Contacts of the helix formed by residues 2095 - 2110 (chain B) in PDB entry 1FAP
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 LYS2095 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE 4.9 9.6 + - - -
37A ASP* 5.8 3.0 - - - +
89A GLY 5.3 2.5 - - - +
90A ILE* 3.8 34.6 - - + +
108A RAP 5.2 2.8 + - - +
2093B ASN* 2.9 21.8 + - - +
2094B VAL* 1.3 87.4 - - + +
2096B ASP* 1.3 61.1 + - - +
2098B THR* 2.8 45.2 + - + +
2099B GLN* 3.2 17.2 + - - +
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Residues in contact with ASP2096 (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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2084B TRP* 3.2 53.2 - - + +
2087B LYS* 3.9 14.3 - - - +
2088B TYR* 3.8 9.9 - - + +
2091B SER* 3.1 24.9 + - - -
2093B ASN* 3.4 14.3 - - + +
2094B VAL 3.3 0.8 - - - +
2095B LYS* 1.3 76.8 - - - +
2097B LEU* 1.3 57.6 + - - +
2099B GLN* 3.1 1.9 + - - +
2100B ALA* 2.8 29.5 + - - +
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Residues in contact with LEU2097 (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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2038B TYR* 4.0 30.5 - - + +
2044B VAL* 3.7 28.3 - - + -
2047B MET* 3.8 24.2 - - + -
2048B PHE* 4.4 1.8 - - + -
2085B CYS* 3.9 18.8 - - - -
2088B TYR* 3.7 43.1 - - + +
2094B VAL* 3.8 15.3 + - + +
2096B ASP* 1.3 77.8 - - - +
2098B THR* 1.3 56.5 + - - +
2100B ALA* 3.0 6.8 - - - +
2101B TRP* 2.8 33.2 + - + +
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Residues in contact with THR2098 (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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87A HIS* 5.8 2.5 - - + +
90A ILE* 5.6 2.0 - - + -
108A RAP 3.1 42.4 - - + +
2038B TYR* 5.0 12.1 - - + +
2039B PHE* 5.7 1.1 - - + -
2094B VAL 3.5 10.9 + - - +
2095B LYS* 2.8 57.9 + - + +
2097B LEU* 1.3 73.9 - - - +
2099B GLN* 1.3 57.8 + - - +
2101B TRP* 3.1 2.6 + - - +
2102B ASP* 2.8 28.2 + - - +
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Residues in contact with GLN2099 (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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2080B GLU* 4.4 3.2 + - - -
2084B TRP* 3.7 44.3 - - + +
2095B LYS 3.2 9.4 + - - +
2096B ASP 3.1 9.5 + - - +
2098B THR* 1.3 81.5 + - - +
2100B ALA* 1.3 59.6 + - - +
2102B ASP* 3.6 26.7 + - - +
2103B LEU* 3.4 20.9 - - - +
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Residues in contact with ALA2100 (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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2081B ALA* 3.5 17.2 - - - +
2084B TRP* 3.3 27.8 - - + +
2085B CYS* 4.0 17.9 - - - +
2096B ASP 2.8 7.0 + - - +
2097B LEU* 3.0 15.0 + - - +
2099B GLN* 1.3 77.4 - - - +
2101B TRP* 1.3 55.3 + - + +
2103B LEU* 3.0 20.8 + - - +
2104B TYR* 3.1 19.7 + - + -
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Residues in contact with TRP2101 (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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108A RAP 3.6 47.8 - - + +
2031B LEU* 3.5 17.0 - - + -
2034B ALA* 4.0 13.2 - - + -
2035B SER* 3.3 42.8 - - - -
2038B TYR* 3.6 22.3 - + - -
2039B PHE* 3.7 16.4 - + + -
2047B MET* 3.4 32.1 - - + +
2051B LEU* 4.9 2.2 - - + -
2097B LEU 2.8 22.2 + - - +
2098B THR* 3.1 4.9 + - - +
2100B ALA* 1.3 73.5 - - + +
2102B ASP* 1.3 64.4 + - - +
2103B LEU 3.2 0.2 - - - -
2104B TYR* 3.4 43.0 - + + -
2105B TYR* 3.2 23.6 + - - +
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Residues in contact with ASP2102 (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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42A ARG* 4.2 28.4 + - - +
44A LYS* 4.0 21.3 + - - +
108A RAP 3.6 13.5 - - - +
2098B THR 2.8 15.3 + - - +
2099B GLN* 3.6 26.9 + - - +
2101B TRP* 1.3 79.2 - - - +
2103B LEU* 1.3 59.1 + - + +
2105B TYR* 3.5 9.3 + - - +
2106B HIS* 3.2 24.6 + - - +
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Residues in contact with LEU2103 (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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2077B ASP* 4.0 29.1 - - + +
2080B GLU* 3.4 38.6 - - - +
2081B ALA* 3.8 19.3 - - + +
2084B TRP* 3.4 15.5 - - + +
2099B GLN* 3.4 24.0 - - - +
2100B ALA 3.0 6.3 + - - +
2102B ASP* 1.3 80.9 - - + +
2104B TYR* 1.3 64.6 + - - +
2106B HIS* 3.2 11.1 + - + +
2107B VAL* 3.1 27.7 + - - +
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Residues in contact with TYR2104 (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 TRP* 4.2 1.3 - + - -
2031B LEU* 3.5 24.2 - - + +
2051B LEU* 3.6 26.9 - - + +
2055B HIS* 2.9 32.6 + - - -
2078B LEU* 3.9 18.4 - - + -
2081B ALA* 3.6 26.8 - - + +
2082B GLN* 4.4 1.0 + - - -
2085B CYS* 4.1 22.1 - - - -
2100B ALA* 3.1 22.5 + - + +
2101B TRP* 3.4 43.1 - + + -
2102B ASP 3.5 0.2 - - - -
2103B LEU* 1.3 74.1 - - - +
2105B TYR* 1.3 58.1 + - - +
2107B VAL* 3.0 6.6 - - - +
2108B PHE* 2.9 32.1 + - - +
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Residues in contact with TYR2105 (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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46A PHE* 4.3 15.7 - + - -
47A LYS* 2.6 31.0 + - + -
48A PHE* 4.6 1.6 - - - -
54A GLU* 5.0 3.1 + - - -
108A RAP 3.2 78.9 - - + +
2101B TRP* 3.2 18.4 + - - +
2102B ASP* 3.6 9.9 - - - +
2103B LEU 3.3 0.2 - - - -
2104B TYR* 1.3 80.2 - - - +
2106B HIS* 1.3 57.4 + - - +
2108B PHE* 4.3 5.6 - + - -
2109B ARG* 2.9 60.4 + - + +
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Residues in contact with HIS2106 (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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44A LYS* 6.1 6.9 - - + +
2077B ASP* 3.3 24.5 - - - -
2102B ASP 3.2 10.7 + - - +
2103B LEU* 3.2 15.3 + - + +
2105B TYR* 1.3 82.1 - - - +
2107B VAL* 1.3 60.8 + - - +
2109B ARG* 3.5 14.8 + - - +
2110B ARG* 3.2 52.3 + - + +
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Residues in contact with VAL2107 (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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2031B LEU* 3.7 9.4 - - + -
2074B TYR* 4.2 28.3 - - + -
2077B ASP* 3.5 37.0 - - + +
2078B LEU* 3.6 31.0 - - + +
2103B LEU 3.1 9.4 + - - +
2104B TYR* 3.0 20.0 - - - +
2106B HIS* 1.3 72.2 - - - +
2108B PHE* 1.3 64.3 + - - +
2110B ARG* 3.1 6.8 + - - +
2111B ILE* 3.0 33.3 + - + +
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Residues in contact with PHE2108 (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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108A RAP 3.4 52.7 - - + -
2028B HIS* 3.2 52.3 - + - -
2031B LEU* 3.8 13.7 - - + -
2032B GLU* 3.7 21.3 - - + -
2104B TYR 2.9 17.8 + - - +
2105B TYR* 3.7 8.5 - + - +
2107B VAL* 1.3 79.4 - - - +
2109B ARG* 1.3 67.4 + - + +
2111B ILE* 3.2 23.8 + - - +
2112B SER* 3.6 15.1 + - - -
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Residues in contact with ARG2109 (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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47A LYS* 3.9 41.3 - - - +
107A GLU* 5.7 0.2 + - - -
2105B TYR* 2.9 55.1 + - + +
2106B HIS* 3.8 18.2 + - - +
2107B VAL 3.3 0.2 - - - -
2108B PHE* 1.3 79.2 - - + +
2110B ARG* 1.3 105.7 + - - +
2112B SER* 3.9 16.4 + - - +
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Residues in contact with ARG2110 (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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2074B TYR* 3.7 29.4 + - + +
2106B HIS* 3.2 33.8 + - + +
2107B VAL* 3.1 9.0 + - - +
2109B ARG* 1.3 119.7 + - + +
2111B ILE* 1.3 57.1 + - - +
2112B SER 3.3 8.9 + - - +
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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