Contacts of the strand formed by residues 2017 - 2023 (chain r) in PDB entry 6FF7
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 ILE2017 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2015r PRO* 3.9 9.6 + - + -
2016r ASN* 1.3 75.2 - - - +
2018r GLU* 1.3 61.4 + - - +
2019r LEU 4.0 1.9 + - - -
2041r LEU* 6.0 3.6 - - + -
2042r GLU 3.3 10.8 - - - +
2043r ARG* 5.1 3.6 - - + -
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Residues in contact with GLU2018 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2016r ASN 4.3 0.2 - - - -
2017r ILE* 1.3 71.3 - - - +
2019r LEU* 1.3 64.1 + - - +
2040r GLN 3.8 0.7 - - - +
2041r LEU* 3.8 1.2 - - - -
2042r GLU* 2.9 39.9 + - + +
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Residues in contact with LEU2019 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017r ILE 4.0 2.4 + - - -
2018r GLU* 1.3 78.3 - - - +
2020r SER* 1.3 66.0 + - - +
2021r TYR* 6.1 1.3 - - + -
2039r VAL* 5.7 4.5 - - + -
2040r GLN 3.1 15.3 - - - +
2041r LEU* 4.4 6.1 - - + +
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Residues in contact with SER2020 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2019r LEU* 1.3 78.3 - - - +
2021r TYR* 1.3 60.4 + - - +
2038r LEU 3.7 1.4 - - - +
2039r VAL* 3.5 1.2 - - - -
2040r GLN* 2.9 41.6 + - - +
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Residues in contact with TYR2021 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2019r LEU* 6.1 1.6 - - + -
2020r SER* 1.3 75.2 - - - +
2022r GLU* 1.3 62.8 + - - +
2037r VAL* 6.5 1.1 - - + -
2038r LEU 3.3 7.4 - - - +
2039r VAL* 4.5 10.3 - - + -
2120r TYR* 6.3 2.2 - - + -
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Residues in contact with GLU2022 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2021r TYR* 1.3 77.1 - - - +
2023r VAL* 1.3 65.3 + - - +
2024r VAL 3.9 0.3 + - - -
2037r VAL* 3.4 5.1 - - - +
2038r LEU* 2.9 38.0 + - + +
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Residues in contact with VAL2023 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022r GLU* 1.3 76.7 - - - +
2024r VAL* 1.3 64.1 + - - +
2025r ASP 3.4 2.6 + - - -
2026r LYS* 3.8 27.1 + - + +
2036r VAL 3.8 6.5 - - - +
2037r VAL* 4.6 4.9 - - + +
2123r SER 5.7 3.1 - - - +
2124r VAL* 5.5 10.5 - - + -
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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