Contacts of the helix formed by residues 2118 - 2131 (chain H) in PDB entry 1F2I
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 ARG2118 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008A C 4.1 0.2 - - - +
2006B C 3.5 33.5 - - - +
2007B G 2.7 47.7 + - - -
1118G ARG* 3.5 50.1 - - + +
1119G SER 5.5 1.3 - - - +
1120G ASP* 4.2 9.6 + - - +
2105H TYR* 3.5 11.2 - - - +
2116H PHE* 3.4 18.4 - - - +
2117H SER* 1.3 89.0 + - - +
2119H SER* 1.3 61.1 + - - +
2120H ASP* 3.0 40.5 + - - +
2121H GLU* 3.2 25.8 + - - +
2122H LEU 3.6 1.6 + - - -
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Residues in contact with SER2119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099G VAL* 3.9 15.8 - - - +
1100G PRO 5.5 0.4 - - - -
1117G SER* 5.8 2.3 - - - -
1118G ARG* 5.7 2.8 - - - +
2105H TYR* 3.5 40.1 + - - -
2118H ARG* 1.3 71.1 - - - +
2120H ASP* 1.3 62.4 + - - +
2121H GLU 3.1 2.0 - - - -
2122H LEU* 3.3 4.1 + - - +
2123H THR* 2.9 31.3 + - - -
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Residues in contact with ASP2120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A G 4.9 10.6 - - + +
1008A C 3.9 13.2 + - - -
1009A G 5.0 0.2 - - - +
2006B C 3.9 8.2 + - - -
1118G ARG* 4.4 8.3 + - - -
2118H ARG* 3.0 51.2 + - - +
2119H SER* 1.3 76.9 + - - +
2121H GLU* 1.3 62.2 + - - +
2123H THR* 3.8 7.3 - - - -
2124H ARG* 3.5 28.3 + - - +
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Residues in contact with GLU2121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004B G 4.6 2.6 + - + -
2005B G 3.3 37.0 + - + +
2006B C 3.7 18.1 - - + -
2116H PHE* 3.0 39.9 - - + +
2117H SER* 3.1 25.1 + - - -
2118H ARG* 3.2 17.7 + - + +
2120H ASP* 1.3 79.5 + - - +
2122H LEU* 1.3 57.6 + - - +
2124H ARG* 3.3 29.9 + - - +
2125H HIS* 3.0 25.5 + - - +
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Residues in contact with LEU2122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097G TYR* 4.9 3.8 - - - +
1099G VAL* 3.9 28.9 - - + -
2105H TYR* 4.0 15.9 - - + -
2106H ALA 3.6 17.3 - - - +
2107H CYS* 3.6 28.7 - - - +
2108H PRO* 4.9 1.3 - - + -
2116H PHE* 3.6 32.9 - - + -
2118H ARG 3.6 6.8 + - - +
2119H SER 3.3 6.8 + - - +
2121H GLU* 1.3 77.2 - - - +
2123H THR* 1.3 64.3 + - - +
2124H ARG 3.1 1.8 - - - -
2125H HIS* 4.0 7.2 - - + -
2126H ILE* 3.0 41.6 + - + +
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Residues in contact with THR2123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099G VAL* 3.3 23.4 - - + +
2119H SER* 2.9 19.6 + - - -
2120H ASP* 4.1 8.9 - - - -
2121H GLU 3.3 0.2 - - - -
2122H LEU* 1.3 77.8 - - - +
2124H ARG* 1.3 61.9 + - - +
2126H ILE* 3.8 9.7 + - - +
2127H ARG* 3.8 30.6 + - - +
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Residues in contact with ARG2124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A G 4.0 6.6 + - - -
2003B G 5.6 1.9 + - - -
2004B G 3.3 21.1 + - - +
2005B G 2.9 50.3 + - - -
2006B C 3.9 9.8 - - - +
2120H ASP 3.5 12.9 + - - +
2121H GLU* 3.3 25.0 + - - +
2123H THR* 1.3 78.7 - - - +
2125H HIS* 1.3 66.1 + - - +
2127H ARG* 3.0 47.3 + - - +
2128H ILE* 4.2 4.0 + - - +
2146H ARG* 3.5 46.2 - - + +
2148H ASP* 5.5 1.2 + - - -
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Residues in contact with HIS2125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004B G 2.6 29.2 + - - +
2107H CYS* 3.9 12.7 - - + +
2112H CYS* 3.4 5.6 - - - -
2114H ARG* 3.5 22.5 - - - +
2116H PHE* 3.5 34.1 - + + -
2121H GLU 3.0 9.0 + - - +
2122H LEU* 3.6 6.3 - - + +
2124H ARG* 1.3 77.3 - - - +
2126H ILE* 1.3 58.0 + - - +
2128H ILE* 2.9 39.1 + - + +
2129H HIS* 3.3 8.5 + + - -
2201H ZN 2.0 37.1 - - - -
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Residues in contact with ILE2126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094G LEU* 3.8 35.0 - - + +
1097G TYR* 3.5 37.5 - - + +
1099G VAL* 4.3 7.2 - - + -
2107H CYS* 5.0 0.7 - - - -
2108H PRO* 3.9 14.1 - - + -
2122H LEU* 3.0 33.1 + - + +
2123H THR* 4.1 7.9 - - - +
2124H ARG 3.3 0.4 - - - -
2125H HIS* 1.3 76.8 - - + +
2127H ARG* 1.3 59.1 + - + +
2128H ILE 3.1 2.2 - - - -
2129H HIS* 3.3 20.0 + - + +
2130H THR* 3.3 15.5 + - + -
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Residues in contact with ARG2127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003B G 6.1 0.4 - - - +
2123H THR* 3.8 28.2 + - - +
2124H ARG* 3.0 39.4 + - - +
2125H HIS 3.0 1.4 + - - -
2126H ILE* 1.3 76.1 - - - +
2128H ILE* 1.3 60.1 + - - +
2129H HIS 3.3 0.2 - - - -
2130H THR* 3.4 7.9 - - - +
2131H GLY* 2.9 27.7 + - - -
2132H GLN* 3.5 33.1 + - + +
2134H PRO* 3.9 16.2 - - - +
2135H PHE* 3.8 22.5 - - - -
2145H SER* 2.8 35.0 + - - -
2146H ARG* 4.3 3.8 - - - +
2147H SER 5.3 0.4 - - - +
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Residues in contact with ILE2128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003B G 3.4 63.7 - - - +
2004B G 3.9 11.7 - - - +
2124H ARG 4.9 2.2 - - - +
2125H HIS* 2.9 24.3 + - + +
2127H ARG* 1.3 79.3 - - - +
2129H HIS* 1.3 74.5 + - + +
2131H GLY* 4.0 5.1 + - - -
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Residues in contact with HIS2129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094G LEU* 3.6 20.2 - - + +
2107H CYS* 3.3 5.7 - - - -
2109H VAL* 3.2 28.0 - - + +
2112H CYS* 4.0 11.9 - - + -
2125H HIS* 3.3 10.5 + + - -
2126H ILE* 3.3 14.8 + - + +
2127H ARG 3.3 0.2 - - - -
2128H ILE* 1.3 89.2 - - + +
2130H THR* 1.3 60.5 + - - +
2201H ZN 2.1 35.6 - - - -
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Residues in contact with THR2130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094G LEU* 3.7 41.1 - - + +
1095G LEU* 4.0 24.9 - - + +
2126H ILE* 3.3 18.4 + - + +
2127H ARG* 3.4 9.7 - - - +
2129H HIS* 1.3 76.8 - - - +
2131H GLY* 1.3 62.9 + - - +
2132H GLN* 3.1 19.2 + - - +
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Residues in contact with GLY2131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127H ARG 2.9 13.5 + - - -
2128H ILE 4.0 4.8 + - - -
2129H HIS 3.5 2.8 - - - -
2130H THR* 1.3 78.1 - - - +
2132H GLN* 1.3 64.7 + - - +
2133H LYS* 3.5 14.2 + - - +
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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