Contacts of the helix formed by residues 2017 - 2027 (chain A) in PDB entry 4M6W
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 GLN2017 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2015A THR* 3.3 23.9 + - - +
2016A HIS* 1.3 84.9 + - - +
2018A LYS* 1.3 90.4 + - - +
2019A ALA 3.3 0.7 - - - -
2020A GLU* 3.2 18.1 + - - +
2021A GLU* 3.3 29.6 + - - +
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Residues in contact with LYS2018 (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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1889A SER 3.5 17.3 + - - +
1890A MET 4.3 9.7 + - - -
1981A ASN* 2.5 36.7 + - - -
1982A ILE* 3.9 13.1 - - + +
1983A SER 5.5 0.2 - - - +
1986A THR* 5.7 1.4 + - - -
2014A VAL* 4.1 19.0 - - + +
2015A THR* 3.7 23.8 - - - +
2016A HIS 3.4 0.6 - - - -
2017A GLN* 1.3 92.8 + - - +
2019A ALA* 1.3 64.1 + - - +
2021A GLU* 3.1 33.8 + - - +
2022A ILE* 3.3 22.5 + - + +
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Residues in contact with ALA2019 (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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2005A LEU* 3.5 29.5 - - + +
2008A ILE* 3.7 27.0 - - + +
2009A SER* 3.6 13.5 - - - -
2014A VAL* 4.0 1.1 - - + +
2015A THR 3.1 17.3 + - - +
2016A HIS 4.0 6.7 - - - +
2017A GLN 3.3 0.2 - - - -
2018A LYS* 1.3 77.8 - - - +
2020A GLU* 1.3 59.5 + - - +
2022A ILE 4.0 0.4 + - - -
2023A TYR* 3.2 23.2 + - - +
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Residues in contact with GLU2020 (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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2005A LEU* 4.5 21.4 - - + +
2016A HIS 3.9 6.2 + - - +
2017A GLN* 3.2 16.2 + - - +
2018A LYS 3.2 0.6 - - - -
2019A ALA* 1.3 77.6 - - - +
2021A GLU* 1.3 60.8 + - + +
2023A TYR* 3.5 9.7 + - + +
2024A ARG* 3.0 30.0 + - + +
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Residues in contact with GLU2021 (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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1981A ASN* 4.7 10.2 + - - -
2017A GLN* 3.5 27.4 + - + +
2018A LYS* 3.1 33.7 + - - +
2020A GLU* 1.3 77.2 - - + +
2022A ILE* 1.3 64.0 + - + +
2024A ARG* 3.5 7.4 + - - +
2025A TYR* 3.2 23.6 + - - +
154B LEU* 4.7 4.2 - - - +
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Residues in contact with ILE2022 (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 ILE* 4.8 15.5 - - + -
1980A PRO 5.7 1.1 - - - +
1982A ILE* 4.0 26.2 - - + -
1990A MET* 4.4 9.9 - - + -
2000A MET* 4.4 16.8 - - - +
2008A ILE* 3.5 37.9 - - + -
2014A VAL* 6.1 1.3 - - + -
2018A LYS* 3.3 20.3 + - + +
2019A ALA 4.0 2.2 - - - +
2021A GLU* 1.3 75.9 - - + +
2023A TYR* 1.3 65.1 + - - +
2025A TYR* 3.3 8.1 - - - +
2026A ILE* 2.9 50.7 + - + +
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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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2003A SER 4.0 18.6 - - - -
2004A SER* 4.9 2.7 - - - -
2005A LEU* 4.5 30.5 - - + -
2008A ILE* 5.5 3.6 - - + -
2019A ALA 3.2 17.1 + - - +
2020A GLU* 3.5 11.7 - - + +
2021A GLU 3.2 0.2 - - - -
2022A ILE* 1.3 85.9 - - - +
2024A ARG* 1.3 59.8 + - + +
2026A ILE* 3.4 1.5 + - - -
2027A HIS* 2.9 85.7 + + + +
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Residues in contact with ARG2024 (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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2020A GLU* 3.0 18.7 + - + +
2021A GLU* 3.8 7.4 - - - +
2023A TYR* 1.3 79.8 - - + +
2025A TYR* 1.3 56.2 + - - +
2027A HIS* 4.0 5.2 - - - +
2028A TYR* 3.1 45.8 + - - +
154B LEU* 3.8 18.1 - - + +
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Residues in contact with TYR2025 (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 ILE* 3.9 26.0 - - + -
1980A PRO* 3.7 24.2 - - + +
2021A GLU 3.2 13.5 + - - +
2022A ILE* 3.3 13.2 - - - +
2023A TYR 3.1 0.8 - - - -
2024A ARG* 1.3 75.6 - - - +
2026A ILE* 1.3 77.2 + - + +
2027A HIS 3.4 0.5 + - - -
2028A TYR* 3.5 9.7 + - - +
154B LEU* 3.8 25.8 - - + -
155B SER 4.5 1.3 - - - -
158B SER* 3.0 28.0 + - - -
159B LEU* 3.3 48.4 + - + +
162B THR* 2.7 28.3 + - + -
184B ILE* 4.1 8.8 - - + +
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Residues in contact with ILE2026 (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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1975A PHE* 5.2 2.5 - - + -
1979A ILE* 4.4 14.1 - - + -
2000A MET* 4.0 24.0 - - + +
2001A ALA* 3.7 41.1 - - + +
2022A ILE* 2.9 33.3 + - + +
2023A TYR* 4.1 1.3 - - - +
2025A TYR* 1.3 84.5 - - + +
2027A HIS* 1.3 66.3 + - + +
2028A TYR 3.7 0.3 + - - -
183B SER* 3.8 0.5 - - - -
184B ILE* 3.3 36.1 + - + -
185B GLN 3.2 24.9 + - - +
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Residues in contact with HIS2027 (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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2001A ALA 3.2 26.4 + - - -
2002A ASN* 5.0 2.4 - - - -
2003A SER 4.9 3.1 - - - -
2023A TYR* 2.9 71.6 + + + +
2024A ARG* 3.9 6.1 - - - +
2026A ILE* 1.3 86.1 - - + +
2028A TYR* 1.3 61.3 + - - +
2029A VAL* 3.4 13.3 + - - +
183B SER* 4.2 6.2 - - - -
185B GLN* 3.2 39.4 + - - +
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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