Contacts of the helix formed by residues 2037 - 2051 (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 SER2037 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2036B GLN* 1.3 75.7 - - - +
2038B GLY* 1.3 63.5 + - - +
2039B PRO* 3.1 13.6 - - - +
2040B THR* 3.0 25.5 + - - -
2041B VAL* 3.3 12.1 + - - +
322E C 3.0 23.4 + - - -
323E T 3.3 30.0 - - - +
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Residues in contact with GLY2038 (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* 6.1 0.2 - - - +
2031B ALA* 4.6 12.9 - - - +
2036B GLN 3.9 1.6 + - - -
2037B SER* 1.3 71.8 - - - +
2039B PRO* 1.3 68.3 - - - +
2041B VAL* 3.5 3.8 + - - +
2042B SER* 3.2 24.6 + - - -
409F C 6.2 3.4 - - - -
410F T 4.6 6.7 - - - -
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Residues in contact with PRO2039 (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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2037B SER* 3.1 12.8 - - - +
2038B GLY* 1.3 87.6 - - - +
2040B THR* 1.3 66.3 + - - +
2042B SER* 3.4 3.6 + - - +
2043B GLN* 3.1 23.7 + - - +
322E C 4.9 4.7 - - - +
323E T 3.1 36.1 - - + +
324E T 4.3 7.2 - - + +
410F T 4.3 19.9 - - + +
411F A 4.1 14.8 - - - +
412F A 4.2 5.6 - - - +
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Residues in contact with THR2040 (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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2036B GLN* 3.8 19.1 - - - +
2037B SER* 3.0 16.0 + - - -
2039B PRO* 1.3 82.6 - - - +
2041B VAL* 1.3 64.1 + - - +
2043B GLN* 3.2 6.2 + - - +
2044B THR* 3.0 34.0 + - - +
320E A 4.7 0.9 - - + -
321E C 3.2 46.9 - - + +
322E C 2.8 29.0 + - - +
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Residues in contact with VAL2041 (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* 3.4 21.5 - - + +
2027B ARG* 3.8 28.5 - - + +
2030B ILE* 4.1 15.5 - - + -
2031B ALA* 3.6 28.5 - - + +
2036B GLN* 4.3 9.0 - - + +
2037B SER 3.3 13.1 + - - +
2038B GLY 3.7 6.7 - - - +
2039B PRO 3.3 0.2 - - - -
2040B THR* 1.3 75.7 - - - +
2042B SER* 1.3 56.8 + - - +
2044B THR* 3.2 2.1 + - - -
2045B VAL* 2.8 48.9 + - + +
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Residues in contact with SER2042 (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* 4.1 27.6 + - - +
2038B GLY 3.2 12.7 + - - -
2039B PRO* 3.8 9.0 - - - -
2040B THR 3.3 0.2 - - - -
2041B VAL* 1.3 78.0 - - - +
2043B GLN* 1.3 58.0 + - - +
2045B VAL* 3.4 2.3 + - - +
2046B ALA* 2.8 29.6 + - - +
409F C 4.6 2.9 + - - -
410F T 3.0 34.2 + - - +
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Residues in contact with GLN2043 (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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2039B PRO 3.1 14.1 + - - +
2040B THR* 3.4 9.8 - - - +
2042B SER* 1.3 77.5 - - - +
2044B THR* 1.3 58.1 + - - +
2046B ALA* 3.2 9.2 - - - +
2047B ARG* 2.9 42.4 + - - +
320E A 3.7 4.7 - - - +
321E C 2.9 42.9 + - - +
322E C 4.9 5.4 - - - +
413F G 5.2 2.6 + - - -
414F G 4.7 3.0 + - - -
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Residues in contact with THR2044 (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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2007B THR* 4.1 13.2 - - + -
2008B THR* 5.5 1.6 - - - +
2011B TYR* 3.4 37.8 + - + -
2040B THR* 3.0 21.4 + - - +
2041B VAL 3.7 0.2 - - - -
2043B GLN* 1.3 72.3 - - - +
2045B VAL* 1.3 67.5 + - - +
2047B ARG* 3.0 39.0 + - - +
2048B MET* 2.8 30.0 + - + +
320E A 4.7 5.1 - - - +
321E C 4.8 2.3 + - - -
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Residues in contact with VAL2045 (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 13.9 - - + -
2027B ARG* 4.0 25.8 - - + +
2030B ILE* 4.6 6.1 - - + -
2041B VAL* 2.8 32.1 + - + +
2042B SER 3.7 4.7 - - - +
2044B THR* 1.3 72.4 - - - +
2046B ALA* 1.3 53.2 + - - +
2048B MET* 3.1 11.6 + - - +
2049B GLU* 2.7 33.3 + - - +
2054B VAL* 4.0 11.6 - - + +
2056B VAL* 4.3 15.7 - - + -
2062B LEU* 3.8 27.4 - - + -
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Residues in contact with ALA2046 (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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2042B SER 2.8 14.9 + - - +
2043B GLN* 3.2 13.0 - - + +
2044B THR 3.1 0.2 - - - -
2045B VAL* 1.3 77.3 - - - +
2047B ARG* 1.3 62.6 + - - +
2049B GLU* 3.0 14.7 + - - +
2050B ARG* 2.9 22.7 + - - +
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Residues in contact with ARG2047 (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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2043B GLN* 2.9 35.4 + - - +
2044B THR* 3.2 46.0 + - - +
2046B ALA* 1.3 74.9 - - - +
2048B MET* 1.3 58.6 + - + +
2050B ARG* 3.1 38.6 + - - +
2051B ASP* 3.0 35.2 + - - +
319E A 3.7 31.0 + - - +
320E A 2.6 65.4 + - - +
321E C 5.3 0.2 - - - -
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Residues in contact with MET2048 (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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2008B THR* 3.7 38.6 - - + +
2011B TYR* 3.7 35.4 - - + -
2012B LEU* 3.2 35.2 - - + -
2015B ILE* 5.4 2.2 - - + -
2044B THR* 2.8 21.1 + - + +
2045B VAL* 3.3 11.7 - - - +
2047B ARG* 1.3 75.0 - - + +
2049B GLU* 1.3 65.1 + - - +
2051B ASP* 3.0 18.6 + - - +
2052B GLY 3.1 0.2 + - - -
2053B LEU* 3.1 28.5 + - + +
2054B VAL* 3.8 15.7 - - + -
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Residues in contact with GLU2049 (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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2045B VAL 2.7 14.9 + - - +
2046B ALA* 3.3 15.1 - - - +
2048B MET* 1.3 72.7 - - - +
2050B ARG* 1.3 62.3 + - - +
2052B GLY* 3.1 12.5 + - - -
2054B VAL* 3.3 26.1 - - + +
2055B VAL* 3.5 10.5 - - + +
2056B VAL* 3.0 48.3 + - + +
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Residues in contact with ARG2050 (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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2046B ALA 2.9 10.8 + - - +
2047B ARG* 3.1 32.1 + - - +
2049B GLU* 1.3 78.0 - - - +
2051B ASP* 1.3 78.2 + - - +
2052B GLY* 3.1 4.7 + - - -
318E T 5.6 0.4 - - - -
319E A 2.9 41.6 + - - -
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Residues in contact with ASP2051 (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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2047B ARG* 3.0 24.6 + - - +
2048B MET* 3.0 11.9 + - - +
2050B ARG* 1.3 103.4 + - - +
2052B GLY* 1.3 62.1 + - - +
2053B LEU* 3.4 21.6 + - + +
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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