Contacts of the helix formed by residues 1462 - 1477 (chain X) in PDB entry 2IWL
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 THR1462 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441X HIS* 4.4 19.1 - - + +
1442X TYR 4.5 7.0 - - - +
1443X ILE* 3.9 23.3 - - + -
1444X TYR* 4.2 2.9 - - - -
1461X ARG* 1.3 76.1 - - - +
1463X PHE* 1.3 60.7 + - - +
1464X ASP* 3.3 10.0 + - - +
1465X GLU* 2.9 51.7 + - - +
1466X PHE* 3.0 14.0 + - - -
1536X ARG* 4.7 0.7 - - - +
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Residues in contact with PHE1463 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1442X TYR 4.9 1.4 + - - -
1444X TYR* 4.0 18.6 - - + -
1462X THR* 1.3 74.2 - - - +
1464X ASP* 1.3 70.0 + - - +
1466X PHE* 3.1 8.9 + - - +
1467X GLN* 2.9 45.2 + - - -
1485X PHE* 3.7 20.2 - + - -
1486X PRO* 3.9 18.8 - - + -
1487X ASN 4.1 12.6 - - - -
1503X ARG* 3.6 53.8 - - + +
1507X LEU* 4.0 29.6 - - + -
2540X SO4 5.8 1.1 - - - -
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Residues in contact with ASP1464 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1462X THR* 3.2 9.0 + - - +
1463X PHE* 1.3 90.4 - - - +
1465X GLU* 1.3 58.3 - - + +
1467X GLN* 3.8 13.3 - - - +
1468X GLU* 3.2 25.5 + - - +
2540X SO4 4.0 17.5 + - - -
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Residues in contact with GLU1465 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1411X PHE* 3.7 44.9 - - + +
1461X ARG* 3.3 10.2 - - + -
1462X THR* 2.9 36.0 + - - +
1464X ASP* 1.3 79.5 - - + +
1466X PHE* 1.3 63.9 + - - +
1467X GLN 3.2 0.9 - - - -
1468X GLU* 3.7 1.9 + - - +
1469X LEU 3.4 12.6 + - - -
1530X PHE* 3.3 13.1 - - - -
1536X ARG* 2.5 49.3 + - - -
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Residues in contact with PHE1466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429X VAL* 4.5 5.6 - - + -
1444X TYR* 4.0 4.7 - - + -
1446X VAL* 3.6 24.7 - - + -
1461X ARG* 3.6 27.4 - - + -
1462X THR 3.0 25.7 + - - -
1463X PHE 3.1 6.5 + - - +
1465X GLU* 1.3 75.0 - - - +
1467X GLN* 1.3 65.2 + - - +
1469X LEU* 3.2 16.2 + - + +
1470X HIS* 3.2 9.5 + - - +
1485X PHE* 3.7 18.7 - - + -
1507X LEU* 3.9 42.2 - - + -
1510X TYR* 5.0 9.7 - + - -
1511X LEU* 3.9 32.8 - - + -
1530X PHE* 3.7 23.3 - + - -
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Residues in contact with GLN1467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463X PHE* 2.9 29.9 + - + +
1464X ASP* 4.0 13.7 - - - +
1465X GLU 3.2 0.2 - - - -
1466X PHE* 1.3 77.4 - - - +
1468X GLU* 1.3 57.2 + - - +
1470X HIS* 2.9 5.7 + - + +
1471X ASN* 2.8 48.4 + - - +
1485X PHE* 3.3 37.5 - - + -
1486X PRO 4.5 4.6 + - - -
1487X ASN* 4.8 5.9 - - - +
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Residues in contact with GLU1468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409X LEU* 3.5 5.3 - - + -
1410X SER* 2.5 52.9 + - - -
1411X PHE* 3.5 16.0 - - + -
1464X ASP 3.2 18.6 + - - +
1465X GLU* 4.0 5.9 - - - +
1466X PHE 3.3 0.2 - - - -
1467X GLN* 1.3 72.8 - - - +
1469X LEU* 1.3 67.0 + - - +
1471X ASN* 3.4 9.1 + - - +
1472X LYS* 2.8 48.1 + - + +
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Residues in contact with LEU1469 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409X LEU* 4.3 13.9 - - + +
1465X GLU 3.4 3.0 + - - +
1466X PHE* 3.2 11.9 + - + +
1468X GLU* 1.3 79.2 - - - +
1470X HIS* 1.3 64.4 + - - +
1472X LYS* 3.2 1.6 + - - +
1473X LEU* 2.9 35.2 + - + +
1510X TYR* 4.8 8.7 - - + -
1511X LEU* 5.5 2.9 - - + -
1514X LEU* 4.2 23.8 - - + -
1526X LEU* 3.9 39.7 - - + +
1527X VAL* 4.3 4.3 - - + +
1530X PHE* 3.8 44.0 - - + -
1531X PHE* 5.9 0.2 - - + -
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Residues in contact with HIS1470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466X PHE 3.2 3.0 + - - +
1467X GLN 2.9 8.0 + - - +
1469X LEU* 1.3 81.1 - - - +
1471X ASN* 1.3 74.2 + - - +
1473X LEU* 3.3 5.5 + - - +
1474X SER* 3.1 24.4 + - - -
1479X LEU* 4.5 15.1 - - + +
1482X LEU* 4.0 22.9 - - + +
1483X PRO 3.4 23.8 - - - -
1484X GLY* 5.3 0.2 - - - -
1485X PHE* 3.6 43.0 + + + +
1510X TYR* 2.6 30.2 + - + +
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Residues in contact with ASN1471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467X GLN* 2.8 38.5 + - - +
1468X GLU* 3.8 8.3 - - - +
1470X HIS* 1.3 87.0 - - - +
1472X LYS* 1.3 60.5 + - + +
1474X SER* 3.3 21.5 + - - -
1475X ILE* 3.3 16.2 + - - +
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Residues in contact with LYS1472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409X LEU* 2.9 38.5 - - + +
1410X SER* 4.0 2.8 - - - +
1468X GLU* 2.8 51.5 + - + +
1469X LEU 3.8 2.7 - - - +
1471X ASN* 1.3 70.4 - - + +
1473X LEU* 1.3 65.2 + - - +
1474X SER 3.3 0.3 + - - -
1475X ILE* 3.4 33.0 + - + +
1476X ILE* 3.6 12.5 + - - +
1526X LEU* 3.7 23.6 - - + +
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Residues in contact with LEU1473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469X LEU* 2.9 33.5 + - + +
1470X HIS 3.6 3.8 - - - +
1472X LYS* 1.3 76.9 - - - +
1474X SER* 1.3 52.1 + - - +
1476X ILE* 3.0 2.5 + - - -
1477X PHE* 2.8 54.9 + - + +
1482X LEU* 3.9 17.3 - - + -
1510X TYR* 4.1 12.3 - - - +
1514X LEU* 4.0 26.0 - - + -
1521X VAL* 4.7 2.5 - - + -
1524X CYS* 3.7 30.5 - - - -
1526X LEU* 3.8 15.0 - - + +
1527X VAL* 4.2 10.1 - - + -
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Residues in contact with SER1474 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1470X HIS* 3.1 21.4 + - - -
1471X ASN* 3.3 12.6 + - - -
1472X LYS 3.1 0.4 - - - -
1473X LEU* 1.3 76.0 - - - +
1475X ILE* 1.3 63.1 + - - +
1477X PHE 3.2 14.0 - - - +
1479X LEU* 4.3 17.3 - - - +
1482X LEU* 3.7 17.0 - - - -
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Residues in contact with ILE1475 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471X ASN 3.3 16.7 + - - +
1472X LYS* 3.5 26.5 - - + +
1474X SER* 1.3 79.1 - - - +
1476X ILE* 1.3 63.6 + - + +
1477X PHE 5.3 0.2 - - - -
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Residues in contact with ILE1476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1472X LYS 3.6 8.0 + - - +
1473X LEU 3.0 6.5 + - - +
1475X ILE* 1.3 83.6 - - + +
1477X PHE* 1.3 92.3 + - + +
1478X PRO* 4.4 2.8 - - - +
1524X CYS* 5.5 3.6 - - + -
1526X LEU* 3.8 29.6 - - + -
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Residues in contact with PHE1477 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473X LEU* 2.8 45.4 + - + +
1474X SER* 3.2 21.2 - - - +
1475X ILE 3.5 0.4 - - - -
1476X ILE* 1.3 105.7 - - + +
1478X PRO* 1.3 79.2 - - + +
1479X LEU 3.4 1.2 + - - -
1481X LYS* 4.1 12.3 - - + -
1482X LEU* 4.1 11.8 - - + +
1520X ASP* 3.3 38.6 - - + -
1521X VAL* 3.7 31.4 - - + -
1524X CYS* 4.1 9.2 - - + -
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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