Contacts of the strand formed by residues 43 - 48 (chain E) in PDB entry 6B0B
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 THR 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E TYR* 5.2 6.7 - - - -
33E GLN* 3.4 5.9 - - - +
34E LEU* 2.9 57.7 + - - +
36E PRO* 5.0 1.1 - - + +
41E THR* 3.8 8.1 + - + +
42E PRO* 1.3 79.4 - - - +
44E ARG* 1.3 63.5 + - - +
66E MET* 5.6 9.8 - - + -
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Residues in contact with ARG 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E TYR* 3.5 17.2 + - - -
33E GLN* 3.1 35.2 + - - +
42E PRO 5.8 0.2 - - - +
43E THR* 1.3 75.3 - - - +
45E GLY* 1.3 59.4 + - - +
146E GLU 4.9 0.4 + - - -
147E ASN* 2.7 60.8 + - - +
148E PHE* 4.1 11.4 - - + +
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Residues in contact with GLY 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E CYS* 3.4 0.2 - - - -
32E TYR* 2.9 57.4 + - - -
44E ARG* 1.3 76.7 - - - +
46E TYR* 1.3 61.5 + - - -
148E PHE* 3.3 11.1 - - - -
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Residues in contact with TYR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 3.5 47.8 + - + +
4E LEU* 3.6 31.2 - - + -
29E LEU* 5.2 7.9 - - + -
30E LEU 3.3 10.3 - - - +
31E CYS* 4.3 12.1 - - - +
32E TYR* 4.6 1.0 + - - -
45E GLY* 1.3 74.8 - - - -
47E PHE* 1.3 69.4 + - - +
48E GLU* 4.2 28.3 + - + -
148E PHE* 4.4 5.3 - + + -
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Residues in contact with PHE 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 3.7 0.8 - - - -
30E LEU* 2.9 42.9 + - + -
32E TYR* 3.3 32.3 - + - -
45E GLY 4.3 0.2 + - - -
46E TYR* 1.3 76.5 - - - +
48E GLU* 1.3 68.3 + - + +
50E LYS* 6.1 0.9 - - + -
55E ALA* 3.3 18.1 - - + +
58E CYS* 3.7 32.5 - - + -
59E PHE* 3.8 14.8 - - + -
62E GLU* 3.5 44.0 - - + -
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Residues in contact with GLU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LYS* 3.5 24.4 + - - +
29E LEU* 3.7 22.6 - - + +
46E TYR* 4.2 20.5 + - + -
47E PHE* 1.3 83.1 - - + +
49E ASN* 1.3 63.0 + - - +
50E LYS* 2.9 49.6 + - + +
55E ALA* 3.8 7.9 - - - +
58E CYS* 5.1 0.3 - - - -
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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