Contacts of the strand formed by residues 29 - 32 (chain A) in PDB entry 2FD6
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ASP* 3.0 35.7 + - - -
19A CYS* 4.2 19.1 - - - -
20A VAL 3.2 11.9 - - - +
21A SER* 4.2 4.9 - - - -
27A ASN 4.2 6.9 + - - +
28A ILE* 1.3 82.3 - - - +
30A TRP* 1.3 72.6 + - - +
31A CYS* 5.3 1.1 - - - -
40A GLN* 2.9 25.8 + - - +
41A HIS* 3.4 7.0 + + - -
501A SO4 3.4 25.9 + - - -
40U LEU* 4.1 0.9 - - - +
42U GLU* 5.8 2.8 + - - -
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Residues in contact with TRP 30 (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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19A CYS* 3.5 4.3 - - - -
20A VAL* 3.1 54.1 + - + +
21A SER* 3.9 18.2 - - - -
22A ASN* 4.4 0.7 - - + -
28A ILE* 3.1 34.1 - - + -
29A HIS* 1.3 84.2 - - - +
31A CYS* 1.3 82.5 + - - +
32A ASN* 5.3 3.7 + - - -
40A GLN* 3.7 13.5 - - + +
29U VAL* 4.3 14.4 - - + -
31U LEU* 3.6 27.5 - - + +
40U LEU* 3.8 17.5 - - + -
57U TYR* 4.0 20.3 + - - -
62U LYS* 5.7 2.5 - - - +
64U THR* 4.1 16.1 + - + +
66U LEU* 3.6 27.1 - - + -
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Residues in contact with CYS 31 (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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12A ASP* 5.1 0.7 - - - -
13A CYS* 2.0 52.9 - - + -
18A THR 3.1 7.4 - - - +
20A VAL* 4.5 0.7 - - - -
29A HIS* 5.3 0.9 - - - -
30A TRP* 1.3 91.7 - - - +
32A ASN* 1.3 65.0 + - - +
33A CYS* 3.8 7.6 + - - -
39A GLY 5.3 1.0 - - - +
40A GLN* 3.2 21.3 + - - +
41A HIS* 3.7 10.1 - - - -
42A CYS* 3.6 17.9 - - - -
31U LEU* 4.7 7.1 - - - +
62U LYS* 4.8 3.1 + - - -
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Residues in contact with ASN 32 (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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16A GLY 3.4 2.4 - - - +
17A GLY* 3.4 4.7 - - - -
18A THR* 2.7 64.4 + - - +
19A CYS 4.7 0.2 + - - -
20A VAL* 4.2 17.8 - - - +
30A TRP* 5.3 1.6 + - - -
31A CYS* 1.3 73.2 - - - +
33A CYS* 1.3 60.8 + - - +
42A CYS* 4.2 0.2 - - - -
62U LYS* 3.2 25.5 + - - +
101U SER* 3.9 32.9 + - - +
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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