Contacts of the strand formed by residues 2020 - 2025 (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 VAL2020 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1964E VAL 3.4 4.0 + - - +
1965E MET* 3.4 27.7 - - + -
1966E ALA 2.9 24.6 + - - -
1984E MET* 4.2 5.2 - - + -
2018E ALA* 3.4 3.0 - - - +
2019E ASP* 1.3 77.5 - - - +
2021E VAL* 1.3 72.6 + - - +
2022E VAL* 4.3 1.3 - - + -
2041E PRO* 3.5 24.0 - - + +
2043E ILE* 4.2 23.1 - - + -
2218E LEU* 4.0 17.5 - - + -
2221E VAL* 4.6 5.2 - - + -
2222E LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2021 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966E ALA* 3.6 10.3 - - + +
1968E MET* 3.8 31.4 - - + -
2011E VAL* 4.5 9.4 - - + +
2014E MET 4.6 0.4 - - - +
2015E SER* 3.9 36.8 - - - +
2018E ALA 5.0 0.4 - - - +
2020E VAL* 1.3 82.2 - - - +
2022E VAL* 1.3 62.1 + - - +
2023E LEU* 4.2 5.6 + - + -
2040E ARG* 4.8 1.8 - - + -
2041E PRO 2.8 13.1 + - - +
2042E VAL* 3.1 20.4 - - + -
2043E ILE* 2.7 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2022 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1965E MET* 4.0 26.2 - - + -
1966E ALA 3.0 9.4 + - - +
1967E SER* 4.8 5.4 - - - -
1968E MET* 2.8 32.2 + - - +
1969E PHE* 4.5 10.7 - - + -
1980E PHE* 3.6 35.0 - - + -
2020E VAL* 5.0 3.1 - - + -
2021E VAL* 1.3 77.2 - - - +
2023E LEU* 1.3 63.0 - - - +
2043E ILE* 3.4 19.3 - - + +
2045E ALA* 3.6 26.2 - - + -
2218E LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2023 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968E MET* 3.2 20.6 - - + +
1970E TYR* 3.7 31.0 - - + -
2007E LEU* 4.3 9.4 - - + -
2011E VAL* 3.9 25.4 - - + -
2021E VAL* 4.7 4.0 - - + -
2022E VAL* 1.3 76.8 - - - +
2024E ARG* 1.3 61.7 + - - +
2025E HIS* 4.7 1.8 - - + -
2030E ALA 4.8 0.7 - - - +
2031E VAL* 4.1 37.3 - - + +
2034E ALA* 4.2 9.0 - - + -
2042E VAL* 4.6 11.2 - - + -
2043E ILE 2.9 10.6 + - - +
2044E ASN* 3.7 7.3 - - - +
2045E ALA* 2.9 23.5 + - - -
2046E GLY 4.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2024 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968E MET 2.9 8.7 + - - -
1969E PHE* 3.5 34.8 - - + -
1970E TYR* 2.8 33.6 + - - +
1971E GLU* 3.6 32.3 - - + +
1972E VAL 3.3 12.2 + - - -
1973E SER* 3.8 2.8 + - - -
1976E THR* 3.5 6.7 + - - -
2023E LEU* 1.3 73.9 - - - +
2025E HIS* 1.3 61.6 + - - +
2045E ALA 2.7 30.8 + - - +
2046E GLY 3.3 5.6 - - - +
2052E HIS* 3.0 11.5 + - - -
2085E ARG* 3.0 25.3 - - - +
3226E PAL 2.8 55.6 + - - -
2003F LYS* 3.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2025 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1970E TYR* 3.4 38.8 - + + -
1971E GLU* 2.7 15.0 - - - +
2007E LEU* 3.9 22.7 - - + +
2023E LEU* 4.2 5.6 - - + -
2024E ARG* 1.3 74.1 - - - +
2026E PRO* 1.4 80.6 - - + +
2027E GLN* 3.2 37.8 + - + +
2030E ALA* 3.6 16.5 - - + +
2031E VAL* 4.2 16.3 - - + +
2046E GLY 2.8 6.7 + - - -
2047E ASP* 3.1 8.5 - - - -
2048E GLY 2.9 14.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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