Contacts of the helix formed by residues 2084 - 2095 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2080E ASP 3.3 17.0 + - - -
2081E LEU 3.5 3.0 + - - -
2082E LYS 3.3 4.0 + - - -
2083E HIS* 1.3 73.5 - - - +
2085E ARG* 1.3 64.6 + - - -
2086E THR* 3.1 4.9 + - - -
2087E VAL* 3.2 10.8 + - - -
2088E HIS* 3.0 31.3 + - - -
2145E THR* 5.9 2.0 - - - -
2148E GLN* 5.0 8.3 - - - -
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Residues in contact with ARG2085 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1971E GLU* 2.7 36.5 + - - +
2024E ARG* 3.0 29.8 - - - +
2046E GLY* 3.8 26.1 - - - -
2047E ASP 4.4 0.7 - - - +
2048E GLY 3.4 28.7 + - - +
2049E VAL 4.5 0.2 - - - -
2050E GLY 3.8 11.1 - - - +
2051E GLU* 3.5 19.1 - - - +
2052E HIS* 3.2 29.1 + - + -
2083E HIS 3.0 7.6 + - - +
2084E GLY* 1.3 71.4 - - - -
2086E THR* 1.3 60.7 + - + +
2088E HIS* 3.7 2.2 + - - -
2089E SER* 3.3 12.6 + - - -
2148E GLN* 5.2 0.6 + - - +
2151E ARG* 4.8 0.8 - - - +
3226E PAL 2.5 47.1 + - - +
2003F LYS* 4.0 4.8 - - - +
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Residues in contact with THR2086 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052E HIS* 3.5 36.8 - - + -
2055E GLN* 3.6 19.7 - - + -
2056E ALA* 5.1 1.4 - - - +
2059E ASP* 4.5 2.0 - - - +
2084E GLY* 4.9 1.9 - - - -
2085E ARG* 1.3 75.7 - - + +
2087E VAL* 1.3 65.1 + - - +
2088E HIS 3.3 0.7 - - - -
2089E SER* 3.7 2.6 + - - +
2090E LEU* 3.0 30.3 + - - +
2143E TYR* 3.4 24.3 + - - -
2145E THR* 5.6 1.0 - - - +
2184E PRO* 3.9 10.0 - - + +
3226E PAL 3.8 22.8 - - + +
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Residues in contact with VAL2087 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2077E MET* 3.3 28.9 - - + -
2081E LEU* 3.8 13.5 - - + +
2084E GLY* 3.2 13.4 + - - +
2086E THR* 1.3 77.5 + - - +
2088E HIS* 1.3 64.4 + - - +
2090E LEU* 4.0 4.9 - - - -
2091E ALA* 3.2 21.8 + - - +
2111E MET* 3.5 23.9 - - + +
2143E TYR* 3.6 29.6 - - + -
2145E THR* 3.7 22.0 - - + -
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Residues in contact with HIS2088 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2049E VAL 3.1 19.7 + - - -
2050E GLY 3.0 27.9 + - - +
2051E GLU* 5.0 4.0 - - + -
2081E LEU 2.8 27.8 + - - -
2082E LYS 3.2 18.3 + - - -
2084E GLY 3.0 27.0 + - - +
2085E ARG 4.0 0.7 - - - +
2086E THR 3.3 0.2 - - - -
2087E VAL* 1.3 75.8 - - - +
2089E SER* 1.3 66.1 + - - +
2091E ALA* 4.0 1.0 - - - +
2092E CYS* 3.1 29.5 + - - +
2111E MET* 3.6 14.1 - - + -
2112E PRO* 3.5 17.2 - - + +
2115E VAL* 3.9 18.8 - - + +
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Residues in contact with SER2089 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929E VAL* 3.4 11.7 - - - +
2051E GLU* 3.1 27.2 + - - +
2052E HIS 2.7 38.5 + - - -
2056E ALA* 3.6 21.3 - - - -
2085E ARG 3.5 5.1 + - - -
2086E THR 4.0 2.7 - - - -
2087E VAL 3.5 0.2 - - - -
2088E HIS* 1.3 77.8 - - - +
2090E LEU* 1.3 51.9 + - - +
2092E CYS* 3.2 2.1 + - - -
2093E LEU* 2.7 33.1 + - - +
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Residues in contact with LEU2090 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056E ALA* 3.9 9.8 - - + +
2059E ASP* 4.1 25.1 - - + +
2060E ILE* 3.9 20.9 - - + +
2063E ILE* 5.2 5.8 - - + -
2075E ILE* 5.0 4.5 - - + -
2077E MET* 3.5 23.8 - - + -
2086E THR 3.0 19.2 + - - +
2089E SER* 1.3 75.1 - - - +
2091E ALA* 1.3 54.3 + - - +
2093E LEU* 3.1 1.0 + - - +
2094E LEU* 2.7 61.8 + - + +
2143E TYR* 4.2 32.1 - - + -
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Residues in contact with ALA2091 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2077E MET* 3.6 17.0 - - + +
2087E VAL 3.2 18.6 + - - +
2088E HIS 4.0 2.5 - - - +
2090E LEU* 1.3 79.7 - - - +
2092E CYS* 1.3 63.4 + - - +
2094E LEU* 3.7 8.4 + - - +
2095E THR* 3.7 16.6 + - - +
2101E LEU* 4.3 10.1 - - + +
2103E TYR* 4.2 10.5 - - - +
2111E MET* 4.6 1.8 - - - -
2115E VAL* 4.0 19.1 - - + -
2119E VAL* 3.9 11.6 - - + +
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Residues in contact with CYS2092 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929E VAL* 3.9 13.5 - - + -
1930E GLN* 4.0 12.3 - - - +
2051E GLU* 5.6 2.5 - - - +
2088E HIS 3.1 19.3 + - - +
2089E SER* 3.5 3.4 - - - +
2091E ALA* 1.3 80.0 - - - +
2093E LEU* 1.3 56.1 + - - +
2095E THR* 2.5 27.5 + - - -
2096E GLN* 5.2 1.2 - - - +
2115E VAL* 4.4 22.9 - - - -
2118E PHE* 3.4 41.4 - - + -
2119E VAL* 4.7 0.4 - - - -
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Residues in contact with LEU2093 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1929E VAL* 3.6 33.1 - - + +
1932E PHE* 4.3 8.3 - - + -
1937E MET* 3.7 41.9 - - + +
2056E ALA* 3.7 33.7 - - + +
2057E LEU* 4.1 12.6 - - + +
2060E ILE* 3.7 6.9 - - + +
2089E SER 2.7 21.6 + - - +
2090E LEU* 3.7 4.0 - - - +
2092E CYS* 1.3 71.8 - - - +
2094E LEU* 1.3 65.7 + - - +
2095E THR 3.0 1.6 + - - -
2096E GLN* 3.0 26.9 + - - +
2097E TYR* 5.0 0.7 - - - -
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Residues in contact with LEU2094 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2060E ILE* 3.6 27.4 - - + -
2063E ILE* 4.7 4.5 - - + -
2070E VAL* 4.0 21.5 - - + -
2075E ILE* 4.2 18.2 - - + -
2077E MET* 4.3 0.7 - - + -
2090E LEU* 2.7 50.2 + - + +
2091E ALA* 3.9 5.6 - - - +
2092E CYS 3.4 0.2 - - - -
2093E LEU* 1.3 72.2 - - - +
2095E THR* 1.3 56.7 + - - +
2096E GLN 2.9 0.7 - - - -
2097E TYR* 2.8 31.6 + - + +
2099E VAL* 3.6 20.8 - - + +
2101E LEU* 3.9 28.3 - - + -
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Residues in contact with THR2095 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2091E ALA 3.7 13.4 + - - +
2092E CYS 2.5 22.8 + - - +
2093E LEU 3.1 0.2 - - - -
2094E LEU* 1.3 74.0 - - - +
2096E GLN* 1.3 59.6 + - - +
2097E TYR 3.1 10.5 + - - +
2101E LEU* 5.7 0.2 - - + -
2118E PHE* 4.0 9.5 - - + -
2119E VAL* 3.9 25.4 - - + -
2122E ARG* 3.7 36.4 - - + +
2124E THR* 3.5 26.9 + - + +
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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