Contacts of the helix formed by residues 2026 - 2034 (chain B) in PDB entry 1F5T
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 LEU2026 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2018B LEU* 4.2 0.2 - - - +
2024B THR* 2.8 21.2 + - + +
2025B PRO* 1.3 78.3 - - - +
2027B ARG* 1.3 57.9 + - - +
2028B ALA* 4.3 2.2 - - + +
2029B ARG* 2.8 49.2 + - + +
2030B ILE* 3.3 6.1 + - - +
2059B ASP 4.2 7.9 - - - +
2060B ARG* 3.0 52.7 - - + +
2061B SER* 3.9 3.4 - - - +
2062B LEU* 3.6 4.0 - - - -
408F G 4.4 24.0 - - - +
409F C 3.8 13.2 - - - +
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Residues in contact with ARG2027 (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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2026B LEU* 1.3 75.1 - - - +
2028B ALA* 1.3 63.1 + - - +
2029B ARG 3.2 0.2 + - - -
2030B ILE* 3.3 6.9 + - + +
2031B ALA* 3.0 23.3 + - - +
2038B GLY 6.1 0.2 - - - +
2041B VAL* 3.8 13.9 - - + +
2042B SER* 4.1 27.5 + - - +
2045B VAL* 4.0 30.4 - - + +
2056B VAL* 4.1 29.4 - - - +
2060B ARG* 4.1 14.1 + - - +
2062B LEU* 3.4 15.9 - - + +
409F C 3.4 46.8 + - - +
410F T 3.3 28.8 + - - -
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Residues in contact with ALA2028 (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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2026B LEU* 3.1 2.7 - - + -
2027B ARG* 1.3 74.5 - - - +
2029B ARG* 1.3 81.2 + - - +
2031B ALA* 3.3 8.8 - - - +
2032B GLU* 3.1 28.1 + - - +
408F G 3.8 24.5 - - + +
409F C 2.8 22.2 + - - +
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Residues in contact with ARG2029 (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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2018B LEU* 3.8 22.4 - - + -
2023B VAL* 4.0 22.9 - - - -
2024B THR 3.7 5.4 - - - +
2026B LEU* 2.8 37.1 + - + +
2028B ALA* 1.3 79.8 - - - +
2030B ILE* 1.3 56.2 + - - +
2031B ALA 3.1 0.9 - - - -
2032B GLU* 2.4 52.4 + - - +
2033B ARG* 2.7 41.7 + - + +
408F G 2.8 42.0 + - - -
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Residues in contact with ILE2030 (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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2011B TYR* 4.1 19.3 - - + +
2014B THR* 3.7 25.1 - - + -
2015B ILE* 3.8 31.9 - - + -
2018B LEU* 4.7 4.9 - - + -
2026B LEU 3.3 6.7 + - - +
2027B ARG* 3.3 10.9 + - - +
2029B ARG* 1.3 75.4 - - - +
2031B ALA* 1.3 65.2 + - - +
2033B ARG* 4.4 0.2 - - - -
2034B LEU* 2.8 48.4 + - + +
2041B VAL* 4.1 14.8 - - + -
2045B VAL* 4.6 13.2 - - + -
2062B LEU* 4.5 16.4 - - + -
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Residues in contact with ALA2031 (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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2027B ARG 3.0 13.2 + - - +
2028B ALA* 3.3 14.8 - - - +
2030B ILE* 1.3 77.4 - - - +
2032B GLU* 1.3 62.6 + - - +
2035B GLU* 3.1 3.3 + - - -
2036B GLN* 3.0 39.8 + - - +
2038B GLY* 4.6 12.8 - - - +
2041B VAL* 3.6 20.6 - - + +
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Residues in contact with GLU2032 (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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2028B ALA* 3.1 9.5 - - - +
2029B ARG* 2.4 52.0 + - - +
2031B ALA* 1.3 76.6 - - - +
2033B ARG* 1.3 71.8 + - + +
2035B GLU* 3.5 15.7 + - - +
408F G 4.9 2.6 + - - -
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Residues in contact with ARG2033 (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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2014B THR* 4.4 24.3 + - + +
2017B GLU* 5.2 6.7 + - - +
2018B LEU* 3.0 38.8 - - - +
2021B GLU* 3.3 31.5 + - - -
2023B VAL* 4.4 7.9 - - - +
2029B ARG* 2.7 32.0 + - + +
2030B ILE 3.8 2.7 - - - +
2032B GLU* 1.3 79.5 + - + +
2034B LEU* 1.3 64.6 + - + +
2035B GLU* 3.6 6.2 + - - +
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Residues in contact with LEU2034 (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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2004B LEU* 4.6 21.2 - - + +
2010B MET* 4.0 36.3 - - + +
2011B TYR* 3.4 39.5 - - + -
2014B THR* 3.8 18.2 - - - +
2030B ILE* 2.8 28.6 + - + +
2033B ARG* 1.3 75.4 - - + +
2035B GLU* 1.3 74.5 + - - +
2036B GLN* 3.1 21.0 + - + +
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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