Contacts of the helix formed by residues 19 - 32 (chain B) in PDB entry 1ZBQ
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 ALA 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLY 3.7 6.1 - - - +
17B ALA 3.4 0.8 - - - -
18B GLY* 1.3 78.8 - - - +
20B GLY* 1.3 68.0 + - - +
21B LEU 3.5 0.2 + - - -
22B GLY 3.4 5.2 + - - -
23B ARG* 3.1 21.8 + - - +
199B ARG* 4.8 13.5 - - - +
1002B NAD 3.5 31.5 + - - +
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA* 1.3 73.9 - - - +
21B LEU* 1.3 64.6 + - - -
23B ARG* 3.6 5.1 + - - +
24B ALA* 3.2 21.3 + - - +
197B GLY 5.3 0.7 - - - -
198B SER* 4.4 11.2 - - - -
215B PRO* 3.9 15.8 - - - +
1002B NAD 3.4 15.5 - - - -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY* 1.3 71.5 - - - -
22B GLY* 1.3 56.5 - - - +
24B ALA* 3.2 2.4 + - - +
25B TYR* 2.9 53.4 + - + +
99B ASN* 3.6 12.3 - - - +
194B PRO* 3.7 29.6 - - + -
196B ALA* 3.7 18.2 - - + -
198B SER* 5.4 0.4 - - - -
215B PRO* 3.8 13.0 - - + +
218B VAL* 3.7 33.2 - - + -
1002B NAD 2.8 49.0 + - + +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.7 9.6 - - - +
16B GLY 3.7 6.7 - - - -
17B ALA* 3.7 7.6 - - - -
19B ALA 3.4 3.2 + - - -
20B GLY 3.3 0.4 - - - -
21B LEU* 1.3 76.7 - - - +
23B ARG* 1.3 57.8 + - - +
25B TYR* 3.1 14.0 + - - +
26B ALA* 2.9 30.5 + - - +
99B ASN* 3.6 23.7 - - - +
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 3.3 17.2 + - - +
18B GLY 4.1 8.5 - - - -
19B ALA* 3.1 26.6 + - - +
20B GLY 3.6 4.0 + - - +
22B GLY* 1.3 75.2 - - - +
24B ALA* 1.3 64.3 + - - +
26B ALA* 3.2 3.5 + - - +
27B LEU* 3.1 45.3 + - + +
58B VAL* 3.9 20.4 - - + -
61B GLU* 2.6 40.2 + - - -
65B ARG* 4.5 5.9 - - - +
216B GLU* 5.2 7.1 + - - -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY 3.2 3.8 + - - +
21B LEU 3.5 8.3 - - - +
23B ARG* 1.3 80.0 - - - +
25B TYR* 1.3 63.4 + - + +
27B LEU* 3.6 7.8 + - - +
28B ALA* 3.1 25.5 + - - +
215B PRO* 3.7 40.6 - - + +
216B GLU* 4.1 16.8 - - + +
219B ALA* 4.1 4.9 - - + +
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 4.2 9.0 - - + -
21B LEU* 2.9 49.5 + - + +
22B GLY* 3.4 12.8 - - - +
24B ALA* 1.3 71.6 - - - +
26B ALA* 1.3 59.2 + - - +
28B ALA* 3.2 2.0 + - - +
29B PHE* 2.9 49.8 + - + -
97B VAL* 3.6 29.2 - - + -
99B ASN* 3.8 18.0 + - + -
149B THR* 5.3 1.6 + - - +
192B ILE* 3.4 14.3 - - + +
194B PRO* 4.8 0.3 - - - +
215B PRO 4.7 1.1 - - - -
218B VAL* 3.4 21.2 - - + +
219B ALA* 3.9 33.0 - - + -
222B VAL* 3.7 24.2 - - + -
223B LEU* 5.0 0.9 - - - -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 4.4 10.1 - - + -
17B ALA* 4.1 17.7 - - + -
22B GLY 2.9 15.7 + - - +
23B ARG 3.7 4.3 - - - +
25B TYR* 1.3 77.1 - - - +
27B LEU* 1.3 58.3 + - - +
29B PHE* 3.9 3.2 - - - +
30B ALA* 3.1 30.3 + - - +
36B VAL* 3.9 10.8 - - + +
38B VAL* 4.1 18.8 - - + -
58B VAL* 4.3 4.9 - - + -
62B ILE* 3.9 8.5 - - + +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 3.1 56.0 + - + +
24B ALA* 3.9 6.1 - - - +
26B ALA* 1.3 74.3 - - - +
28B ALA* 1.3 65.1 + - - +
30B ALA* 3.4 1.2 + - - +
31B GLU* 3.0 27.4 + - - +
58B VAL* 4.6 5.4 - - + +
61B GLU* 4.3 10.5 - - + -
62B ILE* 3.5 36.3 - - + +
65B ARG* 4.4 25.3 - - - +
216B GLU* 6.2 0.4 - - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 3.1 19.0 + - - +
25B TYR 3.8 0.2 - - - +
27B LEU* 1.3 79.2 - - - +
29B PHE* 1.3 60.6 + - - +
31B GLU* 3.6 5.1 + - - +
32B ARG* 3.1 36.2 + - - +
219B ALA* 4.1 12.6 - - + -
223B LEU* 3.8 27.6 - - + -
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.7 38.7 - + - +
12B VAL* 3.6 32.3 - - + -
14B VAL* 4.2 3.8 - - + -
25B TYR* 2.9 35.1 + - + +
26B ALA 3.9 3.1 - - - +
28B ALA* 1.3 75.6 - - - +
30B ALA* 1.3 58.2 + - - +
32B ARG* 3.0 20.4 + - - +
33B GLY 3.4 0.3 + - - -
34B ALA* 3.2 27.7 + - + +
36B VAL* 4.1 6.5 - - + -
95B VAL* 4.4 0.7 - - + -
97B VAL* 3.9 11.0 - - + -
222B VAL* 3.7 32.1 - - + -
223B LEU* 3.9 18.4 - - + +
226B CYS* 3.9 19.7 - - + -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA 3.1 19.0 + - - +
27B LEU 3.4 2.9 + - - +
29B PHE* 1.3 72.0 - - - +
31B GLU* 1.3 64.0 + - - +
33B GLY* 3.1 13.9 + - - -
34B ALA 3.9 14.6 + - - +
36B VAL* 3.9 10.3 - - + +
62B ILE* 3.5 35.7 - - + -
67B GLY* 4.1 16.9 - - - -
68B LYS 4.5 0.9 - - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 3.6 12.0 + - - -
27B LEU 3.0 18.7 + - - +
28B ALA* 3.8 7.4 - - - +
29B PHE 3.2 0.2 - - - -
30B ALA* 1.3 76.6 - - - +
32B ARG* 1.3 83.8 + - - +
33B GLY 3.3 1.6 + - - -
65B ARG* 5.9 6.2 + - + -
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A MET 5.4 1.8 + - - -
265A THR* 4.9 7.3 - - - +
266A PRO* 3.3 29.1 - - - +
267A GLU* 4.7 6.7 + - - -
5B LEU 3.9 20.7 + - - +
6B ARG* 3.4 25.9 - - - +
7B PHE* 2.8 43.4 + - + -
8B ASP 3.5 1.2 + - - -
28B ALA* 3.1 28.1 + - - +
29B PHE 3.0 8.4 + - - +
31B GLU* 1.3 101.8 + - - +
33B GLY* 1.3 55.1 + - - +
34B ALA 3.5 3.1 - - - -
223B LEU* 3.5 23.3 - - + +
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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