Contacts of the strand formed by residues 2020 - 2025 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1964B VAL 3.6 2.0 + - - +
1965B MET* 3.4 22.2 - - + +
1966B ALA 2.9 24.8 + - - -
1984B MET* 4.6 0.7 - - + -
2018B ALA* 3.6 2.6 - - - +
2019B ASP* 1.3 79.0 - - - +
2021B VAL* 1.3 70.9 + - - +
2022B VAL* 4.9 1.1 - - + -
2040B ARG* 4.8 0.9 - - - -
2041B PRO* 3.4 22.0 - - + +
2043B ILE* 3.5 31.9 - - + -
2218B LEU* 4.0 17.9 - - + -
2221B VAL* 4.8 3.8 - - + -
2222B LEU* 4.1 22.9 - - + -
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Residues in contact with VAL2021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966B ALA* 3.5 15.3 - - + +
1968B MET* 3.6 29.2 - - - -
2011B VAL* 4.7 7.9 - - + +
2014B MET* 4.9 1.1 - - + -
2015B SER* 3.3 33.2 - - - +
2018B ALA* 5.1 1.3 - - + -
2020B VAL* 1.3 79.1 - - - +
2022B VAL* 1.3 66.3 + - - +
2023B LEU* 4.4 8.5 - - + -
2038B CYS* 4.3 1.3 - - - -
2040B ARG* 5.1 2.7 - - + -
2041B PRO 2.9 9.2 + - - +
2042B VAL* 3.2 21.9 - - + -
2043B ILE* 2.6 35.0 + - - +
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Residues in contact with VAL2022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965B MET* 3.9 27.4 - - + -
1966B ALA 2.7 13.3 + - - +
1967B SER* 4.5 4.7 - - - -
1968B MET* 2.6 35.2 + - - +
1969B PHE* 4.0 11.1 - - + -
1980B PHE* 3.7 32.1 - - + -
2020B VAL* 4.9 1.3 - - + -
2021B VAL* 1.3 78.7 - - - +
2023B LEU* 1.3 59.5 + - - +
2043B ILE* 3.6 22.0 - - + +
2045B ALA* 3.5 23.8 - - + -
2218B LEU* 5.2 0.7 - - + -
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Residues in contact with LEU2023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968B MET* 3.3 17.0 - - + +
1970B TYR* 4.0 21.5 - - + -
2007B LEU* 4.2 13.9 - - + -
2011B VAL* 4.5 8.3 - - + -
2021B VAL* 4.1 6.9 - - + -
2022B VAL* 1.3 73.8 - - - +
2024B ARG* 1.3 62.3 + - - +
2025B HIS* 4.4 4.5 - - + -
2030B ALA 4.6 0.9 - - - +
2031B VAL* 3.7 42.8 - - + +
2034B ALA* 3.9 21.1 - - + -
2042B VAL* 4.1 19.7 - - + -
2043B ILE 3.0 8.4 + - - +
2044B ASN* 3.8 4.5 - - - -
2045B ALA* 2.9 23.2 + - - -
2046B GLY 3.9 0.2 + - - -
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Residues in contact with ARG2024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968B MET 3.0 8.1 + - - +
1969B PHE* 3.6 29.3 - - + -
1970B TYR* 2.8 33.4 + - - +
1971B GLU* 3.7 28.9 - - + +
1972B VAL 3.0 19.8 + - - -
1973B SER* 3.4 5.5 - - - -
1976B THR* 3.4 4.6 + - - -
2023B LEU* 1.3 73.7 - - - +
2025B HIS* 1.3 62.0 + - - +
2045B ALA* 3.3 25.4 + - + +
2046B GLY 3.3 10.5 - - - +
2052B HIS* 3.4 7.1 + - - -
2085B ARG* 3.4 18.8 - - - +
3226B PAL 3.0 62.0 + - - -
2003C LYS* 3.9 1.4 - - - +
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Residues in contact with HIS2025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1970B TYR* 3.5 38.0 - + - -
1971B GLU* 4.2 4.8 - - - +
2007B LEU* 4.0 24.0 - - + +
2023B LEU* 4.1 6.3 + - + -
2024B ARG* 1.3 73.9 - - - +
2026B PRO* 1.4 68.6 - - + +
2027B GLN* 3.3 44.7 + - + +
2030B ALA* 3.6 12.3 - - + +
2031B VAL* 4.2 17.4 - - + +
2046B GLY 2.9 9.7 + - - +
2047B ASP* 3.3 2.9 - - - -
2048B GLY 2.8 28.9 + - - -
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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