Contacts of the helix formed by residues 2074 - 2079 (chain D) in PDB entry 5DFV
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 THR2074 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2021D GLY* 4.6 4.3 - - - -
2022D ALA 4.2 0.2 - - - -
2073D LEU* 1.3 93.1 - - - +
2075D LYS* 1.3 66.8 + - - +
2076D ASP* 3.3 19.7 + - + +
2077D GLU* 3.2 41.9 + - + +
2078D TYR* 3.1 5.7 + - - +
2080D ARG* 5.7 1.1 - - - +
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Residues in contact with LYS2075 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017D LEU* 3.8 19.4 + - + +
2018D THR 4.4 12.3 + - - -
2020D GLY* 3.5 15.1 - - - +
2021D GLY* 3.3 37.6 - - - +
2022D ALA* 3.9 5.2 - - - -
2074D THR* 1.3 73.2 + - - +
2076D ASP* 1.3 97.0 + - - +
2078D TYR* 3.2 11.1 + - - +
2079D GLU* 3.3 30.1 + - + +
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Residues in contact with ASP2076 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2074D THR* 3.3 11.9 + - + +
2075D LYS* 1.3 100.9 - - - +
2077D GLU* 1.3 61.8 + - - +
2079D GLU* 3.2 17.1 + - - +
2080D ARG* 3.3 31.7 + - - +
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Residues in contact with GLU2077 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2042D ILE* 6.2 1.2 - - + +
2049D ASN* 3.7 22.4 + - - -
2073D LEU* 4.0 16.2 - - + +
2074D THR* 3.2 31.0 + - + +
2076D ASP* 1.3 79.3 - - - +
2078D TYR* 1.3 61.4 + - - +
2079D GLU 3.5 0.2 + - - -
2080D ARG* 3.6 30.8 + - - +
2081D HIS* 3.6 24.8 + - + -
2084D TYR* 4.1 1.0 + - - -
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Residues in contact with TYR2078 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011D PRO* 4.1 4.2 - - - +
2012D PRO* 3.8 29.3 + - + +
2017D LEU* 3.7 29.6 - - + +
2022D ALA* 3.5 18.8 - - + -
2024D VAL* 4.3 5.6 - - + -
2073D LEU* 3.5 11.8 - - + +
2074D THR 3.1 5.3 + - - -
2075D LYS 3.5 8.3 - - - +
2076D ASP 3.2 0.4 - - - -
2077D GLU* 1.3 78.5 - - - +
2079D GLU* 1.3 78.4 + - - +
2080D ARG 3.0 6.5 + - - -
2081D HIS 3.7 0.5 + - - -
2084D TYR* 2.6 59.6 + + - -
2101D PHE* 3.5 20.9 - + - -
2103D ARG* 3.3 30.7 - - + +
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Residues in contact with GLU2079 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017D LEU* 4.2 17.7 - - - +
2075D LYS* 3.3 25.4 - - + +
2076D ASP* 3.2 9.5 + - - +
2078D TYR* 1.3 91.9 - - + +
2080D ARG* 1.3 61.7 + - - +
2081D HIS 3.9 0.4 - - - -
2103D ARG* 3.2 38.4 + - - +
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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