Contacts of the helix formed by residues 41 - 48 (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 ASN 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TYR* 2.9 35.4 + - + -
39B LYS 3.7 1.2 + - - -
40B ALA* 1.3 73.5 - - - +
42B SER* 1.3 58.7 + - - +
43B PHE* 3.0 30.4 + - - +
44B ALA* 3.1 11.8 + - + +
45B ALA* 2.8 26.9 + - - +
59B ASP* 4.7 6.9 + - - +
62B GLN* 5.6 5.5 - - - +
63B ILE* 3.5 30.3 - - - +
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Residues in contact with SER 42 (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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40B ALA 3.3 5.5 + - - -
41B ASN* 1.3 74.9 + - - +
43B PHE* 1.3 62.8 + - - +
45B ALA* 3.9 5.4 - - - +
46B TYR* 3.1 24.9 + - - +
51B SER* 5.7 0.2 - - - -
53B LYS* 4.3 28.2 + - - +
55B PRO* 4.0 8.7 - - - +
59B ASP* 3.6 27.1 + - - -
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Residues in contact with PHE 43 (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* 3.9 26.0 - + - -
22B LEU* 3.9 19.5 - - + -
41B ASN* 3.0 9.7 + - - +
42B SER* 1.3 75.0 - - - +
44B ALA* 1.3 65.0 + - - +
46B TYR* 3.3 2.8 + - - +
47B VAL* 3.0 35.1 + - + +
55B PRO* 3.7 15.8 - - + +
59B ASP* 4.3 11.5 - - - +
60B ILE* 3.9 32.3 - - + -
63B ILE* 3.8 33.7 - - + -
64B LEU* 4.9 1.8 - - + -
174B VAL* 4.0 1.6 - - + -
178B ILE* 3.6 35.4 - - + -
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Residues in contact with ALA 44 (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 LEU* 3.7 22.6 - - + +
25B TYR* 3.6 34.8 - - + -
33B LEU* 3.8 11.4 - - + -
41B ASN* 3.1 16.9 + - - +
43B PHE* 1.3 76.0 - - - +
45B ALA* 1.3 64.7 + - - +
47B VAL* 3.3 1.0 + - - +
48B PHE* 3.0 32.6 + - + +
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Residues in contact with ALA 45 (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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33B LEU* 3.6 16.8 - - + +
37B PRO 4.5 6.7 - - - +
40B ALA* 4.3 9.6 - - + +
41B ASN 2.8 21.2 + - - +
42B SER* 3.9 7.4 - - - +
43B PHE 3.3 0.2 - - - -
44B ALA* 1.3 72.9 - - - +
46B TYR* 1.3 61.8 + - - +
49B GLY 3.2 2.6 + - - -
50B ALA* 2.9 35.6 + - + +
51B SER* 3.2 21.8 + - - -
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Residues in contact with TYR 46 (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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42B SER 3.1 17.5 + - - +
43B PHE 3.7 2.2 - - - +
45B ALA* 1.3 75.0 - - - +
47B VAL* 1.3 67.2 + - - +
49B GLY* 3.3 11.1 + - - -
51B SER* 3.5 17.8 - - - +
52B ASP* 3.6 15.3 - - + -
53B LYS 3.3 22.0 - - - +
54B LYS* 3.6 38.3 - - + +
55B PRO* 3.7 19.1 - - + -
177B LYS* 3.5 62.6 + - + -
178B ILE* 4.2 12.6 - - + -
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Residues in contact with VAL 47 (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 LEU* 4.3 6.1 - - + -
43B PHE* 3.0 46.1 + - + +
44B ALA 3.9 3.1 - - - +
46B TYR* 1.3 77.7 - - + +
48B PHE* 1.3 80.2 + - + +
49B GLY 3.3 0.7 + - - -
170B PHE* 4.5 4.3 - - + -
173B TYR* 3.7 28.1 + - + -
174B VAL* 3.9 34.8 - - + -
177B LYS* 4.3 13.8 - - + +
178B ILE* 4.6 9.0 - - + -
197B PHE* 6.2 0.4 - - + -
212B ILE* 4.3 2.7 - - + +
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Residues in contact with PHE 48 (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* 4.3 6.5 - - + -
22B LEU* 4.6 10.5 - - + -
26B ALA* 3.6 28.7 - - + -
33B LEU* 4.3 22.0 - - + -
44B ALA* 3.0 28.9 + - - +
45B ALA 4.6 0.7 - - - +
47B VAL* 1.3 89.1 - - + +
49B GLY* 1.3 57.3 + - - +
50B ALA* 3.2 2.7 - - + +
170B PHE* 3.8 25.6 - + - -
197B PHE* 4.2 9.0 - + - -
201B LEU* 4.2 17.3 - - + -
208B LEU* 3.8 24.7 - - + +
211B ILE* 3.2 21.3 - - - +
212B ILE* 3.5 32.1 + - + +
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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