Contacts of the helix formed by residues 19 - 29 (chain B) in PDB entry 5W4A
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 PHE 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B THR* 3.0 14.0 + - - +
18B PHE* 1.3 92.5 - - + +
20B PRO* 1.3 66.0 - - - +
21B ASN 3.4 2.5 - - - -
22B LEU* 3.2 15.1 + - + -
23B ALA* 3.1 19.4 + - - +
43B PHE* 3.9 24.2 - + - -
64B LEU* 4.0 14.1 - - + -
80B THR* 3.5 18.6 - - + -
84B LEU* 5.1 6.7 - - + -
170B PHE* 4.0 7.8 - - + -
171B ASP* 3.6 17.3 - - - -
174B VAL* 3.5 38.1 - - + -
175B PHE* 3.7 39.3 - + - -
178B ILE* 6.0 0.7 - - + -
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Residues in contact with PRO 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 VAL* 3.7 24.5 - - + -
11B PHE* 3.4 16.7 - - + -
16B THR* 3.6 11.9 - - + +
17B TYR 3.3 17.5 - - - +
18B PHE 3.4 4.3 - - - +
19B PHE* 1.3 90.2 - - - +
21B ASN* 1.3 59.0 + - + +
23B ALA* 3.4 1.2 + - - +
24B LEU* 3.0 23.6 + - - +
64B LEU* 6.1 0.4 - - + -
73B THR* 6.1 6.5 - - + +
76B THR* 4.6 11.9 - - + -
77B SER* 5.6 5.4 - - - +
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE 3.4 0.4 - - - -
20B PRO* 1.3 79.7 - - + +
22B LEU* 1.3 59.9 + - - +
24B LEU* 4.2 19.0 - - - +
25B TYR* 2.9 29.6 + - - +
62B GLN 4.7 0.2 + - - -
63B ILE* 2.9 43.7 + - + +
64B LEU* 5.4 2.2 - - - +
66B PRO* 3.6 28.0 - - + +
73B THR* 6.3 2.2 - - + -
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Residues in contact with LEU 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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19B PHE* 3.2 18.3 + - + +
21B ASN* 1.3 76.8 - - - +
23B ALA* 1.3 64.7 + - - +
25B TYR* 3.3 6.3 + - + +
26B ALA* 3.0 21.5 + - - +
43B PHE* 3.9 32.1 - - + +
44B ALA* 3.7 39.3 - - + +
47B VAL* 4.3 6.5 - - + -
48B PHE* 4.6 6.1 - - + -
63B ILE* 3.8 18.9 - - + +
170B PHE* 3.9 23.3 - - + -
174B VAL* 4.0 16.8 - - + -
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Residues in contact with ALA 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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11B PHE* 3.9 15.9 - - + -
14B ILE* 3.5 38.9 - - + +
16B THR* 3.9 9.2 - - + -
19B PHE 3.1 12.5 + - - +
20B PRO 3.6 7.4 - - - +
22B LEU* 1.3 77.6 - - - +
24B LEU* 1.3 62.5 + - - +
26B ALA* 3.2 4.6 + - - +
27B VAL* 3.1 26.5 + - - +
170B PHE* 4.4 4.8 - - + -
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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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12A LEU* 6.2 0.7 - - + -
24A LEU* 4.5 6.7 - - + -
27A VAL* 4.1 19.5 - - + -
28A ASN* 4.2 2.7 - - - +
11B PHE* 3.9 39.8 - - + -
20B PRO 3.0 16.9 + - - +
21B ASN* 3.9 17.9 - - - +
23B ALA* 1.3 77.2 - - - +
25B TYR* 1.3 62.9 + - - +
27B VAL* 3.2 4.7 + - + +
28B ASN* 2.9 52.9 + - - +
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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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21B ASN* 2.9 20.7 + - - +
22B LEU* 3.5 8.5 - - - +
23B ALA 3.3 0.2 - - - -
24B LEU* 1.3 77.8 - - - +
26B ALA* 1.3 60.6 + - - +
28B ASN* 4.8 0.9 - - - +
29B ASN* 2.8 67.5 + - + +
32B LEU* 4.0 12.6 - - - +
33B LEU* 4.7 10.1 - - + -
39B LYS 4.4 1.2 + - - -
40B ALA* 3.5 9.6 - - + -
41B ASN* 2.9 34.2 + - + -
44B ALA* 3.6 30.5 - - + -
63B ILE* 4.4 18.8 - - + -
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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 ILE* 4.2 7.9 - - + -
22B LEU 3.0 9.6 + - - +
23B ALA 3.2 7.6 + - - +
25B TYR* 1.3 77.6 - - + +
27B VAL* 1.3 57.4 + - - +
30B ASP* 3.0 33.8 + - - +
33B LEU* 4.0 17.0 - - + -
48B PHE* 3.6 38.4 - - + -
208B LEU* 4.0 7.7 - - + +
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Residues in contact with VAL 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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11A PHE* 4.2 13.0 - - + -
24A LEU* 4.3 20.1 - - + +
11B PHE* 3.6 28.9 - - + +
12B LEU* 3.9 34.3 - - + +
14B ILE* 4.2 10.8 - - + -
23B ALA 3.1 16.6 + - - +
24B LEU* 3.8 6.7 - - + +
26B ALA* 1.3 77.5 - - - +
28B ASN* 1.3 62.6 + - - +
30B ASP* 3.3 14.4 - - - +
205B LYS* 4.3 13.4 + - + +
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Residues in contact with ASN 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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24A LEU* 3.6 14.5 - - - +
28A ASN* 3.0 42.2 + - - +
24B LEU* 2.9 37.3 + - - +
25B TYR* 4.8 0.4 - - - +
27B VAL* 1.3 76.0 - - - +
29B ASN* 1.3 75.5 + - - +
30B ASP 3.7 0.7 - - - -
31B GLU* 3.6 15.2 - - - +
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Residues in contact with ASN 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 TYR* 2.8 64.3 + - + +
26B ALA 3.7 2.5 - - - -
28B ASN* 1.3 93.4 - - - +
30B ASP* 1.3 66.1 + - - +
31B GLU* 3.1 11.0 - - - +
32B LEU* 3.0 34.3 + - + +
33B LEU* 3.2 13.1 + - - +
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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