Contacts of the helix formed by residues 2029 - 2037 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2028C PRO* 1.3 71.4 - - - +
2030C ALA* 1.3 57.5 + - - +
2031C VAL 3.4 2.7 - - - -
2032C GLU* 3.5 15.4 + - - +
2033C LEU* 3.1 25.5 + - - +
2047C ASP* 3.3 11.7 + - - -
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Residues in contact with ALA2030 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007C LEU* 3.4 24.6 - - + +
2023C LEU* 5.1 0.2 - - - -
2025C HIS* 3.8 23.3 - - + +
2027C GLN* 3.1 38.0 + - - +
2028C PRO 3.3 1.0 + - - -
2029C GLY* 1.3 76.1 - - - +
2031C VAL* 1.3 60.1 - - - +
2033C LEU* 3.7 7.5 - - + +
2034C ALA* 3.1 22.7 + - - +
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Residues in contact with VAL2031 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927C LEU* 3.8 13.2 - - + -
2023C LEU* 3.8 35.8 - - + +
2025C HIS* 4.5 9.6 - - + -
2029C GLY 3.4 0.6 - - - -
2030C ALA* 1.3 75.0 - - - +
2032C GLU* 1.3 61.3 + - - +
2034C ALA* 3.9 0.9 - - - +
2035C ALA* 2.9 28.2 + - - +
2042C VAL* 3.6 24.9 - - + -
2044C ASN* 3.5 38.6 - - + +
2046C GLY 4.7 0.7 - - - +
2047C ASP* 4.0 14.5 - - + +
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Residues in contact with GLU2032 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1927C LEU* 4.2 30.6 - - + +
2029C GLY* 3.5 15.6 + - - +
2031C VAL* 1.3 80.2 - - - +
2033C LEU* 1.3 60.5 + - - +
2035C ALA* 3.5 6.6 - - - +
2036C LYS* 3.3 20.1 + - - +
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Residues in contact with LEU2033 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007C LEU* 5.4 7.0 - - + -
2008C ALA* 5.8 7.0 - - + -
2027C GLN* 6.1 0.9 - - - +
2029C GLY 3.1 17.3 + - - +
2030C ALA* 3.8 9.6 - - + +
2031C VAL 3.3 0.2 - - - -
2032C GLU* 1.3 73.1 - - - +
2034C ALA* 1.3 68.3 + - - +
2035C ALA 3.2 0.9 + - - -
2036C LYS* 3.2 25.5 + - + +
2037C HIS* 3.9 3.6 + - - +
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Residues in contact with ALA2034 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007C LEU* 3.7 26.9 - - + +
2008C ALA* 4.7 12.4 - - - +
2011C VAL* 4.0 29.7 - - + +
2023C LEU* 4.3 6.7 - - + -
2030C ALA 3.1 15.0 + - - +
2031C VAL 4.2 2.7 - - - +
2033C LEU* 1.3 81.6 - - - +
2035C ALA* 1.3 62.6 + - - +
2037C HIS* 3.4 17.8 + - - +
2038C CYS 4.0 0.2 + - - -
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Residues in contact with ALA2035 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1925C HIS* 4.1 18.5 + - + +
1927C LEU* 4.3 10.1 - - + -
2031C VAL 2.9 20.4 + - - +
2032C GLU* 3.5 9.9 - - - +
2033C LEU 3.1 0.2 - - - -
2034C ALA* 1.3 72.5 - - - +
2036C LYS* 1.3 56.5 + - - +
2037C HIS 3.0 2.2 - - - -
2038C CYS* 2.6 37.2 + - - +
2042C VAL* 3.9 30.2 - - + +
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Residues in contact with LYS2036 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1925C HIS* 5.0 2.9 + - - -
2032C GLU 3.3 9.0 + - - +
2033C LEU* 3.2 18.9 + - + +
2035C ALA* 1.3 77.1 - - - +
2037C HIS* 1.3 65.3 + - + +
2038C CYS 3.3 4.5 + - - +
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Residues in contact with HIS2037 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2193B VAL* 5.5 10.8 - - + -
2196B ASP* 5.7 9.0 - - + +
2008C ALA* 5.0 19.2 - - + +
2012C GLN* 3.7 43.6 + - + +
2033C LEU 3.9 3.0 + - - +
2034C ALA 3.4 11.3 + - - +
2035C ALA 2.7 5.2 + - - -
2036C LYS* 1.3 79.0 - - + +
2038C CYS* 1.3 57.7 + - - +
2039C ARG 4.3 0.4 - - - -
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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