Contacts of the helix formed by residues 1506 - 1516 (chain B) in PDB entry 5DKD
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 ASP1506 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1485B PHE 3.5 11.4 - - - +
1486B ILE 3.5 9.6 - - - +
1487B GLN* 3.4 3.8 - - - +
1488B LEU* 2.7 40.1 + - + +
1505B VAL* 1.3 76.9 - - - +
1507B PHE* 1.3 67.8 + - - +
1508B LYS* 3.6 5.0 + - - +
1509B LYS* 3.0 24.8 + - - +
1510B ILE* 3.1 21.8 + - - +
1532B LEU* 3.6 10.8 - - - -
1605B 5BW 4.0 5.8 - - + -
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Residues in contact with PHE1507 (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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1466B VAL* 4.2 15.3 - - + -
1469B VAL* 4.1 25.8 - - + -
1470B ILE* 4.0 25.8 - - + -
1482B SER* 4.2 15.9 - - - -
1485B PHE* 3.0 48.2 + + + +
1486B ILE* 4.0 15.7 - - + -
1506B ASP* 1.3 72.2 - - - +
1508B LYS* 1.4 57.3 + - - +
1510B ILE* 3.3 19.8 + - + +
1511B LYS* 2.9 34.8 + - - +
1529B VAL* 4.5 19.5 - - + -
1532B LEU* 3.6 17.2 - - + +
1533B CYS* 6.0 1.1 - - - -
1553B LEU* 4.7 10.8 - - + -
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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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1526A GLU* 4.7 12.5 + - - -
1486B ILE 2.9 18.7 + - - +
1487B GLN* 3.4 26.9 - - + +
1506B ASP* 3.7 6.7 - - - +
1507B PHE* 1.4 75.3 - - - +
1509B LYS* 1.3 57.5 + - - +
1511B LYS* 3.3 23.3 + - - +
1512B GLU* 3.1 36.8 + - - +
1602B EDO 3.4 26.2 - - - +
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Residues in contact with LYS1509 (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 PRO 5.3 2.0 - - - +
1505B VAL* 4.3 11.0 - - + -
1506B ASP* 3.0 28.8 + - - +
1508B LYS* 1.3 72.9 - - - +
1510B ILE* 1.3 61.0 + - - +
1512B GLU* 3.2 34.3 + - - +
1513B ARG* 2.8 91.0 + - - +
1516B ASN* 5.5 1.8 - - - +
1518B LYS* 5.5 3.0 - - - +
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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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1466B VAL* 4.1 17.9 - - + -
1505B VAL* 3.7 13.2 - - + -
1506B ASP 3.1 9.0 + - - +
1507B PHE* 3.3 13.0 + - + +
1509B LYS* 1.3 74.5 - - - +
1511B LYS* 1.3 62.9 + - - +
1513B ARG* 3.3 2.8 + - - +
1514B ILE* 3.0 22.3 + - + +
1519B TYR* 3.7 17.9 - - - +
1525B LEU* 3.5 29.4 - - + -
1528B ASP* 4.0 16.4 - - + +
1529B VAL* 3.9 23.8 - - + +
1532B LEU* 4.0 24.5 - - + -
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Residues in contact with LYS1511 (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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1466B VAL* 4.2 17.7 - - + -
1467B ASP* 5.0 9.6 - - - +
1470B ILE* 4.1 19.6 - - + +
1486B ILE* 4.2 17.4 - - - +
1487B GLN* 5.7 0.4 + - - -
1507B PHE* 2.9 25.4 + - - +
1508B LYS* 3.6 21.9 - - - +
1509B LYS 3.2 0.2 - - - -
1510B ILE* 1.3 75.6 - - - +
1512B GLU* 1.3 56.0 + - - +
1514B ILE* 3.5 11.6 - - + +
1515B ARG* 3.0 28.5 + - - +
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Residues in contact with GLU1512 (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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1558A THR* 4.0 26.0 + - - +
1508B LYS* 3.1 23.2 + - + +
1509B LYS* 3.2 40.6 + - - +
1511B LYS* 1.3 74.8 - - - +
1513B ARG* 1.3 59.3 + - - +
1515B ARG* 3.3 25.6 + - - +
1516B ASN* 2.8 52.5 + - - +
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Residues in contact with ARG1513 (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 PRO 5.3 5.5 + - - -
1505B VAL* 5.1 2.6 - - - +
1509B LYS* 2.8 75.8 + - - +
1510B ILE 3.3 0.6 + - - +
1512B GLU* 1.3 69.4 - - - +
1514B ILE* 1.3 64.6 + - - +
1516B ASN* 3.5 1.0 + - - +
1517B HIS 3.2 3.1 + - - -
1518B LYS* 2.8 61.2 + - + +
1519B TYR* 3.5 23.3 + - + +
1528B ASP* 3.4 26.3 + - - -
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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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1459B THR* 3.6 35.9 + - + +
1462B MET* 3.9 28.4 - - + +
1463B LYS* 4.0 15.5 - - + +
1466B VAL* 3.7 32.5 - - + -
1510B ILE* 3.0 22.0 + - + +
1511B LYS* 3.5 14.1 - - + +
1512B GLU 3.3 0.2 - - - -
1513B ARG* 1.3 75.9 - - - +
1515B ARG* 1.3 64.0 + - - +
1517B HIS* 3.0 21.1 + - - -
1518B LYS 5.1 0.4 - - - +
1519B TYR* 3.8 20.4 - - + +
1525B LEU* 4.3 1.8 - - + -
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Residues in contact with ARG1515 (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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1526A GLU* 4.7 6.5 + - - -
1530A MET* 3.7 44.1 - - - +
1537A GLN* 4.8 2.9 - - - +
1551A ILE* 3.7 12.8 - - - +
1554A GLN* 3.0 40.9 + - - +
1558A THR* 4.2 4.0 - - - +
1459B THR* 4.8 6.9 - - - +
1463B LYS* 5.7 3.6 - - - +
1511B LYS 3.0 14.5 + - - +
1512B GLU* 3.3 28.5 + - - +
1514B ILE* 1.3 81.6 - - - +
1516B ASN* 1.3 86.0 + - - +
1517B HIS* 3.5 5.0 + - - -
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Residues in contact with ASN1516 (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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1551A ILE* 3.9 14.7 - - + +
1554A GLN* 3.1 28.8 + - - +
1555A SER* 4.0 23.8 - - - +
1509B LYS* 5.5 1.2 - - - +
1512B GLU* 2.8 43.3 + - - +
1513B ARG* 5.1 0.4 - - - +
1514B ILE 3.1 0.4 - - - -
1515B ARG* 1.3 89.5 + - - +
1517B HIS* 1.3 68.2 + - - +
1518B LYS* 3.3 33.1 + - + +
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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