Contacts of the helix formed by residues 17 - 33 (chain B) in PDB entry 4BL8
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ILE* 4.5 4.5 - - - +
16B LYS* 1.3 72.5 - - - +
18B TYR* 1.3 60.3 + - - -
21B LEU* 3.4 23.7 + - - +
294B VAL* 3.9 16.6 - - - +
297B ASP* 3.1 28.5 - - - -
298B LYS* 3.6 17.4 + - - +
300B LEU* 6.0 0.6 - - - +
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Residues in contact with TYR 18 (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 ILE* 3.7 26.5 - - + -
13B ASN 4.5 0.7 - - - -
14B GLY* 3.1 28.5 - - - -
16B LYS 3.1 13.2 + - - -
17B GLY* 1.3 73.7 - - - -
19B ASN* 1.3 89.0 + - - +
20B GLY 3.5 0.4 - - - -
21B LEU* 3.9 2.9 - - - -
22B ALA* 3.1 24.3 + - - +
38B VAL* 3.9 14.4 - - + +
40B HIS* 3.2 46.1 + + + -
297B ASP* 3.4 0.8 + - - -
298B LYS* 5.5 4.7 - - - -
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TYR* 1.3 110.3 + - - +
20B GLY* 1.3 64.1 + - - +
21B LEU 3.3 0.2 - - - -
22B ALA* 3.3 8.2 + - - +
23B GLU* 3.1 26.2 + - - +
297B ASP* 3.0 18.0 + - - +
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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
----------------------------------------------------------
17B GLY 4.1 0.4 + - - -
19B ASN* 1.3 74.8 - - - +
21B LEU* 1.3 61.9 + - - +
23B GLU* 3.1 22.9 + - - +
24B VAL* 3.2 15.9 + - - +
293B ALA* 3.2 27.4 - - - +
294B VAL* 4.2 4.7 - - - -
297B ASP* 2.9 20.2 + - - -
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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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10B ILE* 4.0 26.2 - - + -
12B ILE* 3.8 33.2 - - + -
17B GLY 3.4 19.1 + - - +
18B TYR 4.0 3.8 - - - +
19B ASN 3.3 0.4 - - - -
20B GLY* 1.3 75.6 - - - +
22B ALA* 1.3 57.8 + - - +
23B GLU 3.3 0.2 - - - -
24B VAL* 3.4 4.4 + - + +
25B GLY* 3.1 21.0 + - - -
38B VAL* 4.4 11.3 - - + +
62B PHE* 4.2 7.4 - - + -
280B PHE* 3.8 24.7 - - + -
285B LEU* 4.1 29.2 - - + -
294B VAL* 3.9 11.7 - - + +
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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
----------------------------------------------------------
18B TYR 3.1 19.7 + - - +
19B ASN* 3.5 12.3 - - - +
20B GLY 3.2 0.4 - - - -
21B LEU* 1.3 76.1 - - - +
23B GLU* 1.3 59.2 + - - +
25B GLY* 3.1 3.0 + - - +
26B LYS* 2.9 40.1 + - + +
36B VAL 5.7 0.7 - - - +
38B VAL* 4.1 18.4 - - + -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN 3.1 17.4 + - - +
20B GLY* 3.1 19.9 + - - +
22B ALA* 1.3 73.8 - - - +
24B VAL* 1.3 63.9 + - - +
26B LYS* 3.1 22.9 + - + +
27B LYS* 3.2 13.2 + - - +
293B ALA* 4.1 17.1 - - + +
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Residues in contact with VAL 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 12.6 + - - +
21B LEU* 3.6 9.6 - - + +
22B ALA 3.3 0.4 - - - -
23B GLU* 1.3 76.7 - - - +
25B GLY* 1.3 61.2 + - - +
27B LYS* 3.3 9.1 + - + +
28B PHE* 3.2 21.1 + - - +
280B PHE* 3.5 22.2 - - + -
284B TYR* 4.0 23.2 - - + +
285B LEU* 4.0 11.2 - - + +
290B GLY* 3.6 31.2 - - - +
293B ALA* 3.7 10.3 - - + -
294B VAL* 4.5 6.7 - - + -
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 3.1 14.1 + - - -
22B ALA* 3.1 7.2 + - - -
24B VAL* 1.3 74.9 - - - +
26B LYS* 1.3 61.3 + - - +
28B PHE* 3.9 0.7 - - - -
29B GLU* 3.3 18.7 + - - +
36B VAL* 3.6 36.8 + - - +
280B PHE* 3.8 15.2 - - - -
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Residues in contact with LYS 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* 2.9 26.7 + - + +
23B GLU* 3.1 17.1 + - + +
25B GLY* 1.3 76.8 - - - +
27B LYS* 1.3 64.4 + - - +
29B GLU* 3.1 11.3 + - - +
30B LYS* 3.0 23.5 + - - +
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Residues in contact with LYS 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 GLU 3.2 8.6 + - - +
24B VAL* 3.3 12.3 + - + +
26B LYS* 1.3 78.6 - - - +
28B PHE* 1.3 61.5 + - - +
30B LYS* 3.5 11.5 + - + +
31B ASP* 3.2 43.7 + - - +
284B TYR* 4.0 17.0 - - + -
289B GLU* 5.8 9.6 - - + -
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Residues in contact with PHE 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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8B LEU* 4.3 9.4 - - + -
24B VAL 3.2 15.6 + - - +
25B GLY 3.7 5.4 - - - +
26B LYS 3.1 0.2 - - - -
27B LYS* 1.3 76.2 - - - +
29B GLU* 1.3 60.3 + - - +
31B ASP* 3.3 1.2 + - - -
32B THR* 2.9 55.9 + - + -
34B ILE* 4.0 29.6 - - + -
36B VAL* 3.6 17.7 - - + -
276B LEU* 3.9 24.5 - - + -
279B GLU* 4.2 11.0 - - + -
280B PHE* 3.9 29.2 - + + -
284B TYR* 3.4 42.8 - + + -
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Residues in contact with GLU 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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25B GLY 3.3 10.2 + - - +
26B LYS* 3.1 14.9 + - - +
28B PHE* 1.3 78.8 - - - +
30B LYS* 1.3 58.2 + - - +
33B GLY* 2.9 29.7 + - - +
34B ILE 3.1 24.6 + - - +
35B LYS* 3.3 38.9 - - - +
36B VAL 3.7 5.5 + - - +
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Residues in contact with LYS 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 LYS 3.0 12.3 + - - +
27B LYS* 3.6 15.9 - - + +
28B PHE 3.2 0.2 - - - -
29B GLU* 1.3 80.3 - - - +
31B ASP* 1.3 72.9 + - - +
32B THR 3.5 0.3 + - - -
33B GLY* 4.5 0.9 + - - -
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Residues in contact with ASP 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 LYS* 3.2 36.7 + - - +
28B PHE 4.1 0.7 - - - +
30B LYS* 1.3 93.7 - - - +
32B THR* 1.3 59.4 + - - +
284B TYR* 3.5 25.8 + - - +
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Residues in contact with THR 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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28B PHE* 2.9 37.7 + - + -
30B LYS 3.3 0.6 - - - -
31B ASP* 1.3 82.5 - - - +
33B GLY* 1.3 60.3 + - - +
34B ILE* 3.7 26.0 - - + +
276B LEU* 5.0 4.9 - - + -
279B GLU* 5.5 1.0 + - - -
284B TYR* 3.7 13.5 + - - -
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Residues in contact with GLY 33 (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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29B GLU* 2.9 23.5 + - - +
30B LYS 4.5 1.0 + - - -
32B THR* 1.3 78.7 - - - +
34B ILE* 1.3 64.5 + - - +
35B LYS 3.9 1.9 + - - -
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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