Contacts of the helix formed by residues 19 - 31 (chain B) in PDB entry 5IZL
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 GLY 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ASP 3.1 2.2 - - - -
18B SER* 1.3 70.5 - - - +
20B LYS* 1.3 56.5 + - - +
21B THR 3.4 1.6 - - - -
22B ALA* 3.5 1.4 + - - +
23B LEU* 2.9 32.1 + - - +
116B VAL* 4.5 3.4 - - - -
146B ASN* 3.7 12.6 + - - -
1002B GCP 2.4 46.9 + - - -
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Residues in contact with LYS 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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12B VAL* 3.6 31.9 - - + +
13B LEU* 3.6 11.0 - - - +
14B GLY 3.4 26.4 + - - +
15B HIS 2.8 27.1 + - - -
18B SER* 3.4 12.6 - - - +
19B GLY* 1.3 74.0 - - - +
21B THR* 1.3 57.1 + - - +
23B LEU* 3.5 2.1 + - - +
24B ALA* 3.0 28.1 + - - +
92B ASP* 3.7 8.0 - - - +
93B CYS 3.2 21.8 - - - -
94B PRO 3.6 14.6 - - - -
95B GLY* 3.5 6.1 - - - -
116B VAL* 4.4 4.5 - - + -
1002B GCP 2.7 34.7 + - - +
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Residues in contact with THR 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 LYS* 1.3 71.9 - - - +
22B ALA* 1.3 66.8 + - - +
24B ALA* 3.3 3.4 + - + +
25B ARG* 3.0 24.9 + - + +
45B ARG 6.6 0.2 - - - -
46B GLY 5.3 4.5 - - - +
48B THR* 3.0 3.5 + - - +
92B ASP* 2.7 26.4 + - - +
1001B MG 2.3 29.8 - - - -
1002B GCP 2.9 12.1 + - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.7 7.2 - - - +
20B LYS 3.4 0.2 - - - -
21B THR* 1.3 76.1 - - - +
23B LEU* 1.3 56.2 + - - +
25B ARG* 3.3 6.4 + - - +
26B ALA* 3.0 27.9 + - - +
186B ALA* 3.8 9.8 - - + +
187B LYS* 4.4 10.5 - - + -
1002B GCP 3.2 42.3 + - + +
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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
----------------------------------------------------------
12B VAL* 4.2 10.8 - - + -
19B GLY 2.9 18.8 + - - +
20B LYS 3.8 1.6 - - - +
22B ALA* 1.3 74.1 - - - +
24B ALA* 1.3 60.1 + - - +
25B ARG 3.1 1.6 - - - -
26B ALA* 4.0 0.8 - - - +
27B LEU* 3.0 35.5 + - + +
114B MET* 4.3 17.5 - - - -
116B VAL* 4.0 26.2 - - + -
144B VAL* 4.3 11.4 - - + -
146B ASN* 4.6 4.5 - - - +
184B VAL* 4.1 20.4 - - + -
186B ALA* 3.6 19.0 - - + +
202B ILE* 5.5 7.0 - - + -
205B LEU* 3.9 20.0 - - + -
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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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12B VAL* 4.4 14.1 - - + -
20B LYS 3.0 17.6 + - - +
21B THR* 3.8 7.2 - - - +
23B LEU* 1.3 78.0 - - - +
25B ARG* 1.3 56.7 + - - +
27B LEU* 4.6 2.9 - - - -
28B SER* 2.9 33.8 + - - -
54B SER* 4.3 11.0 + - - +
90B LEU* 3.8 20.6 - - + +
92B ASP* 4.6 12.8 - - + +
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Residues in contact with ARG 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 THR* 3.0 15.7 + - + +
22B ALA* 3.6 9.6 - - - +
24B ALA* 1.3 76.7 - - - +
26B ALA* 1.3 65.4 + - - +
28B SER* 3.2 4.1 + - - -
29B THR* 3.1 42.0 + - + +
45B ARG 6.2 0.2 - - - +
54B SER* 5.4 1.6 - - - -
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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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22B ALA 3.0 15.9 + - - +
23B LEU* 3.5 3.8 + - + +
25B ARG* 1.3 77.2 - - - +
27B LEU* 1.3 60.2 + - - +
29B THR* 3.2 7.0 + - - -
30B THR* 3.1 29.6 + - - -
186B ALA* 4.1 13.7 - - + +
199B PRO* 4.1 13.5 - - + -
202B ILE* 2.8 30.3 - - + -
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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
----------------------------------------------------------
23B LEU* 3.0 34.0 + - + +
24B ALA* 4.0 3.6 - - - +
26B ALA* 1.3 79.6 - - - +
28B SER* 1.3 57.4 + - - +
29B THR 3.2 3.5 + - - -
30B THR 3.7 0.2 + - - -
31B ALA* 3.6 16.5 + - - +
56B PHE* 4.0 20.2 - - + -
90B LEU* 4.1 24.7 - - + -
114B MET* 4.1 15.9 - - + -
202B ILE* 4.0 9.6 - - + -
205B LEU* 3.8 28.5 - - + -
206B ILE* 3.6 34.0 - - + +
209B LEU* 4.4 9.4 - - + -
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Residues in contact with SER 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 2.9 21.6 + - - -
25B ARG* 3.2 4.4 + - - -
27B LEU* 1.3 74.8 - - - +
29B THR* 1.3 60.6 + - - +
31B ALA* 4.7 2.8 - - - +
32B SER* 5.5 1.7 + - - -
54B SER* 3.3 18.7 - - - -
55B CYS 4.0 13.6 + - - +
56B PHE* 3.9 15.0 - - - +
90B LEU* 3.1 19.9 - - - +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.1 29.6 + - + +
26B ALA* 3.2 13.5 + - - -
28B SER* 1.3 81.0 - - - +
30B THR* 1.3 69.0 + - - +
31B ALA 3.1 2.2 - - - -
32B SER* 2.9 25.4 + - - +
199B PRO* 5.9 1.2 - - - +
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 3.1 16.0 + - - -
29B THR* 1.3 82.5 + - - +
31B ALA* 1.3 57.9 + - - +
32B SER 2.9 15.5 + - - +
199B PRO* 5.5 2.3 - - - +
202B ILE* 3.4 26.9 - - + +
203B PRO* 4.2 20.5 - - + +
206B ILE* 3.7 19.3 - - + -
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Residues in contact with ALA 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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27B LEU 3.6 7.3 + - - +
28B SER 5.2 2.2 - - - +
29B THR 3.1 1.8 - - - -
30B THR* 1.3 76.4 - - - +
32B SER* 1.3 57.1 + - - +
56B PHE* 3.9 40.2 - - + -
57B SER 4.1 13.8 - - - +
58B VAL* 5.3 3.8 - - + -
206B ILE* 4.2 8.9 - - + +
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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