Contacts of the helix formed by residues 2084 - 2094 (chain F) 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 GLY2084 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2080F ASP 3.3 20.1 + - - -
2081F LEU 3.5 1.3 + - - -
2082F LYS 3.5 1.8 - - - -
2083F HIS* 1.3 73.6 - - - +
2085F ARG* 1.3 64.5 + - - -
2086F THR* 3.1 6.7 - - - -
2087F VAL* 3.0 26.1 - - - +
2088F HIS* 3.1 12.8 - - - -
2145F THR* 6.1 2.7 - - - -
2148F GLN* 4.4 13.0 - - - +
3226F PAL 6.0 1.3 - - - -
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Residues in contact with ARG2085 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003D LYS* 4.3 4.4 - - - +
1971F GLU* 3.3 21.6 + - - +
1972F VAL 5.3 0.2 + - - -
2024F ARG* 3.4 22.7 - - - +
2046F GLY* 3.5 28.6 + - - -
2048F GLY 3.0 27.4 + - - +
2049F VAL 3.7 4.5 - - - +
2051F GLU* 3.6 31.9 - - - +
2052F HIS* 3.3 24.0 + - + -
2083F HIS 2.8 6.2 + - - +
2084F GLY* 1.3 71.6 - - - -
2086F THR* 1.3 62.7 + - - +
2088F HIS* 3.6 13.8 - - - +
2089F SER* 3.3 16.1 + - - -
2148F GLN* 5.7 0.4 + - - -
2151F ARG* 3.5 14.2 - - - +
3226F PAL 2.7 42.4 + - - +
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Residues in contact with THR2086 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052F HIS* 4.1 15.5 - - + -
2055F GLN* 3.7 25.6 - - + -
2056F ALA* 5.0 2.1 - - - +
2059F ASP* 4.9 0.4 - - - +
2084F GLY* 3.1 3.9 + - - -
2085F ARG* 1.3 73.7 - - - +
2087F VAL* 1.3 69.7 + - - +
2088F HIS 3.4 0.2 + - - -
2089F SER* 3.4 4.1 + - - -
2090F LEU* 2.8 31.4 + - - +
2143F TYR* 3.0 29.3 + - - +
2145F THR* 5.2 2.8 - - - +
2184F PRO* 3.9 7.5 - - + +
3226F PAL 3.8 34.3 - - + +
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Residues in contact with VAL2087 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2077F MET* 3.5 32.9 - - + +
2080F ASP 4.6 0.4 - - - +
2081F LEU* 3.8 33.0 - - + +
2084F GLY* 3.0 22.2 - - - +
2086F THR* 1.3 78.5 + - - +
2088F HIS* 1.3 58.2 + - + +
2090F LEU* 4.1 5.6 - - - -
2091F ALA* 2.7 38.0 + - - +
2111F MET* 4.0 4.9 - - + -
2143F TYR* 3.5 29.8 - - + -
2145F THR* 4.0 13.2 - - + -
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Residues in contact with HIS2088 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2049F VAL* 2.8 30.6 + - + -
2050F GLY 3.4 13.6 + - - +
2051F GLU* 5.0 1.8 - - + -
2081F LEU 2.6 26.8 + - - -
2082F LYS 3.0 21.1 + - - -
2083F HIS 4.0 0.4 - - - -
2084F GLY 3.1 21.1 + - - -
2085F ARG* 3.6 6.8 - - - +
2086F THR 3.3 0.2 - - - -
2087F VAL* 1.3 77.6 - - - +
2089F SER* 1.3 63.4 + - - +
2091F ALA* 3.9 1.7 - - - +
2092F CYS* 3.2 27.5 + - - +
2111F MET* 3.9 13.0 - - - -
2112F PRO* 3.6 16.4 - - + +
2115F VAL* 4.4 19.8 - - + +
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Residues in contact with SER2089 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929F VAL* 3.6 14.4 - - - +
2051F GLU* 2.5 42.6 + - - +
2052F HIS 3.1 30.3 + - - -
2056F ALA* 3.9 3.8 - - - -
2085F ARG 3.3 7.8 + - - -
2086F THR 3.8 2.2 - - - -
2088F HIS* 1.3 79.3 - - - +
2090F LEU* 1.3 57.7 + - - +
2092F CYS* 3.6 2.5 - - - +
2093F LEU* 2.9 30.5 + - - +
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Residues in contact with LEU2090 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056F ALA* 3.9 18.4 - - + +
2059F ASP* 4.0 11.9 - - + +
2060F ILE* 3.8 30.3 - - + +
2063F ILE* 5.3 5.6 - - + -
2075F ILE* 5.3 2.9 - - + -
2077F MET* 3.7 19.3 - - + -
2086F THR 2.8 22.8 + - - +
2087F VAL* 3.8 2.9 - - - +
2089F SER* 1.3 71.5 - - - +
2091F ALA* 1.3 60.4 + - - +
2093F LEU* 3.9 1.0 - - - +
2094F LEU* 3.0 41.7 + - + +
2143F TYR* 3.5 41.1 - - + -
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Residues in contact with ALA2091 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2077F MET* 3.7 15.2 - - + +
2087F VAL 2.7 20.6 + - - +
2088F HIS 3.9 2.9 - - - +
2090F LEU* 1.3 70.5 - - - +
2092F CYS* 1.3 67.1 + - - +
2094F LEU* 3.1 15.5 + - - +
2095F THR* 3.4 11.8 + - - +
2101F LEU* 4.4 10.5 - - + +
2103F TYR* 4.0 19.7 - - - +
2111F MET* 4.1 7.9 - - + -
2115F VAL* 4.3 4.7 - - + -
2119F VAL* 4.0 14.4 - - + +
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Residues in contact with CYS2092 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929F VAL* 3.6 17.3 - - + -
1930F GLN* 3.5 21.7 - - - +
2051F GLU* 5.9 2.2 - - - -
2088F HIS 3.2 18.6 + - - +
2089F SER* 3.6 4.7 - - - +
2091F ALA* 1.3 78.6 - - - +
2093F LEU* 1.3 54.3 + - - +
2095F THR* 2.6 36.6 + - - +
2115F VAL* 4.7 15.5 - - - -
2118F PHE* 3.9 26.9 - - - -
2119F VAL* 4.1 1.5 - - - +
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Residues in contact with LEU2093 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929F VAL* 3.6 33.4 - - + +
1932F PHE* 4.0 20.9 - - + +
1937F MET* 3.8 26.2 - - + -
2056F ALA* 3.9 18.6 - - + -
2057F LEU* 4.2 6.1 - - - +
2060F ILE* 3.2 31.9 - - + -
2089F SER 2.9 17.9 + - - +
2090F LEU 4.1 2.0 - - - +
2091F ALA 3.2 0.2 - - - -
2092F CYS* 1.3 70.8 - - - +
2094F LEU* 1.3 58.3 + - - +
2095F THR 3.0 5.4 - - - -
2096F GLN* 3.1 32.1 + - + +
2097F TYR* 4.2 3.6 - - - -
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Residues in contact with LEU2094 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2060F ILE* 4.3 12.6 - - + -
2063F ILE* 4.8 6.5 - - + -
2070F VAL* 3.8 28.7 - - + -
2075F ILE* 3.8 30.7 - - + -
2077F MET* 4.5 2.2 - - + -
2090F LEU* 3.0 43.1 + - + +
2091F ALA 3.1 6.0 + - - +
2093F LEU* 1.3 71.4 - - - +
2095F THR* 1.3 56.4 + - - +
2096F GLN 3.1 5.4 - - - -
2097F TYR* 2.9 36.2 + - + +
2099F VAL* 3.3 22.2 - - + +
2101F LEU* 4.3 13.0 - - + -
2124F THR* 5.1 1.3 - - - -
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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