Contacts of the strand formed by residues 2042 - 2047 (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 VAL2042 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1925E HIS* 3.1 18.4 + - - +
1926E ILE 3.0 21.1 + - - -
1927E LEU* 3.8 13.0 - - + +
2011E VAL* 4.2 10.5 - - + -
2021E VAL* 3.1 17.5 - - + +
2023E LEU* 4.6 12.6 - - + -
2031E VAL* 4.2 15.7 - - + +
2035E ALA* 3.9 18.6 - - + -
2038E CYS* 3.7 34.8 - - + -
2040E ARG 4.0 0.9 - - - +
2041E PRO* 1.3 74.7 - - - +
2043E ILE* 1.3 65.1 + - - +
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Residues in contact with ILE2043 (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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1926E ILE* 3.5 27.1 - - + -
1980E PHE* 3.9 35.7 - - + -
2020E VAL* 4.2 20.6 - - + -
2021E VAL 2.7 15.1 + - - +
2022E VAL* 3.4 8.8 - - + +
2023E LEU* 2.9 29.3 + - - +
2041E PRO* 5.4 0.4 - - + -
2042E VAL* 1.3 79.9 - - - +
2044E ASN* 1.3 63.6 - - - +
2045E ALA 3.3 2.9 + - - -
2054E THR* 3.9 19.7 - - + -
2217E LEU* 4.6 10.1 - - + -
2218E LEU* 4.6 7.2 - - + -
2221E VAL* 4.6 14.4 - - + -
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Residues in contact with ASN2044 (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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1926E ILE 2.8 18.9 + - - +
1927E LEU* 3.3 19.6 + - - +
2023E LEU 3.7 2.9 - - - -
2031E VAL* 3.3 38.7 - - + +
2042E VAL 4.2 0.4 + - - -
2043E ILE* 1.3 74.9 - - - +
2045E ALA* 1.3 58.5 + - - +
2046E GLY 3.2 19.5 + - - -
2047E ASP* 2.9 22.8 + - - +
2051E GLU* 3.7 4.0 + - - +
2052E HIS* 4.6 0.2 + - - -
2053E PRO* 3.3 42.8 - - + +
2054E THR* 4.5 5.2 + - - -
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Residues in contact with ALA2045 (chain E).
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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1969E PHE* 4.3 7.9 - - + -
1976E THR* 3.4 24.0 - - + -
1980E PHE* 4.3 3.8 - - + -
2022E VAL* 3.6 26.0 - - + -
2023E LEU 2.9 14.5 + - - +
2024E ARG* 2.7 38.3 + - - -
2043E ILE 3.3 1.0 + - - -
2044E ASN* 1.3 72.7 - - - +
2046E GLY* 1.3 50.9 + - - +
2052E HIS* 4.0 11.9 - - - -
2054E THR* 5.1 1.8 - - - -
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Residues in contact with GLY2046 (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* 3.9 0.7 - - - +
2024E ARG* 3.3 3.9 - - - -
2025E HIS 2.8 33.7 + - - +
2031E VAL* 4.0 0.9 - - - +
2044E ASN* 3.2 13.4 + - - +
2045E ALA* 1.3 78.1 - - - +
2047E ASP* 1.3 54.2 + - - +
2051E GLU 3.7 11.8 + - - -
2052E HIS* 4.5 3.4 + - - +
2085E ARG* 3.8 22.4 - - - -
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Residues in contact with ASP2047 (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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2025E HIS 3.1 4.3 - - - +
2027E GLN 3.9 5.2 - - - +
2028E PRO* 3.6 8.5 - - - +
2029E GLY* 2.9 33.4 + - - +
2031E VAL* 3.6 22.6 - - + +
2044E ASN* 2.9 25.2 + - - -
2046E GLY* 1.3 72.3 - - - -
2048E GLY* 1.3 60.5 + - - +
2049E VAL 3.2 0.3 + - - -
2050E GLY* 2.9 26.7 + - - -
2051E GLU* 3.0 22.9 + - - +
2085E ARG* 4.2 0.6 - - - +
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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