYS* 3.1 28.6 + - + +
71A VAL* 3.7 21.1 - - + -
72A LYS 3.4 35.0 - - - -
73A CYS* 3.4 32.3 - - + -
307A ALA 6.1 0.2 - - - -
332A SER* 4.2 23.6 - - - -
335A ALA* 4.5 5.6 - - + -
336A TRP* 3.3 46.1 - + - -
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Residues in contact with GLU 24 (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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14A GLN* 3.8 18.0 + - - +
20A ARG* 3.1 28.2 + - + +
21A ILE* 3.9 4.9 - - - +
23A TRP* 1.3 82.3 - - - +
25A LEU* 1.3 61.0 + - - +
27A LYS* 3.1 37.5 + - - +
28A GLU* 2.8 32.4 + - - +
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Residues in contact with LEU 25 (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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21A ILE* 3.1 18.6 + - + +
22A ILE* 3.4 13.9 - - - +
24A GLU* 1.3 76.4 - - - +
26A ILE* 1.3 57.6 + - - +
28A GLU* 4.3 12.6 - - - +
29A LYS* 2.8 67.9 + - + +
394A THR* 5.1 4.7 - - + -
395A PHE* 3.6 37.2 - - + -
398A MET* 4.1 28.5 - - + -
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Residues in contact with ILE 26 (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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22A ILE* 2.8 30.6 + - + +
23A TRP* 3.3 11.0 - - + +
25A LEU* 1.3 73.0 - - - +
27A LYS* 1.3 57.6 + - - +
30A LEU* 2.8 31.9 + - + +
31A ILE* 3.1 21.9 + - + -
332A SER* 3.6 33.7 - - - +
333A ILE* 3.6 35.2 - - + +
336A TRP* 3.7 27.8 - - + +
359A LEU* 6.1 0.2 - - + -
398A MET* 4.2 14.8 - - + -
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Residues in contact with LYS 27 (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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12A GLU* 2.7 36.6 + - - +
14A GLN* 3.5 15.0 - - - +
23A TRP* 3.1 13.3 + - - +
24A GLU* 3.1 34.4 + - - +
26A ILE* 1.3 75.2 - - - +
28A GLU* 1.3 62.1 + - - +
31A ILE* 4.0 8.7 - - + -
32A PHE* 2.9 67.2 + - + +
39A LEU* 5.1 1.6 - - - +
336A TRP* 3.6 33.7 - - + -
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Residues in contact with GLU 28 (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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24A GLU 2.8 20.4 + - - +
25A LEU* 4.1 18.2 - - - +
27A LYS* 1.3 74.5 - - - +
29A LYS* 1.3 67.7 + - + +
32A PHE* 4.6 6.9 - - - +
33A PRO* 3.2 24.4 - - - +
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Residues in contact with LYS 29 (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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25A LEU* 2.8 47.4 + - + +
28A GLU* 1.3 86.7 + - + +
30A LEU* 1.3 74.7 + - + +
31A ILE 3.9 0.2 - - - -
33A PRO* 3.7 12.7 - - - +
34A TYR* 4.3 7.8 + - - -
395A PHE 5.5 0.2 - - - -
398A MET* 4.4 22.4 - - + +
399A ASP* 3.1 30.6 + - - +
402A GLY* 5.1 6.9 - - - -
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Residues in contact with LEU 30 (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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26A ILE* 2.8 22.3 + - + +
29A LYS* 1.3 84.5 - - + +
31A ILE* 1.3 61.2 + - + +
34A TYR* 3.4 13.1 - - - -
333A ILE* 3.7 29.2 - - + -
355A PHE* 3.3 21.1 - - - -
359A LEU* 4.4 18.8 - - + -
398A MET* 3.7 29.4 - - + +
401A LEU* 4.3 9.6 - - + +
402A GLY* 3.9 26.7 - - - +
405A LEU* 3.7 24.3 - - + +
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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