Contacts of the helix formed by residues 2035 - 2043 (chain B) in PDB entry 4D0N
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 GLU2035 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2029B MET* 4.0 2.7 - - - -
2033B LEU 4.2 8.7 - - - +
2034B PHE* 1.3 76.5 - - - +
2036B GLN* 1.3 67.9 + - + +
2037B GLN* 3.1 9.6 - - + +
2038B MET* 3.0 37.3 + - - +
2039B VAL* 3.4 9.5 + - - +
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Residues in contact with GLN2036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2029B MET* 3.5 31.2 - - + +
2035B GLU* 1.3 73.0 - - - +
2037B GLN* 1.3 64.0 + - + +
2039B VAL* 3.2 17.8 + - - +
2040B GLU* 3.2 39.9 + - + +
2047B ASP* 4.6 12.5 + - - +
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Residues in contact with GLN2037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2035B GLU* 3.1 7.2 - - + +
2036B GLN* 1.3 78.1 - - + +
2038B MET* 1.3 62.6 + - - +
2040B GLU* 3.6 19.1 + - + +
2041B LYS* 3.6 18.1 - - + +
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Residues in contact with MET2038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2033B LEU 5.0 1.3 - - - +
2034B PHE* 3.6 51.2 - - + -
2035B GLU* 3.0 35.3 + - - +
2037B GLN* 1.3 76.7 - - - +
2039B VAL* 1.3 65.5 + - - +
2041B LYS* 3.1 29.9 + - + +
2042B LEU* 3.7 4.3 + - - +
2114B TYR* 3.4 30.3 - - - +
2118B LEU* 5.2 3.6 - - + -
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Residues in contact with VAL2039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025B SER* 3.2 37.9 - - - +
2028B MET* 4.6 5.6 - - + -
2029B MET* 3.7 31.2 - - + -
2034B PHE* 4.1 15.7 - - + -
2035B GLU 3.8 7.6 - - - +
2036B GLN* 3.2 13.5 + - - +
2038B MET* 1.3 77.1 - - - +
2040B GLU* 1.3 51.1 + - - +
2042B LEU* 3.0 9.0 + - + +
2043B PHE* 2.8 49.4 + - + +
2046B LEU* 5.6 1.3 - - + -
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Residues in contact with GLU2040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036B GLN* 3.2 36.2 + - + +
2037B GLN* 3.6 17.7 - - + +
2038B MET 3.2 0.2 - - - -
2039B VAL* 1.3 78.2 - - - +
2041B LYS* 1.3 56.2 + - - +
2042B LEU 3.3 0.2 - - - -
2043B PHE 3.9 10.7 - - - +
2044B PRO* 3.2 21.7 - - - +
2045B CYS* 3.1 27.2 + - - -
2046B LEU* 4.4 6.1 + - - +
2047B ASP* 5.1 3.8 + - - +
2103B LYS* 5.0 7.6 + - - -
2107B GLN* 3.2 15.2 + - - +
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Residues in contact with LYS2041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037B GLN* 3.6 17.9 + - + +
2038B MET* 3.1 18.4 + - + +
2040B GLU* 1.3 77.2 - - - +
2042B LEU* 1.3 58.4 + - - +
2107B GLN* 3.1 20.7 + - - +
2110B GLN 4.6 0.5 - - - +
2111B SER* 3.3 16.8 + - - -
2114B TYR* 3.6 48.2 - - + +
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Residues in contact with LEU2042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2028B MET* 3.5 40.2 - - + -
2034B PHE* 4.7 7.4 - - + -
2038B MET 3.7 2.9 + - - +
2039B VAL* 3.0 7.9 + - - +
2041B LYS* 1.3 80.0 - - - +
2043B PHE* 1.3 76.4 + - + +
2044B PRO* 3.5 5.4 - - - +
2104B PHE* 4.9 0.5 - - - -
2111B SER* 3.4 38.9 - - - +
2114B TYR* 3.8 16.6 - - + -
2115B PHE* 3.6 29.2 - - + +
2118B LEU* 4.8 1.8 - - + -
2125B PHE* 4.5 11.9 - - + -
2143B ILE* 4.6 8.7 - - + -
2147B ILE* 3.4 9.2 - - + +
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Residues in contact with PHE2043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2020B MET* 3.5 60.3 - - + -
2024B TYR* 3.7 21.5 - + + -
2025B SER 4.3 2.5 - - - -
2028B MET* 4.4 9.4 - - + -
2039B VAL* 2.8 32.4 + - + +
2040B GLU* 3.9 9.7 - - - +
2042B LEU* 1.3 84.7 - - + +
2044B PRO* 1.3 68.2 - - - +
2045B CYS 3.5 0.2 + - - -
2046B LEU* 3.4 31.1 + - + +
2104B PHE* 4.5 4.0 - + - -
2143B ILE* 4.0 29.6 - - + -
2147B ILE* 4.0 16.6 - - + -
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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