Contacts of the strand formed by residues 1974 - 1982 (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 GLU1974 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1946A THR* 5.2 1.0 + - - -
1963A THR* 2.7 43.1 + - - +
1964A ALA 4.5 2.2 - - - -
1965A VAL* 4.0 23.8 - - + +
1973A GLY* 1.3 70.1 - - - -
1975A ILE* 1.3 56.9 + - - +
1976A LYS* 3.6 6.1 + - - +
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Residues in contact with ILE1975 (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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1963A THR* 3.6 0.2 - - - -
1964A ALA 3.1 35.1 + - - +
1967A ILE* 3.8 19.5 - - + -
1968A LEU* 3.2 43.1 - - + -
1972A SER* 3.2 34.8 - - - +
1973A GLY 3.1 1.8 + - - -
1974A GLU* 1.3 72.0 - - - +
1976A LYS* 1.3 68.3 + - - +
1977A VAL* 3.7 5.2 + - + +
2013A LEU* 4.8 4.5 - - + -
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Residues in contact with LYS1976 (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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1948A ARG* 3.7 17.9 - - - +
1961A GLU* 4.1 10.5 - - - -
1962A GLY 3.4 8.7 - - - +
1963A THR* 4.3 2.0 - - - +
1974A GLU 4.7 5.6 - - - +
1975A ILE* 1.3 80.6 - - - +
1977A VAL* 1.3 64.3 + - - +
2013A LEU* 5.5 0.7 - - - +
2027A GLU* 5.4 0.7 - - - -
2028A LEU* 3.9 25.1 + - + +
2030A GLU* 3.6 29.8 + - - +
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Residues in contact with VAL1977 (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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1945A LEU* 4.0 23.3 - - + -
1961A GLU* 3.5 8.3 - - - +
1962A GLY 2.8 44.3 + - - +
1963A THR 4.1 0.2 - - - -
1964A ALA* 4.0 13.0 - - + -
1967A ILE* 4.5 4.3 - - + -
1975A ILE* 3.9 10.3 - - + +
1976A LYS* 1.3 80.9 - - - +
1978A ALA* 1.3 61.6 + - - +
1979A VAL* 4.2 6.1 - - + -
2013A LEU* 4.2 16.2 - - + -
2025A ILE* 3.8 22.4 - - + -
2026A LEU 3.6 10.8 - - - +
2028A LEU* 3.8 10.5 - - - +
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Residues in contact with ALA1978 (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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1951A LEU* 4.5 3.6 - - + -
1959A VAL* 4.7 2.5 - - + -
1960A TYR 3.4 7.9 - - - +
1977A VAL* 1.3 72.3 - - - +
1979A VAL* 1.3 68.5 + - - +
2025A ILE* 3.5 4.0 - - - +
2026A LEU* 2.8 35.9 + - + +
2027A GLU 4.3 0.2 - - - +
2028A LEU* 3.9 13.4 - - + +
3230A 5P8 3.5 43.1 - - + +
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Residues in contact with VAL1979 (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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1945A LEU* 4.2 17.7 - - + -
1947A LEU* 4.2 13.7 - - + -
1958A GLU 3.7 1.4 - - - +
1959A VAL* 3.2 9.1 - - - -
1960A TYR* 2.7 41.7 + - + +
1962A GLY 4.9 4.3 - - - +
1977A VAL* 4.2 7.2 - - + -
1978A ALA* 1.3 80.9 - - - +
1980A LYS* 1.3 62.8 + - - +
1981A THR* 3.9 5.4 + - + +
2023A TYR* 3.6 33.4 - - + -
2024A ILE 3.5 2.0 - - - -
2025A ILE* 3.4 29.2 - - + -
2026A LEU* 5.5 0.2 - - - -
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Residues in contact with LYS1980 (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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1954A GLY* 3.8 11.3 + - - +
1955A ALA* 3.7 26.1 - - - +
1958A GLU 3.9 2.2 - - - +
1959A VAL* 4.5 8.5 - - + +
1978A ALA 4.3 0.6 - - - -
1979A VAL* 1.3 73.2 - - - +
1981A THR* 1.3 63.9 + - - +
1994A PHE* 3.6 17.4 - - + -
1997A GLU* 3.1 32.3 - - - +
2001A MET* 6.4 1.8 - - + -
2023A TYR* 3.3 5.2 - - - -
2024A ILE* 2.7 56.6 + - + +
2026A LEU* 4.3 13.4 - - + +
2102A ASP* 4.7 12.0 + - - -
3230A 5P8 4.2 23.2 - - + +
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Residues in contact with THR1981 (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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1947A LEU* 5.0 0.4 - - + -
1954A GLY 5.0 0.2 - - - +
1955A ALA* 5.7 0.7 - - - +
1957A GLY* 3.5 18.7 + - - -
1958A GLU* 2.8 29.2 + - - +
1960A TYR* 3.9 22.7 - - + -
1979A VAL* 4.1 5.2 - - + +
1980A LYS* 1.3 79.2 - - - +
1982A LEU* 1.3 61.1 + - - +
1983A LYS* 2.9 22.6 + - - -
1994A PHE* 3.8 9.0 - - - -
2021A PRO* 4.7 4.9 - - + -
2022A GLN 3.2 7.6 - - - -
2023A TYR* 3.6 26.5 - - + -
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Residues in contact with LEU1982 (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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1955A ALA* 6.4 0.4 - - + -
1956A PHE* 3.9 16.6 - - + +
1981A THR* 1.3 73.9 - - - +
1983A LYS* 1.3 88.2 + - - +
1986A SER* 2.8 29.2 - - - +
1990A GLU* 4.3 15.0 - - + +
1991A LYS* 4.3 18.6 - - - -
1994A PHE* 3.7 35.2 - - + -
2020A GLU* 3.2 18.4 - - - +
2021A PRO* 3.4 14.0 - - - +
2022A GLN* 3.1 33.3 + - + -
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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