Contacts of the strand formed by residues 33 - 38 (chain E) in PDB entry 43C9
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 33 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E MET* 3.9 7.6 - - + -
23E CYS* 3.9 21.8 - - - -
27E LEU* 3.6 24.0 - - - +
31E ASN 2.9 6.7 + - - -
32E TYR* 1.3 75.8 - - - +
34E ALA* 1.3 63.0 + - - +
35E TRP* 3.7 24.0 - - + +
48E VAL* 4.2 0.3 - - - +
49E TYR 3.6 0.9 - - - -
50E PHE 3.0 9.1 + - - +
51E ALA* 2.9 26.9 + - - +
71E PHE* 3.0 54.1 - - + -
88E CYS* 4.3 2.2 - - + -
89E GLN 3.5 16.8 - - - +
91E HIS* 5.0 1.1 - - - -
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Residues in contact with ALA 34 (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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33E LEU* 1.3 75.1 - - - +
35E TRP* 1.3 65.3 + - - +
36E TYR* 3.6 28.5 - - + +
46E LEU* 3.9 6.5 - - + -
48E VAL 3.1 13.7 - - - +
49E TYR* 4.3 6.7 - - + -
88E CYS* 3.1 27.5 - - - +
89E GLN 3.0 10.6 + - - +
91E HIS* 3.9 14.6 - - + +
95F TYR* 6.0 0.7 - - + -
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Residues in contact with TRP 35 (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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6E GLN* 3.9 21.3 - - - -
21E MET* 3.6 24.9 - - + -
22E SER 3.8 4.5 - - - -
23E CYS* 3.4 28.9 - - + -
33E LEU* 3.7 17.3 - - + +
34E ALA* 1.3 77.0 - - - +
36E TYR* 1.3 58.8 + - - +
46E LEU* 3.4 6.6 - - - +
47E LEU* 2.7 31.6 + - + -
48E VAL* 2.9 37.2 + - + +
51E ALA 4.4 8.7 + - - -
64E GLY* 4.8 1.0 - - - -
65E SER 4.8 0.2 + - - -
71E PHE* 4.2 5.0 - - + +
72E THR 3.7 15.8 + - - -
73E LEU* 3.3 56.6 - - + +
86E TYR* 5.0 4.0 - - + -
87E PHE 3.3 18.2 - - - -
88E CYS* 4.0 5.4 - - + -
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Residues in contact with TYR 36 (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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34E ALA* 3.6 25.6 - - + +
35E TRP* 1.3 74.1 - - - +
37E GLN* 1.3 60.5 + - - +
44E PRO* 4.0 15.0 - - + -
45E LYS 3.3 7.4 - - - +
46E LEU* 3.6 32.1 - - + -
47E LEU* 4.1 4.7 - - - +
85E ASP 3.7 0.3 - - - +
86E TYR* 3.4 13.3 - - - +
87E PHE* 2.8 48.0 + - + +
89E GLN* 3.0 31.9 + - + -
91E HIS* 3.0 12.1 + - - -
98E PHE* 4.8 4.0 - + - -
95F TYR* 2.5 31.2 + + - -
101F SER* 5.2 0.4 - - - -
103F TRP* 3.4 28.3 - + - -
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Residues in contact with GLN 37 (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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36E TYR* 1.3 74.0 - - - +
38E GLN* 1.3 65.6 + - - +
39E LYS* 3.9 19.7 + - + +
43E SER 4.0 0.3 - - - +
44E PRO* 3.2 2.1 - - - +
45E LYS* 2.8 66.5 + - + +
47E LEU* 3.7 27.6 - - + +
62E PHE* 4.7 8.7 - - - -
82E ASP* 3.9 10.2 + - - +
84E ALA* 3.8 15.8 - - + +
85E ASP 3.6 3.1 - - - -
86E TYR* 2.7 36.1 + - + -
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Residues in contact with GLN 38 (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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37E GLN* 1.3 76.7 - - - +
39E LYS* 1.3 64.1 + - - +
40E PRO* 4.8 0.2 - - - +
42E GLN 3.0 26.7 + - - +
43E SER* 4.2 2.2 - - - +
44E PRO* 3.5 22.4 - - + +
84E ALA* 3.1 4.2 - - - +
85E ASP* 2.9 47.3 + - + +
87E PHE* 3.2 23.1 - - + -
39F GLN* 3.1 40.4 + - - +
91F TYR* 4.3 1.8 + - - -
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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