Contacts of the strand formed by residues 2022 - 2027 (chain A) in PDB entry 4UXL
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 GLN2022 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1981A THR* 3.2 1.9 - - - -
1982A LEU* 3.1 44.0 + - + -
1991A LYS* 3.0 44.2 + - - +
1994A PHE* 3.3 22.8 - - + -
1995A LEU* 5.6 4.4 - - - +
2016A CYS 3.3 10.1 - - - +
2017A LEU* 4.1 23.8 + - + +
2019A ASN 3.3 15.4 - - - +
2020A GLU* 3.7 13.6 - - - +
2021A PRO* 1.3 73.1 - - - +
2023A TYR* 1.3 70.1 + - - +
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Residues in contact with TYR2023 (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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1942A ARG* 3.4 37.9 + - + -
1945A LEU* 3.6 25.4 - - + -
1947A LEU* 3.4 27.3 - - + +
1979A VAL* 3.6 19.7 - - + -
1980A LYS 3.3 1.3 - - - -
1981A THR* 3.6 21.5 - - + -
1994A PHE* 4.6 0.2 - - - -
2015A VAL* 3.3 5.7 - - - +
2016A CYS* 2.8 56.1 + - + -
2017A LEU* 3.9 1.2 - - - +
2021A PRO* 4.0 11.6 - - + +
2022A GLN* 1.3 83.3 - - - +
2024A ILE* 1.3 66.2 + - - +
2025A ILE* 3.9 7.2 - - + -
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Residues in contact with ILE2024 (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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1979A VAL* 3.5 1.9 - - - -
1980A LYS* 2.7 53.0 + - + +
1994A PHE* 3.4 33.7 - - + +
1995A LEU* 6.4 0.2 - - + -
1997A GLU* 6.0 2.2 - - + +
1998A ALA* 3.4 30.5 - - + +
2001A MET* 5.0 4.0 - - + -
2012A GLN* 3.1 22.0 - - + +
2014A GLY 3.9 0.7 - - - -
2015A VAL* 3.5 18.6 - - + -
2017A LEU* 4.4 4.0 - - + -
2023A TYR* 1.3 74.7 - - - +
2025A ILE* 1.3 63.6 + - - +
2026A LEU* 3.7 25.0 + - + +
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Residues in contact with ILE2025 (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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1940A PHE* 5.1 6.7 - - + -
1945A LEU* 3.5 20.6 - - + -
1964A ALA* 4.9 1.8 - - + -
1967A ILE* 4.3 15.7 - - + -
1977A VAL* 3.8 33.4 - - + -
1978A ALA 3.5 0.7 - - - -
1979A VAL* 3.4 39.5 - - + -
2012A GLN* 3.5 2.9 - - - -
2013A LEU* 2.6 36.7 + - + -
2014A GLY* 2.7 31.8 + - - +
2015A VAL 4.7 0.7 - - - +
2016A CYS* 4.7 5.8 - - - -
2023A TYR* 3.9 9.9 - - + -
2024A ILE* 1.3 72.3 - - - +
2026A LEU* 1.3 56.8 + - - +
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Residues in contact with LEU2026 (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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1977A VAL* 3.6 5.5 - - - +
1978A ALA* 2.8 39.2 + - + +
1979A VAL 5.5 0.2 - - - -
1980A LYS* 4.3 18.8 - - + +
2001A MET* 3.4 35.2 - - + -
2010A LEU* 3.8 13.5 - - + -
2011A LYS 3.5 8.7 - - - +
2012A GLN* 4.1 3.8 - - - -
2013A LEU* 4.3 3.6 - - - -
2024A ILE* 3.8 20.4 - - + +
2025A ILE* 1.3 75.2 - - - +
2027A GLU* 1.3 60.5 + - - +
2028A LEU 3.4 0.2 + - - -
2101A GLY 5.7 0.4 - - - +
3230A 5P8 3.6 49.6 - - + +
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Residues in contact with GLU2027 (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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1976A LYS 5.4 0.2 - - - -
1977A VAL* 5.1 0.7 - - - +
2010A LEU* 3.3 16.7 - - + +
2011A LYS* 2.7 48.3 + - + +
2013A LEU* 3.7 24.2 - - + +
2026A LEU* 1.3 70.7 - - - +
2028A LEU* 1.3 61.2 + - - +
2029A MET* 3.5 13.9 + - - +
2099A LYS* 3.0 35.9 + - - +
3230A 5P8 2.9 22.5 + - - -
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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