Contacts of the helix formed by residues 2109 - 2121 (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 SER2109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A LEU* 5.5 0.2 - - - +
1100A GLU* 3.0 33.1 + - - -
1103A ARG* 3.5 10.0 - - - +
2078B LYS* 3.7 0.7 - - - -
2108B MET* 1.3 77.0 - - - +
2110B ASP* 1.3 59.5 + - - +
2111B GLU* 3.6 11.6 - - - +
2112B VAL* 3.3 14.6 + - - +
2113B GLU* 2.8 25.5 + - - +
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Residues in contact with ASP2110 (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 ARG* 6.3 0.2 - - - -
2078B LYS* 3.1 25.3 + - - +
2109B SER* 1.3 70.9 - - - +
2111B GLU* 1.3 71.5 + - - +
2113B GLU* 2.8 15.8 + - - +
2114B ARG* 2.8 44.9 + - - +
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Residues in contact with GLU2111 (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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1092A LEU* 4.0 20.6 - - + +
1093A ASP* 4.5 5.9 - - - +
1096A LYS* 3.3 42.1 + - + +
2109B SER* 3.6 12.5 - - - +
2110B ASP* 1.3 81.8 - - - +
2112B VAL* 1.3 62.6 + - - +
2114B ARG* 3.3 24.2 + - - +
2115B ARG* 3.0 20.7 + - - +
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Residues in contact with VAL2112 (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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1086A LEU* 4.4 5.2 - - + -
1090A ILE* 4.7 12.8 - - + -
1092A LEU* 3.5 32.3 - - + +
1100A GLU* 3.5 26.0 - - + +
1104A TRP* 4.3 13.5 - - + -
2108B MET* 3.9 16.6 - - + -
2109B SER* 3.3 11.7 + - - +
2111B GLU* 1.3 79.7 - - - +
2113B GLU* 1.3 54.9 + - - +
2115B ARG* 3.1 7.7 + - - -
2116B LEU* 2.6 48.4 + - + +
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Residues in contact with GLU2113 (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 ARG* 2.9 49.3 + - - +
2078B LYS* 2.9 36.0 + - + +
2081B LEU* 3.4 33.1 - - + +
2108B MET* 4.5 8.5 - - - -
2109B SER 2.8 13.6 + - - +
2110B ASP* 2.8 21.9 + - - +
2112B VAL* 1.3 73.7 - - - +
2114B ARG* 1.3 68.1 + - - +
2116B LEU* 3.4 1.0 + - - +
2117B VAL* 3.1 15.6 + - - +
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Residues in contact with ARG2114 (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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2110B ASP* 2.8 45.5 + - + +
2111B GLU* 3.7 30.9 + - - +
2113B GLU* 1.3 74.7 - - + +
2115B ARG* 1.3 67.1 + - - +
2117B VAL* 2.8 33.5 + - + +
2118B LYS* 3.4 8.7 + - - +
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Residues in contact with ARG2115 (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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1090A ILE* 2.9 39.2 + - + +
1091A GLY* 3.0 22.0 + - - +
1092A LEU* 4.6 7.2 - - + +
2111B GLU 3.0 12.0 + - - +
2112B VAL* 3.3 12.3 - - - +
2114B ARG* 1.3 81.1 - - - +
2116B LEU* 1.3 61.9 + - - +
2118B LYS* 3.2 34.7 + - - +
2119B VAL* 3.1 38.0 + - - +
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Residues in contact with LEU2116 (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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1090A ILE* 3.8 35.4 - - + -
2081B LEU* 3.7 27.8 - - + +
2085B LEU* 4.0 22.7 - - + -
2108B MET* 3.8 28.0 - - + -
2112B VAL* 2.6 25.0 + - + +
2113B GLU 3.6 4.3 - - - +
2115B ARG* 1.3 71.7 - - - +
2117B VAL* 1.3 64.4 + - - +
2119B VAL* 4.1 8.5 - - + -
2120B LEU* 2.9 51.8 + - + +
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Residues in contact with VAL2117 (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 LEU* 4.5 22.4 - - + +
2113B GLU 3.1 10.8 + - - +
2114B ARG* 2.8 30.8 + - + +
2116B LEU* 1.3 76.2 - - - +
2118B LYS* 1.3 72.3 + - + +
2120B LEU* 4.2 2.7 - - - +
2121B LYS* 3.7 33.5 + - - +
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Residues in contact with LYS2118 (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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2114B ARG* 3.9 14.8 - - - +
2115B ARG* 3.2 32.5 + - - +
2116B LEU 3.2 0.2 - - - -
2117B VAL* 1.3 86.6 - - + +
2119B VAL* 1.3 66.6 + - - +
2121B LYS* 3.0 28.5 - - - +
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Residues in contact with VAL2119 (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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1089A ILE 3.7 17.9 - - - +
1090A ILE* 3.4 31.6 - - + +
2089B ILE* 4.0 22.8 - - + +
2115B ARG* 3.1 29.6 - - - +
2116B LEU* 3.3 12.3 + - + +
2118B LYS* 1.3 78.6 - - - +
2120B LEU* 1.3 70.8 + - + +
2121B LYS* 4.3 1.2 - - - +
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Residues in contact with LEU2120 (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 LEU* 4.8 5.6 - - + +
2084B ARG* 3.5 46.2 - - + +
2085B LEU* 4.2 11.4 - - + +
2088B ASP* 4.1 14.6 - - + +
2089B ILE* 4.3 24.5 - - + -
2116B LEU* 2.9 60.7 + - + +
2117B VAL* 4.2 4.7 - - - +
2119B VAL* 1.3 80.0 - - + +
2121B LYS* 1.3 75.0 + - - +
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Residues in contact with LYS2121 (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 ARG* 4.6 8.9 + - - +
2117B VAL* 3.7 26.2 + - - +
2118B LYS* 3.0 26.5 - - - +
2119B VAL 4.3 1.1 - - - +
2120B LEU* 1.3 85.1 - - - +
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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