Contacts of the helix formed by residues 1467 - 1481 (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 THR1467 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1514A ARG* 6.1 2.9 - - - +
1466B TYR* 1.3 74.4 - - - +
1468B ALA* 1.3 67.9 + - - +
1469B GLU* 3.5 13.9 + - - +
1470B ALA* 3.1 8.3 + - - +
1471B ASP* 2.9 24.4 + - - -
1512B THR* 4.4 14.6 - - + -
1513B VAL 3.9 1.4 + - - -
1514B ARG* 2.8 44.3 + - + -
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Residues in contact with ALA1468 (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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1467B THR* 1.3 76.5 - - - +
1469B GLU* 1.3 69.3 + - + +
1470B ALA 3.3 0.2 + - - -
1471B ASP* 3.3 13.7 + - - +
1472B LYS* 3.4 20.2 + - - +
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Residues in contact with GLU1469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467B THR* 3.6 11.1 + - - +
1468B ALA* 1.3 79.2 - - + +
1470B ALA* 1.3 61.6 + - - +
1472B LYS* 3.5 6.6 + - - +
1473B ALA* 3.4 20.1 + - - +
1514B ARG* 3.3 25.8 - - - +
1515B GLU* 5.2 9.3 - - + +
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Residues in contact with ALA1470 (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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1466B TYR* 3.7 13.5 - - + -
1467B THR* 3.1 19.6 + - - +
1469B GLU* 1.3 79.5 - - - +
1471B ASP* 1.3 64.1 + - - +
1472B LYS 3.3 0.7 + - - -
1473B ALA* 3.4 6.3 + - - +
1474B ILE* 3.3 28.5 + - - +
1513B VAL* 3.0 30.3 - - + +
1514B ARG 3.5 6.7 + - - +
1515B GLU* 4.6 7.6 - - - +
1516B VAL* 5.0 2.2 - - + +
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Residues in contact with ASP1471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1448B LYS* 3.3 14.8 + - - +
1466B TYR* 3.0 34.6 - - - +
1467B THR 2.9 22.1 + - - +
1468B ALA* 3.3 7.5 + - - +
1470B ALA* 1.3 72.2 - - - +
1472B LYS* 1.3 63.6 + - + +
1474B ILE* 3.8 6.8 - - - +
1475B GLN* 3.2 26.0 + - - +
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Residues in contact with LYS1472 (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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1468B ALA* 3.4 13.6 + - - +
1469B GLU* 3.9 9.6 - - - +
1470B ALA 3.3 0.8 - - - -
1471B ASP* 1.3 76.5 - - + +
1473B ALA* 1.3 55.8 + - - +
1475B GLN* 3.3 18.0 + - - +
1476B ARG* 2.6 70.4 + - + +
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Residues in contact with ALA1473 (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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1469B GLU 3.4 10.2 + - - +
1470B ALA* 3.4 7.9 + - - +
1472B LYS* 1.3 73.6 - - - +
1474B ILE* 1.3 68.5 + - - +
1476B ARG* 2.8 17.5 + - - +
1477B TYR* 2.7 35.2 + - + +
1515B GLU* 6.1 0.9 - - + -
1516B VAL* 3.8 31.9 - - + +
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Residues in contact with ILE1474 (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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1446B SER* 5.8 0.7 - - - +
1447B ILE* 4.0 25.1 - - + -
1448B LYS* 3.7 21.1 - - + -
1451B ILE* 5.9 0.4 - - + -
1466B TYR* 3.4 39.9 - - + -
1470B ALA 3.3 13.8 + - - +
1471B ASP* 3.8 6.1 - - - +
1473B ALA* 1.3 78.8 - - - +
1475B GLN* 1.3 57.5 + - - +
1477B TYR* 2.8 26.2 + - - +
1478B GLU* 2.8 37.7 + - - +
1516B VAL* 4.4 17.3 - - + -
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Residues in contact with GLN1475 (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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1471B ASP 3.2 16.6 + - - +
1472B LYS* 3.4 17.2 + - - +
1474B ILE* 1.3 81.8 - - - +
1476B ARG* 1.3 65.1 + - - +
1478B GLU* 4.3 7.6 - - - +
1479B SER* 3.0 29.4 + - - -
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Residues in contact with ARG1476 (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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1472B LYS* 2.6 58.3 + - - +
1473B ALA* 2.8 16.2 + - - +
1475B GLN* 1.3 76.9 - - + +
1477B TYR* 1.3 70.6 + - + +
1479B SER* 3.1 3.9 + - - -
1480B LEU* 3.1 35.7 + - + +
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Residues in contact with TYR1477 (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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1229B TYR* 4.4 16.2 + + - -
1447B ILE* 4.6 4.7 - - + -
1473B ALA* 2.7 28.7 + - + +
1474B ILE* 2.8 9.7 + - - +
1476B ARG* 1.3 77.5 - - + +
1478B GLU* 1.3 50.3 + - - +
1480B LEU* 2.6 35.7 + - + +
1481B GLY 2.7 14.7 + - - -
1482B TYR* 3.3 21.7 + - + +
1516B VAL* 2.9 50.6 + - + -
1517B ARG* 3.5 1.6 - - - -
1518B LEU* 3.0 52.9 + - + +
1524B LEU* 4.4 9.6 - - + -
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Residues in contact with GLU1478 (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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1446B SER* 3.5 12.4 + - - -
1447B ILE* 3.0 53.0 + - + +
1474B ILE* 2.8 26.2 + - - +
1475B GLN* 4.3 6.9 - - - +
1477B TYR* 1.3 74.6 - - - +
1479B SER* 1.3 60.4 + - - +
1481B GLY* 3.2 13.1 + - - +
1483B GLY* 3.8 13.4 - - - +
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Residues in contact with SER1479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475B GLN* 3.0 23.7 + - - -
1476B ARG* 3.4 7.2 - - - -
1478B GLU* 1.3 76.4 - - - +
1480B LEU* 1.3 68.7 + - - +
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Residues in contact with LEU1480 (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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1229B TYR* 4.8 8.3 - - + -
1233B GLY 5.0 4.7 - - - +
1235B PRO* 3.6 35.7 - - + -
1476B ARG* 3.1 25.4 + - + +
1477B TYR* 2.6 18.8 + - + +
1479B SER* 1.3 91.3 - - - +
1481B GLY* 1.3 54.3 + - - -
1482B TYR* 3.7 22.2 - - + -
1518B LEU* 6.0 0.7 - - + -
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Residues in contact with GLY1481 (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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1477B TYR 2.7 9.1 + - - -
1478B GLU 3.2 10.9 + - - -
1480B LEU* 1.3 77.1 - - - +
1482B TYR* 1.3 51.1 + - - -
1483B GLY 2.6 18.7 + - - -
1484B ASN* 3.6 18.4 + - - -
1485B LEU* 5.8 0.3 - - - +
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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