Contacts of the strand formed by residues 39 - 42 (chain A) in PDB entry 1D7E
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 ILE 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.3 1.6 - - + -
32A GLN 3.7 4.7 - - - +
33A LEU* 3.7 17.0 - - + -
38A ASN* 1.3 71.6 - - - +
40A LEU* 1.3 63.8 + - - +
41A GLN 3.6 25.4 - - - +
42A TYR* 4.1 14.1 - - + -
57A VAL* 3.6 33.0 - - + +
58A ILE* 3.7 12.6 - - + +
59A GLY* 2.8 28.1 + - - +
60A LYS 2.9 18.0 + - - +
62A PHE* 4.0 21.3 - - + -
66A VAL* 3.9 24.5 - - + -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 2.8 29.9 + - - +
33A LEU 3.9 4.9 - - - +
34A ASP* 3.8 39.9 - - + +
38A ASN* 4.2 5.8 - - + +
39A ILE* 1.3 76.8 - - - +
41A GLN* 1.3 64.6 + - + +
58A ILE* 3.9 16.9 - - - +
116A ASP 4.6 0.7 - - - -
117A SER* 3.7 23.6 - - - +
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET 4.7 10.3 + - - -
19A ASP 5.3 0.8 + - - -
20A ASP* 4.2 17.1 + - - +
23A LEU* 3.6 32.6 - - + +
30A ALA 4.5 0.2 - - - -
31A ILE* 3.4 8.9 - - - +
32A GLN* 2.8 59.8 + - + +
39A ILE* 3.6 1.7 - - - +
40A LEU* 1.3 84.2 - - + +
42A TYR* 1.3 63.4 + - - +
58A ILE* 4.0 6.3 - - - -
119A TRP* 3.7 11.9 - - - -
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.8 2.2 - - - +
24A ASP* 4.5 1.6 - - - +
30A ALA 3.5 5.6 - - - -
31A ILE* 3.8 23.8 - - + -
39A ILE* 4.1 11.9 - - + -
41A GLN* 1.3 76.2 - - - +
43A ASN* 1.3 67.2 + - - +
46A GLU* 3.3 16.8 - - + +
47A GLY* 3.7 17.0 - - - -
50A THR* 2.8 19.6 + - - -
52A ARG* 3.4 18.8 - - + +
54A PRO* 3.3 30.2 - - + +
57A VAL* 3.4 32.5 - - + -
58A ILE* 3.9 11.0 - - + +
62A PHE* 5.1 1.3 - + - -
66A VAL* 5.1 1.1 - - + -
126A HC4 2.5 36.5 + + - -
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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