Contacts of the helix formed by residues 2093 - 2105 (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 ASP2093 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1115A ARG* 5.5 0.8 - - - +
2091B GLY 3.9 1.6 + - - -
2092B LEU* 1.3 77.2 - - + +
2094B ILE* 1.3 64.5 + - - +
2095B ASN* 3.0 31.0 + - - +
2096B LYS* 2.8 62.5 + - + +
2097B VAL* 3.2 8.8 + - - +
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Residues in contact with ILE2094 (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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2087B THR* 3.5 36.6 - - + +
2092B LEU 3.1 6.1 + - - +
2093B ASP* 1.3 75.6 + - - +
2095B ASN* 1.3 65.4 + - - +
2096B LYS 2.9 5.9 + - - -
2097B VAL* 3.1 19.2 + - + +
2098B HIS 4.5 1.7 + - - -
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Residues in contact with ASN2095 (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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2093B ASP* 3.0 23.0 + - - +
2094B ILE* 1.3 81.3 - - - +
2096B LYS* 1.3 61.0 + - + +
2098B HIS 5.6 0.2 - - - -
2099B ASP* 4.9 6.6 - - - +
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Residues in contact with LYS2096 (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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1111A GLU* 4.1 28.2 + - + +
2092B LEU* 4.0 19.5 - - + +
2093B ASP* 2.8 41.2 + - + +
2095B ASN* 1.3 83.4 - - + +
2097B VAL* 1.3 69.2 + - - +
2098B HIS 3.7 0.4 - - - -
2099B ASP* 3.3 13.7 - - + +
2100B GLU* 3.1 21.1 + - + +
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Residues in contact with VAL2097 (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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2083B GLU* 3.6 31.9 - - + +
2086B LEU* 3.8 7.6 - - + +
2087B THR* 3.4 31.4 - - - +
2092B LEU* 3.6 22.9 - - + +
2093B ASP 3.2 15.8 + - - +
2094B ILE* 3.1 21.5 + - + +
2096B LYS* 1.3 72.0 - - - +
2098B HIS* 1.3 59.1 + - - +
2100B GLU* 2.7 27.6 + - - +
2101B ALA 2.9 9.5 + - - -
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Residues in contact with HIS2098 (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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254B NI 2.0 35.1 - - + +
2013B ARG* 3.4 18.5 + - - -
2017B GLU* 5.2 2.9 - - - -
2079B HIS* 2.5 15.6 + + - -
2083B GLU* 2.0 29.3 + - - +
2094B ILE 4.5 2.2 + - - +
2095B ASN 5.6 0.2 - - - -
2096B LYS 3.7 0.2 - - - -
2097B VAL* 1.3 78.2 - - - +
2099B ASP* 1.3 64.0 + - - +
2101B ALA* 3.3 0.9 + - - +
2102B ASP* 2.9 25.0 + - + +
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Residues in contact with ASP2099 (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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2095B ASN 4.9 5.9 + - - +
2096B LYS* 3.3 17.7 + - + +
2097B VAL 2.9 0.4 + - - -
2098B HIS* 1.3 82.7 - - - +
2100B GLU* 1.3 60.9 + - - +
2102B ASP* 3.5 16.5 + - - +
2103B ARG* 3.8 16.7 + - - +
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Residues in contact with GLU2100 (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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1109A SER* 2.4 46.4 + - - +
1112A VAL* 3.5 9.1 - - + +
2086B LEU* 3.5 13.2 - - + -
2092B LEU* 3.7 22.2 - - + -
2096B LYS* 3.1 5.9 + - + +
2097B VAL 2.7 14.8 + - - +
2099B ASP* 1.3 72.8 - - - +
2101B ALA* 1.3 59.5 + - - +
2102B ASP 3.1 0.2 - - - -
2103B ARG* 3.0 36.8 + - - +
2104B TRP* 2.3 57.7 + - - -
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Residues in contact with ALA2101 (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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2079B HIS* 3.6 17.7 + - + +
2082B ALA* 4.0 8.5 - - + +
2083B GLU* 3.3 42.6 - - + +
2086B LEU* 3.8 6.0 - - + +
2097B VAL 2.9 6.8 + - - +
2098B HIS 3.7 4.7 - - - +
2100B GLU* 1.3 72.3 - - - +
2102B ASP* 1.3 62.5 + - - +
2103B ARG 3.0 5.4 - - - -
2104B TRP* 4.3 1.6 - - - +
2105B GLU* 3.0 27.9 + - - +
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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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253B NI 1.7 86.1 - - - +
2010B MET* 2.6 17.3 - - - +
2013B ARG* 3.9 12.4 + - - +
2079B HIS* 4.1 2.2 - - + -
2098B HIS* 2.9 17.3 + - + +
2099B ASP* 3.6 15.3 - - - +
2100B GLU 3.1 0.8 - - - -
2101B ALA* 1.3 76.0 - - - +
2103B ARG* 1.3 53.1 + - + +
2105B GLU* 3.1 7.6 - - - -
2106B HIS* 2.7 6.1 + - - -
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Residues in contact with ARG2103 (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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1106A HIS 5.4 0.7 - - - -
1107A VAL* 2.4 55.4 + - + +
1108A MET 4.4 0.2 - - - -
1109A SER* 4.1 10.3 - - - +
2003B ASP 5.2 4.0 - - - +
2005B VAL* 3.5 26.1 - - + +
2099B ASP* 3.8 12.4 + - - +
2100B GLU* 3.0 49.4 + - - +
2101B ALA 3.0 0.2 - - - -
2102B ASP* 1.3 79.8 - - - +
2104B TRP* 1.3 67.8 - - + +
2105B GLU 3.0 1.3 - - - -
2106B HIS* 3.0 22.5 + - - +
2107B VAL* 3.9 5.0 + - - +
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Residues in contact with TRP2104 (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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1085A LEU* 5.6 4.0 - - + -
1104A TRP* 3.4 46.6 - + + -
1107A VAL* 3.2 29.7 + - + -
1108A MET* 4.1 15.9 - - + -
1112A VAL* 3.8 25.6 - - + -
1116A LEU* 5.8 1.6 - - + -
2082B ALA* 4.2 20.4 - - + -
2085B LEU* 4.2 18.2 - - + -
2086B LEU* 4.1 23.1 - - + -
2090B ILE* 5.5 5.4 - - + -
2100B GLU* 2.3 42.2 + - - +
2101B ALA* 4.4 0.9 - - - +
2103B ARG* 1.3 75.4 - - + +
2105B GLU* 1.3 56.9 + - - +
2107B VAL* 2.8 30.3 + - + +
2108B MET* 3.3 19.0 + - + +
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Residues in contact with GLU2105 (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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253B NI 1.7 43.7 - - - +
2009B GLU* 4.4 2.9 - - - +
2010B MET* 2.6 2.3 - - - +
2013B ARG* 2.4 29.1 + - - -
2075B VAL* 3.8 14.2 - - + +
2078B LYS* 3.8 34.5 - - - +
2079B HIS* 3.2 29.2 + - + +
2082B ALA* 4.8 0.8 - - - +
2101B ALA 3.0 12.4 + - - +
2102B ASP* 2.5 7.3 - - - +
2103B ARG 3.0 0.2 + - - -
2104B TRP* 1.3 77.4 - - - +
2106B HIS* 1.3 81.1 + - + +
2107B VAL 3.5 0.9 + - - -
2108B MET* 4.3 0.8 + - - -
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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