Contacts of the helix formed by residues 50 - 58 (chain B) in PDB entry 6E8Y
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 LEU 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.9 23.1 - - + -
41B PHE 4.4 2.0 - - - +
42B GLU* 3.0 5.2 + - - +
43B GLU* 2.9 38.0 + - + +
45B ILE* 4.0 20.0 - - + -
48B LYS 3.5 1.2 + - - -
49B LYS* 1.3 70.8 - - - +
51B THR* 1.3 58.6 + - - +
53B ILE* 3.1 7.1 + - + +
54B ILE* 2.9 40.6 + - + +
60B ASN* 3.8 24.7 - - - +
61B VAL* 4.1 19.5 - - + +
62B LYS* 4.4 5.4 - - + +
63B TYR* 4.2 20.4 - - + -
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Residues in contact with THR 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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40B VAL* 3.9 34.3 - - + +
42B GLU* 2.5 40.0 + - - +
49B LYS* 4.2 3.1 - - - +
50B LEU* 1.3 74.9 - - - +
52B GLU* 1.3 63.6 + - - +
54B ILE* 3.4 2.7 + - - +
55B ASN* 2.9 35.8 + - - -
75B ALA* 4.0 22.9 - - + -
77B PRO* 4.0 19.6 - - + +
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Residues in contact with GLU 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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48B LYS* 4.3 24.9 + - + +
49B LYS* 2.9 37.0 + - + +
51B THR* 1.3 82.0 + - - +
53B ILE* 1.3 58.7 + - - +
55B ASN* 3.3 5.2 + - - +
56B THR* 2.7 41.2 + - + +
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Residues in contact with ILE 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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45B ILE* 3.8 33.4 - - + +
48B LYS* 3.6 29.4 - - + +
49B LYS 2.9 18.1 + - - +
50B LEU* 3.4 8.5 - - + +
52B GLU* 1.3 76.3 - - - +
54B ILE* 1.3 58.1 + - - +
56B THR* 3.6 4.9 - - - -
57B GLN* 2.8 60.4 + - - +
59B GLU 3.8 5.6 - - - +
61B VAL* 3.7 30.3 - - + -
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Residues in contact with ILE 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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38B MET* 4.3 14.1 - - + -
40B VAL* 4.1 22.9 - - + -
50B LEU* 2.9 31.7 + - + +
51B THR 3.7 4.9 - - - +
53B ILE* 1.3 75.4 - - - +
55B ASN* 1.3 63.6 + - - +
58B HIS* 2.9 34.5 + - - +
59B GLU 3.7 20.9 - - - +
60B ASN* 4.0 29.2 - - + +
69B LEU* 4.4 12.6 - - + -
73B VAL 4.9 6.2 - - - +
75B ALA* 3.8 17.9 - - + +
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Residues in contact with ASN 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 THR* 2.9 22.7 + - - +
52B GLU* 3.3 6.3 + - - +
53B ILE 3.2 0.2 - - - -
54B ILE* 1.3 77.8 - - - +
56B THR* 1.3 62.9 + - + +
58B HIS* 3.7 17.6 + - - -
73B VAL 4.0 4.2 - - - +
74B VAL* 3.5 17.5 - - - +
75B ALA* 2.9 47.0 + - - +
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Residues in contact with THR 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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48B LYS* 3.8 15.8 + - - +
52B GLU* 2.7 24.6 + - + +
53B ILE* 3.2 7.1 + - - -
54B ILE 3.2 0.2 - - - -
55B ASN* 1.3 83.7 - - + +
57B GLN* 1.3 63.7 + - - +
58B HIS* 3.5 15.1 + - - -
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Residues in contact with GLN 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 ILE* 2.8 44.4 + - + +
56B THR* 1.3 77.5 + - - +
58B HIS* 1.3 69.9 + - - +
59B GLU* 3.7 22.3 - - - +
61B VAL* 3.9 11.8 - - - +
68B LYS* 3.0 25.7 + - - +
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Residues in contact with HIS 58 (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 ILE 3.6 0.2 + - - -
54B ILE* 2.9 25.0 + - - +
55B ASN* 3.7 25.1 + - - -
56B THR* 3.5 15.6 + - - -
57B GLN* 1.3 79.6 - - - +
59B GLU* 1.3 55.6 + - - +
68B LYS* 3.2 10.9 - - + -
69B LEU* 2.8 52.3 + - - +
70B PRO 4.5 2.0 + - - -
71B PRO* 3.5 45.5 + - + +
73B VAL 4.6 6.6 + - - -
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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