Contacts of the strand formed by residues 2442 - 2446 (chain A) in PDB entry 5DZZ
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 CYS2442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2258A SER* 3.1 17.1 + - - -
2259A CYS 3.5 12.9 + - - +
2260A ILE* 3.8 3.9 - - - -
2261A ALA 3.1 23.0 + - - -
2262A GLY 3.7 0.7 + - - -
2430A LYS* 3.3 33.9 - - + +
2433A CYS* 3.8 21.3 - - + -
2434A ILE 3.2 7.9 - - - -
2435A LYS* 5.6 4.7 - - - -
2440A GLY 5.1 1.1 - - - -
2441A LEU* 1.3 73.5 - - - +
2443A LEU* 1.3 64.5 + - - +
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Residues in contact with LEU2443 (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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2261A ALA* 4.3 3.4 - - + -
2262A GLY* 3.5 33.4 - - - +
2263A ILE 3.9 3.4 - - - +
2264A TYR* 4.1 23.6 - - + +
2271A LYS* 3.7 25.8 - - + -
2304A PRO* 3.8 17.9 - - + -
2433A CYS* 3.3 3.7 - - - -
2434A ILE* 2.8 43.0 + - + +
2436A ASP* 3.2 34.1 - - - +
2441A LEU* 3.7 6.9 + - + +
2442A CYS* 1.3 76.8 - - - +
2444A LEU* 1.3 58.7 + - - +
2445A PRO* 3.2 5.4 - - - +
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Residues in contact with LEU2444 (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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2260A ILE* 4.6 7.4 - - + -
2262A GLY 3.2 14.6 + - - +
2263A ILE* 3.6 16.6 - - + +
2264A TYR 3.1 17.3 + - - -
2283A VAL* 6.1 0.2 - - + -
2291A LEU* 5.4 7.4 - - + -
2417A ASP* 4.0 10.1 - - - +
2418A PRO* 3.9 33.2 - - + -
2419A ASN* 4.9 2.0 - - - +
2429A LEU* 4.1 27.8 - - + -
2432A ARG* 4.0 17.3 - - + +
2433A CYS* 4.0 17.6 - - - -
2443A LEU* 1.3 71.3 - - - +
2445A PRO* 1.3 81.9 - - + +
2446A LEU* 3.5 4.3 + - + +
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Residues in contact with PRO2445 (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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2264A TYR* 3.5 10.7 - - + +
2266A GLU* 3.6 26.2 - - + +
2419A ASN* 2.5 33.7 + - - +
2432A ARG 3.4 23.8 - - - +
2433A CYS* 4.1 0.2 - - - -
2434A ILE* 4.0 28.7 - - + -
2443A LEU 3.2 9.4 - - - +
2444A LEU* 1.3 87.9 - - + +
2446A LEU* 1.3 55.9 + - - +
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Residues in contact with LEU2446 (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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2263A ILE* 3.6 40.4 - - + -
2264A TYR 3.0 8.0 + - - +
2265A ASN* 3.6 4.4 - - - -
2266A GLU* 2.7 36.4 + - - +
2282A LEU* 4.0 24.0 - - + +
2283A VAL* 3.9 15.9 - - + -
2418A PRO* 3.6 22.9 - - + -
2419A ASN* 3.3 24.7 - - - +
2444A LEU* 3.9 10.5 - - + +
2445A PRO* 1.3 83.7 - - - +
2447A LYS* 1.3 67.1 + - - +
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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