Contacts of the helix formed by residues 14 - 26 (chain B) in PDB entry 1Z6Z
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 ARG 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY 3.5 9.9 - - - +
12B ALA 3.4 0.2 - - - -
13B SER* 1.3 84.8 + - - +
15B GLY* 1.3 68.4 + - - +
16B PHE 3.6 1.2 + - - -
17B GLY 3.6 0.3 + - - -
18B ARG* 3.3 16.3 + - - -
39B ARG* 4.3 6.3 - - - +
40B ASN* 6.0 4.3 - - - +
201B ASP* 2.9 35.0 + - - +
802B NAP 2.7 83.9 + - - +
42E GLU* 5.8 10.2 - - - +
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Residues in contact with GLY 15 (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 ARG* 1.3 73.6 - - - +
16B PHE* 1.3 64.8 + - - -
18B ARG* 3.2 5.3 + - - +
19B THR* 3.2 22.9 + - - -
200B THR* 3.8 16.2 - - - -
201B ASP 5.7 0.2 - - - -
231B CYS* 4.3 3.8 - - - -
802B NAP 3.4 17.9 + - - -
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Residues in contact with PHE 16 (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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15B GLY* 1.3 70.8 - - - -
17B GLY* 1.3 56.9 + - - +
19B THR* 3.2 4.0 + - - -
20B LEU* 2.9 40.3 + - + +
97B ASN* 3.5 22.7 - - - +
152B ILE* 3.9 28.5 - - + -
193B TYR* 4.3 12.8 - + - -
195B PRO* 4.2 4.0 - - + -
198B LEU* 3.6 30.7 - - + -
200B THR* 4.0 3.0 - - - +
231B CYS* 4.0 15.7 - - + -
234B SER* 3.8 12.6 - - - -
235B ALA* 3.6 40.4 - - + -
238B LEU* 4.1 15.9 - - + -
802B NAP 2.9 16.5 + - - +
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Residues in contact with GLY 17 (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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9B LEU* 3.4 16.6 - - - +
11B GLY 3.2 19.7 - - - -
12B ALA* 4.0 4.7 - - - +
14B ARG 3.6 1.6 + - - -
15B GLY 3.3 0.4 - - - -
16B PHE* 1.3 78.8 - - - +
18B ARG* 1.3 56.6 + - - +
20B LEU* 4.2 5.6 - - - -
21B ALA* 2.9 27.5 + - - +
97B ASN* 3.5 17.6 - - - +
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 3.3 18.9 + - - +
13B SER 3.3 17.9 + - - +
14B ARG* 3.3 26.6 + - - -
15B GLY 3.2 4.1 + - - +
17B GLY* 1.3 77.1 - - - +
19B THR* 1.3 59.6 + - - +
21B ALA* 4.2 1.4 - - - +
22B PRO* 3.1 24.2 - - - +
43B ALA* 3.6 21.0 + - - +
46B GLN* 3.1 29.7 + - - +
47B LEU* 3.9 20.8 - - - +
50B GLU* 3.1 31.3 + - - -
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Residues in contact with THR 19 (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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15B GLY 3.2 9.8 + - - -
16B PHE 3.8 4.9 - - - -
18B ARG* 1.3 77.5 - - - +
20B LEU* 1.3 64.6 + - - +
22B PRO* 3.3 11.9 - - - +
23B LEU* 3.6 17.5 - - + +
231B CYS* 3.5 23.4 - - + +
232B LYS* 3.5 39.7 - - + +
235B ALA* 4.7 0.7 - - + -
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Residues in contact with LEU 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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9B LEU* 3.9 17.3 - - + -
16B PHE* 2.9 28.6 + - + +
17B GLY 3.3 5.1 + - - +
19B THR* 1.3 76.6 - - - +
21B ALA* 1.3 55.8 - - - +
23B LEU* 3.1 5.2 + - - +
24B LEU* 2.8 41.8 + - + +
95B ILE* 3.8 29.2 - - + -
235B ALA* 3.8 29.8 - - + +
238B LEU* 4.1 17.0 - - + -
239B LEU* 4.1 31.4 - - + -
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Residues in contact with ALA 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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9B LEU* 3.8 17.4 - - + +
17B GLY 2.9 16.1 + - - +
18B ARG 4.2 0.2 - - - +
20B LEU* 1.3 75.6 - - - +
22B PRO* 1.4 59.4 - - + +
24B LEU* 3.5 4.6 - - - +
25B ALA* 2.7 36.7 + - - +
34B LEU* 4.3 4.5 - - + +
36B LEU* 4.1 10.3 - - + -
47B LEU* 3.8 29.4 - - + -
51B LEU* 4.6 2.7 - - + -
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Residues in contact with PRO 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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18B ARG* 3.1 21.1 - - - +
19B THR* 3.3 11.2 - - - +
21B ALA* 1.4 92.7 - - + +
23B LEU* 1.3 62.2 + - + +
25B ALA* 3.4 2.1 + - - +
26B SER* 3.2 24.3 + - - -
47B LEU* 4.2 12.8 - - + -
50B GLU* 5.4 9.9 - - + +
51B LEU* 3.7 18.8 - - + +
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Residues in contact with LEU 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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19B THR* 3.6 14.6 - - + +
20B LEU* 3.1 6.8 + - - +
22B PRO* 1.3 81.6 - - + +
24B LEU* 1.3 61.2 + - - +
26B SER* 3.0 21.5 + - - +
27B LEU* 3.6 14.4 - - - +
232B LYS* 4.1 31.4 - - + +
235B ALA* 3.8 28.3 - - + -
236B GLN* 4.3 17.7 - - + +
239B LEU* 3.8 16.1 - - + +
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Residues in contact with LEU 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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2B LEU* 3.7 28.7 - - + -
7B CYS* 3.4 26.7 - - - -
9B LEU* 4.7 12.8 - - + -
20B LEU* 2.8 26.1 + - + +
21B ALA* 3.5 4.3 - - - +
23B LEU* 1.3 74.7 - - - +
25B ALA* 1.3 67.7 + - - +
27B LEU* 2.9 16.5 + - - +
28B LEU* 3.4 17.3 + - + +
34B LEU* 4.4 9.9 - - + -
93B LEU* 3.8 13.7 - - + -
95B ILE* 3.9 18.8 - - + -
239B LEU* 3.8 20.6 - - + +
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Residues in contact with ALA 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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21B ALA 2.7 21.1 + - - +
22B PRO 3.6 6.1 - - - +
24B LEU* 1.3 73.5 - - - +
26B SER* 1.3 60.5 + - - +
28B LEU* 3.2 33.5 + - - +
34B LEU* 4.0 7.6 - - + +
51B LEU* 3.9 21.5 - - + -
58B LEU* 3.9 24.9 - - + +
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Residues in contact with SER 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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-5B LEU* 6.2 4.7 - - - -
-3B PHE 5.5 5.9 + - - -
-2B GLN* 6.1 0.7 - - - -
-1B GLY 5.7 0.3 + - - -
1B MET* 3.6 18.1 - - - +
22B PRO 3.2 11.7 + - - -
23B LEU* 3.0 18.4 + - - +
24B LEU 3.1 0.4 + - - -
25B ALA* 1.3 75.8 - - - +
27B LEU* 1.3 64.1 + - - +
28B LEU 3.4 1.5 - - - +
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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