Contacts of the helix formed by residues 1487 - 1499 (chain H) in PDB entry 1P3F
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 THR1487 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044G GLY* 4.6 9.4 - - - +
1047G ALA* 3.7 8.5 - - - -
1485H THR* 3.5 23.8 - - + +
1486H ILE* 1.3 76.3 - - - +
1488H SER* 1.3 69.1 + - - +
1489H ARG* 3.0 18.0 + - - +
1490H GLU* 2.5 37.5 + - - +
1491H ILE* 3.0 14.6 + - - +
111I A 5.8 0.4 - - - +
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Residues in contact with SER1488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046G GLY* 3.9 21.6 - - - +
1047G ALA* 3.9 11.6 - - - +
1050G TYR* 3.9 22.6 - - - -
1487H THR* 1.3 76.3 - - - +
1489H ARG* 1.3 65.9 + - - +
1491H ILE* 3.0 6.6 + - - +
1492H GLN* 2.7 26.2 + - - +
1515H VAL* 4.5 9.6 - - - +
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Residues in contact with ARG1489 (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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274F GLU 3.7 4.0 + - - -
275F HIS* 2.6 53.4 + - + +
277F LYS* 3.5 42.7 - - - +
1487H THR* 3.0 15.9 + - - +
1488H SER* 1.3 83.4 + - - +
1490H GLU* 1.3 61.0 + - - +
1492H GLN* 3.1 11.6 + - - +
1493H THR* 3.0 28.0 + - - -
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Residues in contact with GLU1490 (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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275F HIS* 2.7 36.5 + - - +
1474H ALA* 4.0 31.8 - - + +
1477H LEU* 3.9 8.7 - - + +
1478H ALA* 4.4 8.9 + - + +
1483H ARG* 5.3 9.8 - - - +
1485H THR 3.7 7.7 - - - +
1486H ILE* 4.1 7.9 - - + -
1487H THR* 2.5 53.0 + - - +
1489H ARG* 1.3 82.7 + - - +
1491H ILE* 1.3 57.5 + - - +
1493H THR* 3.3 0.9 + - - -
1494H ALA* 2.6 39.1 + - - +
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Residues in contact with ILE1491 (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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1034G LEU* 5.0 5.6 - - + -
1047G ALA* 3.8 24.5 - - + +
1050G TYR* 3.4 28.7 - - + -
1051G LEU* 3.8 33.2 - - + -
1054G VAL* 5.0 0.2 - - + -
1470H ILE* 3.9 21.3 - - + -
1471H ALA* 5.2 1.3 - - - -
1474H ALA* 4.3 8.1 - - + -
1486H ILE* 4.2 15.9 - - + -
1487H THR 3.0 16.2 + - - +
1488H SER 3.0 6.7 + - - +
1490H GLU* 1.3 75.5 - - - +
1492H GLN* 1.3 57.3 + - - +
1494H ALA* 3.4 5.3 + - - +
1495H VAL* 2.8 38.2 + - + +
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Residues in contact with GLN1492 (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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1050G TYR* 2.5 42.5 + - + +
1488H SER 2.7 11.1 + - - +
1489H ARG* 3.1 17.4 - - - +
1491H ILE* 1.3 74.1 - - - +
1493H THR* 1.3 67.1 + - - +
1494H ALA 3.0 1.3 - - - -
1495H VAL* 2.9 5.1 + - - +
1496H ARG* 2.9 48.7 + - - +
1508H VAL* 3.4 21.0 - - + +
1512H THR* 3.7 7.9 + - - -
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Residues in contact with THR1493 (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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271F THR* 3.5 27.8 - - + +
275F HIS* 2.5 34.8 + - + +
1477H LEU* 3.2 33.2 - - + -
1489H ARG* 3.0 5.4 + - - -
1490H GLU 3.9 0.2 - - - -
1492H GLN* 1.3 78.2 - - - +
1494H ALA* 1.3 64.4 + - - +
1496H ARG* 3.2 8.6 + - - +
1497H LEU* 2.9 26.9 + - + +
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Residues in contact with ALA1494 (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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1470H ILE* 3.9 20.6 - - + +
1473H GLU* 3.8 32.3 - - + -
1474H ALA* 4.0 5.6 - - - +
1477H LEU* 4.0 1.3 - - - +
1490H GLU 2.6 22.7 + - - +
1491H ILE* 3.4 7.0 - - - +
1493H THR* 1.3 76.1 - - - +
1495H VAL* 1.3 57.4 + - - +
1497H LEU* 3.0 4.9 + - - +
1498H LEU* 2.8 32.2 + - - +
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Residues in contact with VAL1495 (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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1050G TYR* 4.7 1.6 - - + -
1054G VAL* 3.9 18.8 - - + -
1470H ILE* 3.8 29.8 - - + -
1491H ILE* 2.8 24.3 + - + +
1492H GLN* 2.9 7.1 + - - +
1494H ALA* 1.3 72.4 - - - +
1496H ARG* 1.3 67.9 + - - +
1498H LEU* 4.3 5.2 - - - +
1499H LEU* 2.9 35.8 + - + +
1504H ALA* 4.2 10.0 - - - +
1507H ALA* 3.5 30.5 - - + -
1508H VAL* 4.6 7.9 - - + +
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Residues in contact with ARG1496 (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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271F THR* 4.9 13.0 - - + +
1492H GLN* 2.9 40.1 + - - +
1493H THR* 3.5 11.9 - - - +
1495H VAL* 1.3 80.3 - - - +
1497H LEU* 1.3 62.4 + - - +
1499H LEU 3.8 11.4 - - - +
1504H ALA* 4.7 12.2 - - + +
1505H LYS* 5.8 3.0 - - - +
1508H VAL* 3.9 33.7 - - + +
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Residues in contact with LEU1497 (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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268F ASP* 3.9 30.8 - - + +
271F THR* 3.5 31.9 - - + +
272F TYR* 3.4 36.3 - - + +
292F ARG* 2.8 32.5 + - - +
1473H GLU* 3.7 20.9 - - + +
1477H LEU* 4.9 0.9 - - + -
1493H THR* 2.9 27.0 + - + +
1494H ALA 3.5 5.8 - - - +
1496H ARG* 1.3 77.8 - - - +
1498H LEU* 1.3 59.0 + - - +
1499H LEU 5.1 0.5 - - - +
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Residues in contact with LEU1498 (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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292F ARG* 3.7 17.5 - - - +
1096G LEU* 3.6 11.3 - - - +
1469H ARG* 3.2 60.7 + - + +
1470H ILE* 3.4 19.5 - - + +
1473H GLU* 4.1 13.7 - - + +
1494H ALA 2.8 21.6 + - - +
1495H VAL* 3.1 2.7 + - - +
1497H LEU* 1.3 75.9 - - - +
1499H LEU* 1.3 80.2 + - + +
1500H PRO* 4.1 1.6 - - - +
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Residues in contact with LEU1499 (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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1054G VAL* 4.9 2.5 - - + -
1058G LEU* 3.8 34.1 - - + -
1096G LEU* 3.4 26.2 - - + -
1466H VAL* 5.7 4.9 - - + -
1470H ILE* 5.7 3.1 - - + -
1495H VAL* 2.9 37.1 + - + +
1496H ARG 3.8 7.4 - - - +
1497H LEU 3.6 0.9 - - - +
1498H LEU* 1.3 108.9 - - + +
1500H PRO* 1.3 71.1 - - + +
1501H GLY 3.5 1.6 + - - -
1503H LEU* 4.2 5.2 - - + +
1504H ALA* 3.5 21.8 - - - +
1507H ALA* 4.0 13.2 - - + -
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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