Contacts of the strand formed by residues 41 - 47 (chain E) in PDB entry 3IT8
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 HIS 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E TYR* 3.5 11.9 - - - -
36E ASN* 2.9 22.0 + - - +
39E THR* 3.1 34.1 + - + +
40E ARG* 1.3 79.6 - - - +
42E GLY* 1.3 71.6 + - - +
43E ASN* 3.3 17.0 + - - -
67E ASN* 3.6 23.0 + - - +
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Residues in contact with GLY 42 (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 ILE* 4.2 3.4 - - - -
34E SER 3.4 10.5 - - - -
41E HIS* 1.3 84.0 + - - +
43E ASN* 1.3 67.2 + - - +
63E ASP* 5.2 8.4 - - - +
66E PHE* 3.7 24.0 - - - -
67E ASN* 3.0 15.1 + - - +
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Residues in contact with ASN 43 (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 ILE* 3.2 7.0 - - - +
34E SER* 3.0 31.1 + - - +
36E ASN* 2.9 44.2 - - - +
39E THR* 5.3 0.4 + - - -
41E HIS* 3.3 14.8 + - - -
42E GLY* 1.3 80.8 - - - +
44E VAL* 1.3 66.9 + - - +
45E ASN* 3.3 11.5 + - - +
63E ASP* 6.3 0.7 - - - -
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Residues in contact with VAL 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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31E THR* 4.4 6.3 - - + -
32E LYS 3.4 6.7 - - - +
33E ILE* 3.9 15.7 - - + -
43E ASN* 1.3 73.4 - - - +
45E ASN* 1.3 59.3 + - - +
46E PHE 3.3 28.9 - - - +
47E ARG* 4.5 23.3 - - + +
63E ASP* 3.6 26.2 - - - +
64E TYR* 6.3 0.2 - - + -
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Residues in contact with ASN 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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32E LYS* 2.8 38.2 + - + +
34E SER* 2.5 43.1 + - - +
43E ASN* 3.5 14.9 - - - +
44E VAL* 1.3 75.2 - - - +
46E PHE* 1.3 62.2 - - - +
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Residues in contact with PHE 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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29E LEU* 3.6 49.6 - - + -
30E VAL 4.0 2.9 - - - -
31E THR* 3.3 5.1 - - - -
32E LYS* 3.1 37.6 + - + -
44E VAL* 3.3 11.7 - - - +
45E ASN* 1.3 83.1 - - + +
47E ARG* 1.3 76.3 + - - +
48E ALA* 3.4 27.4 - - + -
49E ASP* 5.9 1.1 - - - -
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Residues in contact with ARG 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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30E VAL 3.3 6.1 - - - -
31E THR* 2.3 50.9 + - - +
44E VAL* 4.5 22.4 - - + +
46E PHE* 1.3 84.5 - - - +
48E ALA* 1.3 72.8 + - - +
49E ASP* 3.3 3.5 + - - -
51E PHE* 4.3 20.1 + - - +
53E ILE* 3.4 37.6 - - - +
63E ASP* 4.9 5.9 + - - -
64E TYR* 3.5 13.1 + - - -
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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