Contacts of the helix formed by residues 1503 - 1523 (chain D) in PDB entry 5EK0
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 SER1503 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1499D ASN 3.7 8.7 - - - -
1500D ILE* 3.1 22.0 - - - -
1501D VAL 3.1 4.8 + - - +
1502D GLU* 1.3 77.5 - - - +
1504D SER* 1.4 71.7 + - - +
1505D PHE* 3.3 16.8 + - - +
1506D PHE 3.6 2.8 + - - -
1507D THR* 3.3 25.4 + - - +
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Residues in contact with SER1504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503D SER* 1.4 71.7 + - - +
1505D PHE* 1.4 66.5 + - - +
1507D THR* 3.3 9.1 + - - +
1508D LYS* 2.9 51.1 + - - +
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Residues in contact with PHE1505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1500D ILE* 5.1 10.1 - - + -
1503D SER* 3.3 11.7 + - - +
1504D SER* 1.4 77.1 - - - +
1506D PHE* 1.4 70.2 + + + +
1508D LYS* 4.1 3.2 - - - +
1509D PHE* 2.9 59.5 + + + +
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Residues in contact with PHE1506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500D ILE* 3.3 30.4 + - + +
1501D VAL* 3.3 43.5 - - + +
1503D SER 3.6 3.0 + - - +
1504D SER 3.4 0.6 - - - -
1505D PHE* 1.4 85.2 - + + +
1507D THR* 1.4 63.0 + - - +
1509D PHE* 4.2 9.8 - + - +
1510D ILE* 3.1 53.6 + - + +
1550D GLU* 3.9 30.1 - - + -
1553D LEU* 4.0 23.3 - - + -
1554D ARG* 4.4 9.0 - - + -
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Residues in contact with THR1507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1501D VAL 5.6 1.1 - - - -
1503D SER 3.3 13.6 + - - +
1504D SER* 3.3 19.7 - - - +
1506D PHE* 1.4 77.1 - - - +
1508D LYS* 1.4 67.3 + - + +
1510D ILE* 3.5 9.0 + - - +
1511D ILE* 3.1 44.4 + - + +
1615D ALA 4.9 2.8 + - - -
1617D PRO* 4.9 9.0 - - + +
1620D ARG* 5.4 1.9 + - - -
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Residues in contact with LYS1508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504D SER* 2.9 38.8 + - - +
1505D PHE* 4.1 2.9 - - - +
1507D THR* 1.4 77.1 - - + +
1509D PHE* 1.3 59.7 + - - +
1511D ILE* 3.3 12.5 + - + +
1512D TYR* 3.0 26.9 + - - +
1618D GLN* 6.0 0.2 + - - -
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Residues in contact with PHE1509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505D PHE* 2.9 47.8 + + + +
1506D PHE* 4.2 10.1 - + - +
1508D LYS* 1.3 75.6 - - - +
1510D ILE* 1.3 70.8 + - + +
1512D TYR* 3.3 20.1 - + + +
1513D LEU* 3.1 56.2 + - + +
1546D LEU* 5.0 8.7 - - + -
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Residues in contact with ILE1510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1506D PHE* 3.1 39.4 + - + +
1507D THR* 3.7 13.2 - - - +
1508D LYS 3.4 0.4 - - - -
1509D PHE* 1.3 82.4 - - + +
1511D ILE* 1.4 67.3 + - + +
1513D LEU* 3.4 27.0 + - + +
1514D ILE* 3.2 28.2 + - + +
1546D LEU 5.3 1.1 - - - +
1547D PHE* 4.0 4.4 - - + -
1550D GLU* 3.6 44.4 - - + +
1611D ARG* 3.8 18.6 - - - +
1615D ALA* 5.7 2.0 - - + -
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Residues in contact with ILE1511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1507D THR* 3.1 32.9 + - + +
1508D LYS* 3.3 11.2 + - + +
1510D ILE* 1.4 75.2 - - + +
1512D TYR* 1.4 64.8 + - - +
1514D ILE* 3.3 11.7 + - + +
1515D VAL* 3.2 30.5 + - + +
1612D LEU* 5.3 2.1 - - + +
1615D ALA* 3.4 43.3 - - + +
1616D VAL* 4.0 20.9 - - + -
1617D PRO* 4.0 15.9 - - + -
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Residues in contact with TYR1512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508D LYS 3.0 13.9 + - - +
1509D PHE* 3.3 26.7 - + - +
1511D ILE* 1.4 77.2 - - - +
1513D LEU* 1.4 60.8 + - + +
1515D VAL* 3.3 11.5 + - + +
1516D LEU* 3.0 67.8 + - + +
1804D PX4 5.9 0.2 - - - +
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Residues in contact with LEU1513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509D PHE* 3.1 47.7 + - + +
1510D ILE* 3.5 27.6 - - + +
1511D ILE 3.3 0.4 - - - -
1512D TYR* 1.4 81.5 - - + +
1514D ILE* 1.4 54.3 + - - +
1516D LEU* 3.6 4.0 + - + -
1517D ASN* 3.1 23.4 + - - +
1543D PHE* 3.3 34.5 - - + -
1546D LEU* 3.9 36.6 - - + +
1547D PHE* 3.7 17.2 - - + -
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Residues in contact with ILE1514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1510D ILE 3.2 17.9 - - - +
1511D ILE* 3.3 17.6 + - + +
1513D LEU* 1.4 72.9 - - - +
1515D VAL* 1.4 53.6 + - - +
1517D ASN* 3.0 5.6 + - - -
1518D MET* 2.9 30.2 + - - +
1547D PHE* 3.6 19.5 - - + -
1608D ARG 3.2 25.1 - - - +
1609D ILE* 3.5 9.9 - - + +
1611D ARG* 3.9 20.6 - - + +
1612D LEU* 3.8 31.6 - - + +
1615D ALA* 3.9 26.5 - - + -
1616D VAL* 6.3 0.2 - - + -
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Residues in contact with VAL1515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1803A PX4 4.6 28.3 - - + -
1511D ILE* 3.2 22.4 + - + +
1512D TYR* 3.5 13.0 - - + +
1514D ILE* 1.4 73.4 - - - +
1516D LEU* 1.3 65.1 + - + +
1518D MET* 3.1 22.9 + - - +
1519D VAL* 3.1 24.0 + - + +
1612D LEU* 4.4 19.3 - - + -
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Residues in contact with LEU1516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512D TYR* 3.0 64.8 + - + +
1513D LEU* 3.8 4.5 - - + +
1514D ILE 3.3 0.2 - - - -
1515D VAL* 1.3 82.5 - - + +
1517D ASN* 1.3 56.7 + - - +
1519D VAL* 3.8 8.7 + - + +
1520D THR* 3.2 33.1 + - - +
1543D PHE* 3.6 22.4 - - + -
1804D PX4 3.9 32.0 - - + +
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Residues in contact with ASN1517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513D LEU 3.1 13.6 + - - +
1514D ILE* 3.0 11.5 + - - +
1516D LEU* 1.3 74.4 - - - +
1518D MET* 1.4 59.4 + - - +
1520D THR* 3.1 14.7 + - - -
1521D MET* 3.2 21.2 + - - +
1540D ASN* 2.8 28.1 + - - -
1543D PHE* 3.3 31.5 - - + +
1547D PHE* 3.7 6.4 - - + -
1608D ARG* 2.8 33.4 + - - +
1609D ILE* 3.7 7.9 - - + -
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Residues in contact with MET1518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1642A LEU* 4.7 5.6 - - + +
1645A TYR* 3.8 31.0 - - + +
1646A ILE* 3.7 33.4 - - + +
1649A ILE* 4.8 6.2 - - + +
1803A PX4 4.3 22.2 - - + -
1514D ILE 2.9 7.0 + - - +
1515D VAL* 3.1 11.8 + - - +
1517D ASN* 1.4 74.8 - - - +
1519D VAL* 1.4 54.2 + - + +
1521D MET* 3.1 5.6 + - - +
1522D MET* 2.8 48.7 + - + +
1609D ILE* 3.4 25.3 - - + +
1612D LEU* 3.7 24.9 - - + -
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Residues in contact with VAL1519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1803A PX4 5.4 7.9 - - + -
1515D VAL* 3.1 25.9 + - + +
1516D LEU* 4.0 10.3 - - + +
1518D MET* 1.4 73.8 - - + +
1520D THR* 1.3 56.4 + - - +
1522D MET* 3.1 22.6 + - + +
1523D VAL* 3.0 33.3 + - + +
1804D PX4 4.7 17.5 - - + -
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Residues in contact with THR1520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516D LEU 3.2 16.4 + - - +
1517D ASN* 3.1 26.9 + - - -
1519D VAL* 1.3 76.1 - - - +
1521D MET* 1.3 59.6 + - - +
1523D VAL* 3.4 12.1 + - - +
1524D GLU* 4.5 1.0 + - - +
1536D LEU* 3.4 28.7 - - - +
1539D ILE* 3.7 31.1 - - + +
1540D ASN* 4.3 7.9 + - - -
1543D PHE* 4.1 4.0 - - + -
1804D PX4 3.8 32.1 - - + -
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Residues in contact with MET1521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1649A ILE* 3.7 36.7 - - + +
1517D ASN* 3.2 24.6 + - - +
1518D MET* 3.1 7.2 + - - +
1520D THR* 1.3 76.3 - - - +
1522D MET* 1.4 61.6 + - - +
1524D GLU* 3.5 11.1 - - - +
1540D ASN* 3.9 13.0 - - - +
1605D ARG* 3.1 71.7 + - + +
1606D ILE 4.1 0.4 - - - +
1608D ARG* 3.5 23.3 - - - -
1609D ILE* 3.8 22.2 - - + -
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Residues in contact with MET1522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645A TYR* 3.8 35.4 - - + +
1649A ILE* 3.7 22.0 - - + -
1666A LEU* 3.7 35.2 - - + +
1802A PX4 5.3 8.1 - - + -
1803A PX4 5.5 5.2 - - + -
1518D MET* 2.8 27.0 + - + +
1519D VAL* 3.1 25.8 + - + +
1521D MET* 1.4 73.1 - - - +
1523D VAL* 1.4 52.4 + - - +
1524D GLU 2.8 26.2 + - - +
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Residues in contact with VAL1523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519D VAL* 3.0 17.3 + - + +
1520D THR* 3.4 20.9 - - - +
1522D MET* 1.4 71.5 - - - +
1524D GLU* 1.3 55.9 + - - +
1525D LYS* 4.3 3.2 + - - +
1528D GLN* 4.6 3.8 - - - +
1532D MET* 5.2 4.9 - - - +
1536D LEU* 3.5 27.9 - - + +
1804D PX4 5.0 12.8 - - + -
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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
------------------------------------------------------------
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