Contacts of the helix formed by residues 2029 - 2037 (chain D) in PDB entry 5G1N
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 GLY2029 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2027D GLN* 5.6 0.7 - - - -
2028D PRO* 1.3 70.6 - - - +
2030D ALA* 1.3 62.0 + - - +
2031D VAL 3.5 1.6 - - - -
2032D GLU* 3.7 11.3 + - - +
2033D LEU* 3.0 24.8 + - - +
2047D ASP* 2.8 16.7 + - - -
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Residues in contact with ALA2030 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2007D LEU* 3.9 13.6 - - + +
2025D HIS* 3.1 34.1 - - + +
2027D GLN* 3.1 31.7 + - + +
2028D PRO 3.2 2.4 + - - -
2029D GLY* 1.3 74.9 - - - +
2031D VAL* 1.3 56.2 + - - +
2033D LEU* 3.0 9.7 + - - +
2034D ALA* 2.7 35.9 + - - +
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Residues in contact with VAL2031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927D LEU* 4.6 3.6 - - + -
2023D LEU* 3.7 41.1 - - + +
2025D HIS* 4.0 13.2 - - + +
2029D GLY 3.5 0.2 - - - -
2030D ALA* 1.3 76.7 - - - +
2032D GLU* 1.3 50.9 + - - +
2034D ALA* 3.2 2.4 + - - +
2035D ALA* 2.7 32.7 + - - +
2042D VAL* 3.8 20.8 - - + +
2044D ASN* 3.7 37.5 - - + +
2047D ASP* 3.8 21.3 - - + -
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Residues in contact with GLU2032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927D LEU* 3.6 43.5 - - + +
1928D SER* 5.5 3.3 - - - -
2029D GLY* 3.7 12.3 + - - +
2030D ALA 3.3 0.6 - - - -
2031D VAL* 1.3 75.0 - - - +
2033D LEU* 1.3 59.8 + - - +
2035D ALA 3.6 0.5 - - - -
2036D LYS* 2.8 34.5 + - + +
2044D ASN* 6.0 0.2 - - - +
2047D ASP* 5.8 0.6 + - - -
3227D EDO 4.5 6.5 + - - +
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Residues in contact with LEU2033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007D LEU* 5.8 4.5 - - + -
2008D ALA* 6.0 1.2 - - - +
2027D GLN* 5.4 6.5 - - - +
2029D GLY 3.0 18.7 + - - +
2030D ALA* 3.0 8.8 + - - +
2032D GLU* 1.3 77.1 - - - +
2034D ALA* 1.3 60.8 + - - +
2036D LYS* 3.4 42.2 - - + +
2037D HIS 4.5 1.0 + - - -
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Residues in contact with ALA2034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007D LEU* 4.1 15.9 - - + +
2008D ALA* 5.3 8.4 - - - +
2011D VAL* 3.6 43.5 - - + +
2023D LEU* 3.9 11.9 - - + -
2030D ALA 2.7 19.2 + - - +
2031D VAL 3.6 4.5 - - - +
2033D LEU* 1.3 73.8 - - - +
2035D ALA* 1.3 58.2 + - - +
2037D HIS 4.5 2.5 + - - -
2038D CYS* 3.6 9.7 + - - +
2042D VAL* 5.1 0.7 - - - -
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Residues in contact with ALA2035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1925D HIS* 3.2 26.8 + - + +
1927D LEU* 3.6 27.6 - - + -
2031D VAL 2.7 20.1 + - - +
2032D GLU 3.8 2.9 - - - +
2033D LEU 3.3 0.2 - - - -
2034D ALA* 1.3 72.5 - - - +
2036D LYS* 1.3 68.3 + - - +
2037D HIS 3.3 1.7 + - - -
2038D CYS* 3.4 6.0 + - - -
2042D VAL* 3.7 26.7 - - + -
3227D EDO 3.9 2.5 - - - -
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Residues in contact with LYS2036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1925D HIS* 5.1 0.3 - - - -
2032D GLU* 2.8 23.9 + - + +
2033D LEU* 3.4 39.3 - - + +
2034D ALA 3.4 0.8 - - - -
2035D ALA* 1.3 77.9 - - - +
2037D HIS* 1.3 84.3 + - + +
2038D CYS 3.9 1.6 + - - +
3227D EDO 3.9 25.1 - - - +
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Residues in contact with HIS2037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2012D GLN* 4.9 8.1 + - - +
2033D LEU 4.5 1.4 + - - -
2034D ALA 4.5 4.5 + - - -
2035D ALA 3.3 0.2 - - - -
2036D LYS* 1.3 103.6 + - + +
2038D CYS* 1.3 58.4 + - - +
2039D ARG* 4.0 20.9 + - - +
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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