Contacts of the helix formed by residues 1408 - 1415 (chain B) in PDB entry 1FP7
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 LEU1408 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1382B ASN* 5.4 1.3 - - - +
1383B ALA* 3.4 33.4 - - + +
1406B VAL* 4.0 4.4 - - + +
1407B ALA* 1.3 68.7 - - - +
1409B SER* 1.3 58.2 + - - +
1412B TRP* 3.4 4.9 - - + +
1413B ALA* 3.7 26.5 - - + +
1414B LYS* 3.1 65.6 + - + +
1418B GLY* 3.5 13.0 + - - -
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Residues in contact with SER1409 (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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1076B THR* 4.7 9.6 - - - -
1077B THR* 5.2 6.7 + - - -
1080B GLY* 3.4 30.4 - - - -
1116B TYR* 4.6 7.0 + - - +
1117B ALA* 5.5 1.1 - - - -
1382B ASN* 6.0 0.4 - - - -
1407B ALA* 3.2 11.7 + - - +
1408B LEU* 1.3 72.0 - - - +
1412B TRP* 1.3 68.4 + - - +
1413B ALA 2.8 4.6 + - - -
1415B GLY* 3.2 32.3 + - - +
1418B GLY* 4.0 0.4 - - - -
1419B GLY* 3.3 24.2 + - - +
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Residues in contact with TRP1412 (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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1009B GLU* 4.8 9.1 + - - -
1076B THR* 4.2 16.5 - - + +
1114B GLY* 4.3 8.7 - - - -
1115B GLY* 3.6 24.3 - - - +
1116B TYR* 3.6 22.2 + - - -
1382B ASN* 4.1 26.0 - - - +
1383B ALA 5.4 8.3 - - - +
1384B PHE* 6.3 5.4 - + - -
1385B PRO* 5.9 9.9 - - + -
1408B LEU* 5.0 4.7 - - + -
1409B SER* 1.3 78.8 - - - +
1413B ALA* 1.3 83.2 + - + +
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Residues in contact with ALA1413 (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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1116B TYR* 4.5 13.9 - - + -
1408B LEU* 3.7 15.5 - - + +
1409B SER 2.8 1.0 + - - -
1412B TRP* 1.3 101.8 - - + +
1414B LYS* 1.3 65.3 + - + +
1415B GLY 3.5 2.9 - - - -
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Residues in contact with LYS1414 (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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1087B ARG* 4.8 0.2 + - - -
1408B LEU* 3.1 54.6 + - + +
1413B ALA* 1.3 80.7 - - - +
1415B GLY* 1.3 68.7 + - - +
1417B GLU* 2.9 33.4 + - + +
1418B GLY* 2.8 21.4 + - - +
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Residues in contact with GLY1415 (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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1080B GLY* 5.4 0.7 - - - -
1083B ASP* 4.8 0.2 - - - -
1087B ARG* 4.6 2.5 - - - -
1116B TYR* 3.8 25.2 - - - +
1264B GLU* 3.7 11.0 - - - -
1409B SER* 3.2 28.2 + - - -
1413B ALA 3.5 2.4 - - - -
1414B LYS* 1.3 83.9 - - - +
1416B GLY* 1.3 61.6 + - - -
1418B GLY 3.3 4.9 + - - -
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Residues in contact with GLY1416 (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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1080B GLY 4.1 4.0 - - - -
1083B ASP* 3.2 36.6 - - - -
1084B ALA* 3.2 8.5 - - - +
1087B ARG* 3.1 7.5 - - - +
1264B GLU* 3.0 12.3 + - - -
1415B GLY* 1.3 73.2 - - - -
1417B GLU* 1.3 63.2 + - - +
1419B GLY 3.1 10.2 + - - -
1420B LEU* 2.9 16.8 - - - +
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Residues in contact with GLU1417 (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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1087B ARG* 3.3 15.1 - - - +
1414B LYS* 2.9 33.6 - - + +
1416B GLY* 1.3 75.3 - - - +
1418B GLY* 1.3 56.9 + - - +
1420B LEU* 2.8 43.8 + - + +
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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