Contacts of the helix formed by residues 1504 - 1522 (chain B) 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 SER1504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1503B SER* 1.3 81.3 + - - +
1505B PHE* 1.4 60.0 + - - +
1506B PHE 3.5 1.1 - - - -
1507B THR* 3.4 6.1 - - - -
1508B LYS* 3.1 41.9 + - - +
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Residues in contact with PHE1505 (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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1500B ILE* 5.9 5.4 - - + -
1503B SER* 3.5 3.3 + - - +
1504B SER* 1.4 76.0 - - - +
1506B PHE* 1.4 62.3 + + + +
1508B LYS* 3.3 8.8 + - - +
1509B PHE* 2.8 56.2 + + + +
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Residues in contact with PHE1506 (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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1500B ILE* 3.2 41.1 - - + +
1501B VAL* 3.6 39.3 - - + -
1502B GLU* 3.8 6.5 - - - +
1503B SER* 3.2 5.0 + - - +
1505B PHE* 1.4 81.6 - + + +
1507B THR* 1.4 68.8 + - - +
1509B PHE* 3.2 7.9 + + - +
1510B ILE* 3.1 62.3 + - + +
1550B GLU* 4.1 17.7 - - + -
1553B LEU* 4.5 15.0 - - + -
1554B ARG* 4.4 11.7 - - + -
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Residues in contact with THR1507 (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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1502B GLU* 4.9 3.6 + - - -
1503B SER 2.7 31.9 + - - +
1504B SER* 3.4 9.2 - - - -
1506B PHE* 1.4 82.6 - - - +
1508B LYS* 1.4 60.5 + - + +
1510B ILE* 3.6 9.0 + - - +
1511B ILE* 3.3 23.7 + - + +
1615B ALA 5.2 9.2 - - - +
1617B PRO* 5.7 9.2 - - + -
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Residues in contact with LYS1508 (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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1504B SER* 3.1 29.2 + - - +
1505B PHE* 3.5 7.0 - - - +
1507B THR* 1.4 74.6 - - + +
1509B PHE* 1.3 62.9 + - - +
1511B ILE* 3.3 15.3 + - + +
1512B TYR* 3.2 20.3 + - - +
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Residues in contact with PHE1509 (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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1505B PHE* 2.8 40.6 + + + +
1506B PHE* 3.2 13.4 + + - +
1508B LYS* 1.3 69.3 - - - +
1510B ILE* 1.3 78.5 + - + +
1512B TYR* 3.3 36.7 - + - +
1513B LEU* 3.1 47.4 + - + +
1546B LEU* 5.5 5.6 - - + -
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Residues in contact with ILE1510 (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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1506B PHE* 3.1 42.0 + - + +
1507B THR* 3.6 6.7 + - - +
1508B LYS 3.3 0.2 - - - -
1509B PHE* 1.3 93.1 - - + +
1511B ILE* 1.4 59.9 + - + +
1513B LEU* 3.2 12.6 + - + +
1514B ILE* 2.9 36.2 + - + +
1547B PHE* 4.2 8.5 - - + -
1550B GLU* 3.4 47.3 - - + +
1611B ARG* 3.5 15.5 - - - +
1615B ALA* 5.7 0.9 - - + -
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Residues in contact with ILE1511 (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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1507B THR* 3.3 22.4 - - + +
1508B LYS* 3.3 15.2 + - + +
1510B ILE* 1.4 75.7 - - + +
1512B TYR* 1.4 52.6 + - - +
1514B ILE* 3.0 10.7 + - + +
1515B VAL* 2.8 40.4 + - + +
1612B LEU* 4.5 15.5 - - + -
1615B ALA* 3.4 44.9 - - + +
1616B VAL* 3.7 28.7 - - + +
1617B PRO* 5.2 2.9 - - + -
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Residues in contact with TYR1512 (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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1508B LYS 3.2 9.2 + - - +
1509B PHE* 3.3 40.2 - + + +
1511B ILE* 1.4 77.6 - - - +
1513B LEU* 1.3 66.5 + - + +
1515B VAL* 3.7 10.2 + - + +
1516B LEU* 3.0 57.6 + - + +
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Residues in contact with LEU1513 (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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1509B PHE* 3.1 47.9 + - + +
1510B ILE* 3.2 17.7 + - + +
1512B TYR* 1.3 83.6 - - + +
1514B ILE* 1.4 55.5 + - - +
1516B LEU* 3.3 3.3 + - + -
1517B ASN* 2.9 31.4 + - - +
1543B PHE* 3.2 30.0 - - + -
1546B LEU* 4.2 37.5 - - + +
1547B PHE* 3.9 18.8 - - + -
1550B GLU* 6.3 0.7 - - + -
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Residues in contact with ILE1514 (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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1510B ILE* 2.9 32.2 + - + +
1511B ILE* 3.4 7.6 - - - +
1513B LEU* 1.4 73.2 - - - +
1515B VAL* 1.3 57.1 + - - +
1517B ASN* 3.3 5.5 + - - +
1518B MET* 3.1 25.1 + - - +
1547B PHE* 3.6 21.5 - - + -
1608B ARG 3.6 20.4 - - - +
1609B ILE* 3.8 10.6 - - - +
1611B ARG* 3.5 26.5 - - + +
1612B LEU* 3.7 31.9 - - + +
1615B ALA* 3.8 23.8 - - + -
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Residues in contact with VAL1515 (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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1511B ILE* 2.8 22.8 + - + +
1512B TYR* 3.9 10.5 - - + +
1514B ILE* 1.3 72.6 - - - +
1516B LEU* 1.3 67.7 + - + +
1518B MET* 3.2 18.1 + - - +
1519B VAL* 3.2 26.0 + - + +
1612B LEU* 3.8 29.4 - - + -
1803B PX4 4.2 30.3 - - + -
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Residues in contact with LEU1516 (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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1512B TYR* 3.0 59.3 + - + +
1513B LEU* 3.3 5.6 + - + +
1515B VAL* 1.3 78.2 - - + +
1517B ASN* 1.3 60.4 + - - +
1519B VAL* 3.7 10.1 + - + +
1520B THR* 3.4 21.1 + - - +
1543B PHE* 3.6 28.3 - - + -
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Residues in contact with ASN1517 (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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1513B LEU 2.9 16.6 + - - +
1514B ILE 3.7 5.4 - - - +
1515B VAL 3.3 0.2 - - - -
1516B LEU* 1.3 74.1 - - - +
1518B MET* 1.4 61.7 + - - +
1520B THR* 3.2 16.1 - - - +
1521B MET* 3.2 13.4 + - - +
1540B ASN* 2.8 27.0 + - - -
1543B PHE* 3.4 32.6 - - + +
1547B PHE* 4.0 6.7 - - + -
1608B ARG* 2.8 39.7 + - - +
1609B ILE* 3.6 8.5 - - + +
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Residues in contact with MET1518 (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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1514B ILE 3.1 9.6 + - - +
1515B VAL* 3.2 12.5 + - - +
1517B ASN* 1.4 75.8 - - - +
1519B VAL* 1.3 54.9 + - + +
1521B MET* 3.1 5.2 + - - +
1522B MET* 2.9 41.8 + - - +
1609B ILE* 3.5 29.1 - - + +
1612B LEU* 3.7 28.3 - - + -
1803B PX4 5.2 12.8 - - - -
1642C LEU* 4.0 11.0 - - + -
1645C TYR* 4.1 25.4 - - + -
1646C ILE* 3.7 29.6 - - + -
1649C ILE* 3.8 12.2 - - + +
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Residues in contact with VAL1519 (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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1515B VAL* 3.2 24.2 + - + +
1516B LEU* 3.7 10.5 + - + +
1517B ASN 3.4 0.2 - - - -
1518B MET* 1.3 77.1 - - + +
1520B THR* 1.4 56.2 + - - +
1522B MET* 3.3 28.9 + - + +
1523B VAL* 3.1 21.5 - - + +
1803B PX4 5.8 7.0 - - + -
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Residues in contact with THR1520 (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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1516B LEU 3.4 14.1 + - - +
1517B ASN* 3.2 35.0 - - - +
1519B VAL* 1.4 75.4 - - - +
1521B MET* 1.3 60.0 + - - +
1522B MET 3.2 0.7 - - - -
1523B VAL* 3.4 14.8 + - - -
1524B GLU 4.7 0.2 + - - -
1536B LEU* 3.4 34.1 - - - +
1539B ILE* 3.7 23.4 - - + +
1540B ASN* 4.3 9.3 + - - +
1543B PHE* 3.7 13.0 - - + -
1605B ARG* 4.9 2.1 + - - -
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Residues in contact with MET1521 (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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1517B ASN* 3.2 10.8 + - - +
1518B MET* 3.1 10.4 + - - +
1520B THR* 1.3 75.6 - - - +
1522B MET* 1.4 55.2 + - - +
1523B VAL 3.3 3.6 - - - -
1524B GLU* 3.3 24.0 - - - +
1540B ASN* 4.0 18.6 - - - +
1605B ARG* 3.3 63.7 - - + +
1606B ILE* 3.8 17.0 - - + -
1608B ARG* 4.2 5.6 - - - -
1609B ILE* 3.4 38.8 - - + -
1649C ILE* 3.6 26.5 - - + +
1666C LEU* 4.6 0.3 - - - +
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Residues in contact with MET1522 (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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1518B MET* 2.9 21.4 + - - +
1519B VAL* 3.3 30.1 - - + +
1520B THR 3.2 0.4 - - - -
1521B MET* 1.4 74.7 - - - +
1523B VAL* 1.4 54.4 + - - +
1524B GLU 3.2 10.0 + - - +
1803B PX4 6.2 3.4 - - - -
1645C TYR* 3.7 35.2 - - + +
1649C ILE* 4.0 8.5 - - + -
1666C LEU* 3.8 44.9 - - + +
1802C PX4 4.9 7.0 - - + +
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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