Contacts of the helix formed by residues 1546 - 1562 (chain A) in PDB entry 2FR1
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 LEU1546 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509A ARG* 4.9 0.2 - - - +
1536A GLU* 3.4 30.1 - - + +
1537A ALA 4.0 3.4 - - - +
1539A PRO* 3.4 27.9 - - + +
1543A PRO 3.5 14.6 + - - +
1544A LEU* 3.0 3.0 - - - +
1545A ALA* 1.3 78.0 - - - +
1547A ALA* 1.3 66.6 + - - +
1548A SER* 3.9 10.3 - - - +
1549A LEU* 3.1 20.5 + - + +
1550A ALA* 3.4 10.0 + - - +
1586A ASN* 3.8 4.7 - - - +
1588A ALA* 3.5 28.9 - - + +
1589A HIS* 3.4 29.2 - - + -
1591A ALA* 6.1 0.2 - - + -
1592A LEU* 4.6 3.8 - - + -
1766A GLY* 5.8 0.2 - - - -
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Residues in contact with ALA1547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479A TYR* 3.1 23.8 + - + +
1508A ALA* 4.2 11.9 - - + -
1509A ARG* 3.8 29.1 - - + +
1536A GLU* 3.4 10.1 + - - +
1545A ALA 3.2 3.6 + - - -
1546A LEU* 1.3 71.6 - - - +
1548A SER* 1.3 58.7 + - - +
1549A LEU 3.2 0.3 + - - -
1550A ALA* 3.2 3.0 + - - +
1551A ASP* 2.8 33.0 + - - +
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Residues in contact with SER1548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479A TYR* 3.3 8.7 + - - -
1532A LEU* 3.8 21.4 - - - +
1533A ALA* 3.9 11.1 - - - +
1536A GLU* 2.6 34.7 + - - -
1546A LEU* 3.9 5.4 - - - +
1547A ALA* 1.3 77.7 - - - +
1549A LEU* 1.3 55.4 + - - +
1551A ASP* 4.6 0.4 - - - -
1552A THR* 2.7 38.4 + - - -
1589A HIS* 4.1 0.2 - - - -
1592A LEU* 3.7 21.0 - - - +
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Residues in contact with LEU1549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1544A LEU* 3.6 29.4 - - + +
1546A LEU* 3.1 16.6 + - + +
1548A SER* 1.3 78.8 + - - +
1550A ALA* 1.3 66.0 + - - +
1552A THR* 3.4 3.6 + - - -
1553A LEU* 3.3 31.0 + - + +
1591A ALA* 4.5 22.0 - - + +
1592A LEU* 4.1 17.0 - - + -
1595A VAL* 4.2 25.4 - - + -
1766A GLY* 4.4 12.1 - - - -
1769A ILE* 4.4 26.0 - - + -
1815A PRO* 5.2 1.6 - - + -
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Residues in contact with ALA1550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509A ARG* 4.7 20.0 - - + +
1546A LEU 3.4 6.7 + - - +
1547A ALA* 3.2 6.8 + - - +
1549A LEU* 1.3 80.6 - - - +
1551A ASP* 1.3 63.0 + - - +
1553A LEU* 3.5 3.5 + - - +
1554A SER* 3.1 29.0 + - - -
1765A THR* 5.8 0.2 - - - -
1766A GLY* 3.7 30.6 + - - +
1767A GLU 4.8 1.3 - - - +
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Residues in contact with ASP1551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479A TYR* 2.4 38.6 + - - +
1506A VAL* 4.5 10.5 - - + -
1507A ASP 4.5 3.4 - - - -
1508A ALA* 3.3 1.8 - - - -
1509A ARG* 2.8 38.0 + - - -
1510A CYS* 3.8 7.3 + - - -
1515A LEU* 4.5 2.0 - - + +
1532A LEU* 3.9 15.6 - - + +
1547A ALA 2.8 14.6 + - - +
1548A SER 4.4 0.2 - - - +
1550A ALA* 1.3 75.8 - - - +
1552A THR* 1.3 59.8 + - - +
1553A LEU 3.3 0.2 - - - -
1554A SER* 3.7 8.1 + - - -
1555A LEU* 2.8 30.5 + - - +
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Residues in contact with THR1552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530A SER* 4.8 4.0 + - - -
1532A LEU* 4.4 9.6 - - - +
1548A SER* 2.7 25.2 + - - -
1549A LEU* 3.4 7.4 + - - -
1551A ASP* 1.3 75.5 - - - +
1553A LEU* 1.3 62.0 + - + +
1555A LEU* 3.3 6.7 + - - +
1556A VAL* 3.0 44.5 + - + +
1568A LEU* 4.9 3.6 - - + -
1570A THR* 4.7 13.1 + - + +
1592A LEU* 4.4 16.6 - - + +
1595A VAL* 5.2 8.3 - - + -
1599A ILE* 4.9 6.3 - - + -
1607A TRP* 4.5 17.9 - - + -
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Residues in contact with LEU1553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549A LEU* 3.3 22.6 + - + +
1550A ALA 3.7 5.6 - - - +
1551A ASP 3.3 0.2 - - - -
1552A THR* 1.3 82.5 - - + +
1554A SER* 1.3 56.4 + - - +
1556A VAL* 3.3 5.0 + - - +
1557A GLN* 2.9 45.2 + - - +
1595A VAL* 4.0 23.6 - - + -
1599A ILE* 4.2 7.0 - - + -
1761A VAL* 4.0 29.2 - - + +
1764A LEU* 4.2 8.3 - - + +
1765A THR* 3.9 7.4 - - - -
1766A GLY* 3.8 19.5 - - - +
1769A ILE* 3.8 26.0 - - + -
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Residues in contact with SER1554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509A ARG* 6.0 0.2 - - - -
1511A GLY* 3.6 35.9 + - - -
1512A ARG* 3.6 6.8 + - - +
1515A LEU* 3.8 10.6 - - - +
1550A ALA 3.1 19.6 + - - -
1551A ASP* 3.7 9.9 + - - -
1552A THR 3.3 0.2 - - - -
1553A LEU* 1.3 77.6 - - - +
1555A LEU* 1.3 56.6 + - - +
1557A GLN* 3.7 11.1 + - - +
1558A ALA* 2.9 31.5 + - - +
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Residues in contact with LEU1555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477A ALA* 3.9 27.4 - - + -
1504A LEU* 4.6 14.4 - - + -
1506A VAL* 5.5 2.0 - - + -
1515A LEU* 3.7 15.7 - - + +
1519A LEU* 4.0 15.0 - - + -
1528A VAL* 4.3 5.4 - - + -
1530A SER* 4.6 2.7 - - - -
1532A LEU* 4.6 11.7 - - + -
1551A ASP 2.8 17.8 + - - +
1552A THR* 3.6 6.1 - - - +
1553A LEU 3.3 0.2 - - - -
1554A SER* 1.3 77.3 - - - +
1556A VAL* 1.3 58.8 + - - +
1558A ALA* 3.3 0.9 + - - +
1559A MET* 2.8 52.7 + - + +
1568A LEU* 3.9 30.1 - - + -
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Residues in contact with VAL1556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1552A THR 3.0 23.9 + - - +
1553A LEU* 3.3 6.3 + - - +
1555A LEU* 1.3 75.3 - - - +
1557A GLN* 1.3 65.2 + - + +
1559A MET* 3.2 11.1 + - - +
1560A VAL* 3.0 31.5 + - + +
1568A LEU* 3.8 21.5 - - + -
1599A ILE* 4.0 30.3 - - + -
1603A ASN* 5.8 0.9 - - + -
1606A VAL* 4.2 16.8 - - + +
1607A TRP* 4.1 18.4 - - + -
1761A VAL* 4.9 9.6 - - + -
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Residues in contact with GLN1557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512A ARG* 3.4 56.5 + - + +
1553A LEU* 2.9 26.1 + - - +
1554A SER* 3.7 8.7 + - - +
1556A VAL* 1.3 78.8 - - + +
1558A ALA* 1.3 63.1 + - - +
1560A VAL* 3.2 9.2 + - - +
1561A SER* 3.0 26.3 + - - -
1761A VAL* 2.8 31.6 + - + +
1762A ASP* 3.8 6.7 - - + +
1764A LEU 2.9 20.6 + - - +
1765A THR* 5.5 2.8 - - - +
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Residues in contact with ALA1558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512A ARG* 3.7 8.9 - - - +
1515A LEU* 3.5 30.3 - - + -
1516A ALA* 3.5 18.7 - - - +
1519A LEU* 3.9 7.0 - - + -
1554A SER 2.9 20.1 + - - +
1555A LEU 3.6 3.8 - - - +
1557A GLN* 1.3 78.1 - - - +
1559A MET* 1.3 56.9 + - - +
1561A SER* 3.1 3.2 + - - +
1562A ALA* 2.9 32.6 + - - +
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Residues in contact with MET1559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519A LEU* 3.7 20.0 - - + -
1528A VAL* 3.3 29.2 - - + -
1555A LEU* 2.8 39.5 + - + +
1556A VAL* 3.2 5.8 + - - +
1558A ALA* 1.3 73.9 - - - +
1560A VAL* 1.3 61.2 + - - +
1562A ALA 3.8 0.4 + - - +
1563A GLU* 3.2 15.6 + - - -
1564A LEU* 3.3 21.2 + - + +
1565A GLY 4.7 1.9 + - - -
1566A CYS* 3.4 33.9 - - - +
1567A PRO 4.0 0.9 - - - +
1568A LEU* 3.8 35.4 - - + -
1606A VAL* 3.7 15.6 - - + +
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Residues in contact with VAL1560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1556A VAL* 3.0 21.9 + - + +
1557A GLN* 3.5 9.2 - - - +
1559A MET* 1.3 79.4 - - - +
1561A SER* 1.3 61.7 + - - +
1563A GLU* 3.3 17.6 + - - +
1603A ASN* 3.5 30.5 - - + +
1606A VAL* 4.1 17.0 - - + -
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Residues in contact with SER1561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512A ARG* 4.4 12.3 + - - -
1516A ALA* 4.4 11.9 - - - -
1520A ARG* 3.2 26.5 + - - -
1557A GLN 3.0 14.4 + - - -
1558A ALA* 3.1 8.0 + - - -
1560A VAL* 1.3 73.5 - - - +
1562A ALA* 1.3 57.2 + - - +
1563A GLU* 3.0 20.9 + - - +
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Residues in contact with ALA1562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516A ALA* 4.0 3.8 - - - +
1519A LEU* 3.7 31.2 - - + +
1520A ARG* 3.8 31.2 - - + +
1558A ALA 2.9 16.3 + - - +
1561A SER* 1.3 74.8 - - - +
1563A GLU* 1.3 70.5 + - - +
1564A LEU* 3.3 13.0 + - + +
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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