Contacts of the helix formed by residues 1286 - 1295 (chain E) in PDB entry 2FO1
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 HIS1286 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D ASN* 5.9 7.4 - - + -
1249E ALA 4.5 2.9 - - - -
1250E GLN 3.8 2.2 + - - -
1251E GLU 3.1 29.8 - - - -
1252E GLY* 2.8 23.6 + - - -
1281E ALA 2.9 17.0 + - - +
1282E GLN* 4.3 0.6 + - - +
1284E ASN* 2.9 45.6 + - + +
1285E ASN* 1.3 74.1 - - - +
1287E HIS* 1.3 55.5 + - - +
1288E ASN* 3.2 11.2 - - - +
1289E ILE* 2.7 42.5 + - + +
1290E VAL* 3.0 13.7 + - - +
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Residues in contact with HIS1287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LYS* 5.4 9.9 - - + -
87D GLU* 2.8 40.7 + - - -
1282E GLN* 4.5 17.6 + - - -
1285E ASN* 3.5 18.7 - - + +
1286E HIS* 1.3 71.0 - - - +
1288E ASN* 1.3 74.4 + - - +
1290E VAL* 2.7 24.3 + - + +
1291E ASP* 2.8 25.9 + - - +
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Residues in contact with ASN1288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 5.3 5.9 + - - -
83D LYS* 4.4 18.1 + - - +
1254E ILE* 3.8 27.1 - - + +
1286E HIS* 3.5 16.8 - - - +
1287E HIS* 1.3 78.7 + - - +
1289E ILE* 1.3 51.4 + - + +
1291E ASP* 3.6 6.1 + - - +
1292E ILE* 2.7 38.4 + - + +
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Residues in contact with ILE1289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249E ALA* 3.6 15.0 - - + +
1252E GLY* 3.4 37.9 - - - +
1253E ARG 4.2 1.8 - - - +
1254E ILE* 3.5 19.7 - - + -
1257E VAL* 4.1 21.1 - - + -
1281E ALA* 3.7 9.0 - - + -
1286E HIS* 2.7 30.5 + - + +
1288E ASN* 1.3 69.6 - - + +
1290E VAL* 1.3 67.5 + - - +
1292E ILE* 2.7 25.8 + - - +
1293E PHE* 3.2 29.7 + - + -
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Residues in contact with VAL1290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278E ARG* 3.9 6.7 - - - +
1281E ALA* 4.5 0.6 - - - +
1282E GLN* 3.2 63.7 - - + +
1286E HIS 3.0 5.6 + - - +
1287E HIS* 2.7 33.1 + - + +
1289E ILE* 1.3 75.5 - - - +
1291E ASP* 1.3 58.9 + - - +
1293E PHE* 2.7 37.1 + - - +
1294E ASP* 3.3 19.4 + - - +
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Residues in contact with ASP1291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287E HIS* 2.8 36.7 + - - +
1288E ASN* 3.8 5.5 + - - +
1290E VAL* 1.3 78.7 - - - +
1292E ILE* 1.3 52.6 + - + +
1294E ASP* 3.1 11.4 + - - +
1295E ARG* 2.6 68.6 + - - +
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Residues in contact with ILE1292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254E ILE* 5.0 3.1 - - + -
1257E VAL* 4.9 13.9 - - + -
1258E MSE 4.1 42.4 - - + -
1261E ILE* 5.8 5.4 - - + +
1288E ASN* 2.7 32.1 - - + +
1289E ILE* 2.7 25.4 + - + +
1291E ASP* 1.3 74.5 - - + +
1293E PHE* 1.3 59.4 + - + +
1295E ARG* 3.6 10.1 + - + +
1296E CYS* 3.4 18.9 + - - +
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Residues in contact with PHE1293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245E ILE* 5.1 5.2 - - + -
1249E ALA* 4.4 5.2 - - + -
1257E VAL* 4.3 9.6 - - + -
1261E ILE* 3.6 30.3 - - + -
1267E VAL* 3.8 24.7 - - + -
1277E ALA* 3.5 21.8 - - + -
1278E ARG* 3.7 54.0 + - + +
1289E ILE* 3.2 39.0 + - + -
1290E VAL* 2.7 10.2 + - - +
1292E ILE* 1.3 75.8 - - + +
1294E ASP* 1.3 56.9 + - - +
1295E ARG 3.1 4.3 - - - -
1296E CYS* 3.1 25.3 + - + +
1297E ARG 3.7 7.6 + - - +
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Residues in contact with ASP1294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278E ARG* 3.7 28.0 + - - -
1290E VAL* 3.3 26.9 + - - +
1291E ASP* 3.1 11.3 + - - +
1293E PHE* 1.3 71.7 - - - +
1295E ARG* 1.3 65.7 + - - +
1296E CYS 3.1 6.0 + - - -
1297E ARG 3.9 13.8 - - - +
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Residues in contact with ARG1295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291E ASP* 2.6 46.8 + - - +
1292E ILE* 3.7 14.4 - - + +
1293E PHE 3.1 0.2 - - - -
1294E ASP* 1.3 83.4 - - - +
1296E CYS* 1.3 63.4 + - - +
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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