Contacts of the helix formed by residues 1603 - 1611 (chain B) in PDB entry 3LQJ
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 SER1603 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1597B SER* 5.9 0.2 - - - -
1601B ASN 4.2 1.2 + - - -
1602B LEU* 1.3 77.9 - - - +
1604B ASP* 1.3 67.0 + - - +
1605B GLU* 3.6 9.7 + - - +
1606B MET* 3.3 27.6 + - - +
1607B TYR* 3.0 20.8 + - - +
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Residues in contact with ASP1604 (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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1584B LYS* 3.3 36.7 + - - +
1597B SER* 5.0 3.5 + - - -
1602B LEU 5.2 0.9 - - - +
1603B SER* 1.3 76.4 - - - +
1605B GLU* 1.3 63.6 + - - +
1607B TYR* 3.1 8.9 + - - +
1608B GLU* 3.0 29.0 + - + +
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Residues in contact with GLU1605 (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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1603B SER* 3.2 8.8 + - - +
1604B ASP* 1.3 79.0 - - - +
1606B MET* 1.3 70.4 + - + +
1608B GLU* 3.2 5.2 + - - +
1609B ILE* 3.0 29.0 + - + +
1640B LEU* 5.2 0.3 - - - +
1722B SER* 3.5 14.3 - - - -
1723B VAL* 3.0 32.1 + - - +
1724B LEU* 3.2 32.2 + - - +
1768B TRP* 3.8 26.6 - - + -
1769B PHE* 4.3 4.6 - - + -
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Residues in contact with MET1606 (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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1602B LEU* 4.3 11.7 - - + -
1603B SER* 3.3 27.9 + - - +
1604B ASP 3.3 0.6 - - - -
1605B GLU* 1.3 83.3 - - - +
1607B TYR* 1.3 61.0 + - - +
1609B ILE* 3.1 15.7 + - + +
1610B LEU* 2.7 31.9 + - - +
1636B LEU* 3.8 41.7 - - + +
1637B GLU* 5.9 1.6 - - - -
1640B LEU* 3.5 33.2 - - + -
1721B THR 4.2 9.2 - - - +
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Residues in contact with TYR1607 (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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1583B SER 3.6 4.9 + - - -
1584B LYS* 3.5 40.1 - - + -
1585B MET 3.4 33.0 + - - -
1586B MET* 4.1 9.0 - - + -
1597B SER* 3.7 24.2 - - - +
1602B LEU* 4.8 4.9 - - + +
1603B SER 3.0 13.3 + - - +
1604B ASP* 3.4 11.4 - - - +
1606B MET* 1.3 77.4 - - - +
1608B GLU* 1.3 63.3 + - + +
1610B LEU* 3.3 6.4 + - + +
1611B SER* 2.9 38.0 + - - -
3T THR* 3.5 17.5 - - + -
4T M3L 3.4 24.1 + - - +
5T GLN* 3.7 15.1 + - + -
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Residues in contact with GLU1608 (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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1584B LYS* 5.2 7.1 - - - -
1604B ASP* 3.0 21.5 + - + +
1605B GLU* 3.4 7.9 - - - +
1607B TYR* 1.3 84.6 - - + +
1609B ILE* 1.3 60.2 - - - +
1611B SER* 3.4 6.3 - - - -
1612B ASN* 3.2 27.0 + - - +
1768B TRP* 3.7 50.9 - - + +
5T GLN* 2.9 35.6 + - - +
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Residues in contact with ILE1609 (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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1605B GLU* 3.0 16.9 + - + +
1606B MET* 3.1 18.8 + - + +
1608B GLU* 1.3 72.3 - - - +
1610B LEU* 1.3 61.5 + - - +
1611B SER 3.1 0.4 - - - -
1612B ASN* 2.9 24.2 + - + +
1613B LEU* 3.2 11.4 + - - +
1636B LEU* 3.7 18.6 - - + +
1639B GLU* 3.7 29.1 - - + +
1640B LEU* 3.7 37.9 - - + +
1643B SER* 5.8 0.7 - - - +
1723B VAL* 4.6 3.1 - - + -
1766B PHE* 4.8 6.3 - - + -
1768B TRP* 3.9 22.4 - - + +
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Residues in contact with LEU1610 (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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1586B MET* 3.6 32.8 - - + -
1602B LEU* 3.9 21.3 - - + -
1606B MET 2.7 20.9 + - - +
1607B TYR* 3.6 7.0 - - - +
1609B ILE* 1.3 72.2 - - - +
1611B SER* 1.3 63.1 + - - +
1612B ASN 3.1 1.2 + - - -
1613B LEU* 3.1 44.3 + - + +
1619B TYR* 4.9 4.7 - - + -
1632B TRP* 4.1 29.2 - - + -
1636B LEU* 3.8 11.0 - - + +
1T ALA* 3.7 26.7 - - + +
3T THR* 4.8 2.7 - - + -
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Residues in contact with SER1611 (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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1607B TYR* 2.9 19.0 + - - -
1608B GLU 3.4 9.6 - - - -
1609B ILE 3.1 0.2 - - - -
1610B LEU* 1.3 76.4 - - - +
1612B ASN* 1.3 61.7 + - - +
1613B LEU 3.5 3.6 + - - +
1T ALA 4.6 7.2 - - - +
3T THR* 2.8 34.8 + - - +
5T GLN* 3.1 28.7 + - - +
6T THR* 5.1 4.8 + - - -
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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
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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