Contacts of the helix formed by residues 47 - 57 (chain B) in PDB entry 6W6Y
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 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS 3.5 1.6 - - - -
46B GLY* 1.3 78.9 - - - +
48B GLY* 1.3 65.7 + - - -
49B VAL 3.6 0.2 + - - -
50B ALA* 3.4 8.8 + - - +
51B GLY* 2.9 20.7 + - - -
201B MES 4.0 14.4 + - - +
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Residues in contact with GLY 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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47B GLY* 1.3 72.8 - - - -
49B VAL* 1.3 63.9 + - - -
52B ALA* 3.1 22.2 + - - +
201B MES 6.1 1.3 - - - -
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Residues in contact with VAL 49 (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 ILE* 4.2 18.2 - - + -
36B VAL 4.5 0.9 - - - +
37B ASN* 4.0 5.8 - - - +
38B ALA* 4.3 11.9 - - + +
47B GLY 3.6 0.2 + - - -
48B GLY* 1.3 71.5 - - - -
50B ALA* 1.3 58.7 + - - +
52B ALA* 3.1 7.5 + - - +
53B LEU* 2.9 50.3 + - + +
125B PRO* 4.0 36.1 - - + -
201B MES 5.4 6.1 + - - +
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Residues in contact with ALA 50 (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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37B ASN* 3.1 25.2 + - - +
38B ALA 3.8 7.2 + - - +
45B HIS* 3.6 24.7 - - - +
47B GLY 3.4 7.3 + - - +
48B GLY 3.2 0.2 - - - -
49B VAL* 1.3 80.0 - - - +
51B GLY* 1.3 56.1 + - - +
53B LEU* 3.4 2.0 + - - +
54B ASN* 3.0 30.7 + - - +
61B MET* 4.7 0.9 - - - +
201B MES 3.8 22.0 - - - -
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Residues in contact with GLY 51 (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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45B HIS 3.5 18.1 + - - -
46B GLY 4.4 0.9 - - - -
47B GLY* 2.9 27.1 + - - +
48B GLY 3.8 1.3 - - - -
50B ALA* 1.3 76.9 - - - +
52B ALA* 1.3 55.8 + - - +
54B ASN* 3.4 1.8 + - - +
55B LYS* 2.8 32.7 + - - +
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Residues in contact with ALA 52 (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 ASP* 5.6 2.0 - - - +
23B ILE* 5.7 2.7 - - + -
24B VAL* 3.6 17.7 - - + +
48B GLY 3.1 14.8 + - - +
49B VAL* 3.6 9.6 - - - +
51B GLY* 1.3 72.2 - - - +
53B LEU* 1.3 67.8 + - + +
55B LYS* 3.4 8.2 + - - +
56B ALA* 3.1 24.1 + - - +
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Residues in contact with LEU 53 (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 ILE* 4.2 14.1 - - + +
24B VAL* 4.2 15.3 - - + -
27B ALA* 5.5 0.7 - - + -
35B VAL* 4.2 18.8 - - + -
36B VAL 3.8 11.2 - - - +
37B ASN* 3.7 35.0 - - + +
49B VAL* 2.9 28.3 + - + +
50B ALA 3.9 3.4 - - - +
52B ALA* 1.3 75.2 - - - +
54B ASN* 1.3 63.4 + - - +
56B ALA* 3.2 4.3 + - - +
57B THR* 3.2 25.6 + - - +
61B MET* 4.0 17.7 - - + -
88B LEU* 3.6 22.1 - - + +
92B CYS* 4.9 2.0 - - - -
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Residues in contact with ASN 54 (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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45B HIS* 3.8 22.4 + - + +
50B ALA 3.0 18.0 + - - +
51B GLY 3.8 3.3 + - - +
53B LEU* 1.3 78.0 - - - +
55B LYS* 1.3 59.1 + - - +
57B THR* 2.7 29.3 + - - -
58B ASN 3.1 5.4 + - - -
59B ASN* 2.8 38.4 + - - +
61B MET* 3.4 11.7 - - - +
62B GLN* 2.8 36.1 + - - +
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Residues in contact with LYS 55 (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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51B GLY 2.8 23.2 + - - +
52B ALA* 3.8 7.2 - - - +
53B LEU 3.3 0.2 - - - -
54B ASN* 1.3 75.0 - - - +
56B ALA* 1.3 57.1 + - - +
58B ASN* 2.9 30.0 + - - +
59B ASN 4.9 0.7 - - - +
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Residues in contact with ALA 56 (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 VAL* 3.5 29.4 - - + -
28B LYS* 4.6 7.8 + - - +
52B ALA 3.1 17.3 + - - +
53B LEU 3.5 6.1 - - - +
54B ASN 3.1 0.4 - - - -
55B LYS* 1.3 75.8 - - - +
57B THR* 1.3 58.2 + - - +
58B ASN* 3.3 9.0 + - - +
87B ASN* 3.0 21.2 + - - -
88B LEU* 4.0 13.7 - - + -
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Residues in contact with THR 57 (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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53B LEU 3.3 13.7 - - - +
54B ASN 2.7 16.6 + - - -
56B ALA* 1.3 75.0 - - - +
58B ASN* 1.3 69.4 + - - +
60B ALA* 3.2 16.8 + - - +
61B MET* 3.1 35.7 + - + +
85B GLY 4.7 0.4 - - - +
86B HIS* 3.9 24.5 - - + -
87B ASN* 3.4 22.2 - - - +
88B LEU* 3.8 16.6 - - + -
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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