Contacts of the strand formed by residues 1607 - 1614 (chain A) in PDB entry 2L29
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 LYS1607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1574A VAL 3.4 2.7 + - - -
1591A VAL* 4.0 17.3 - - + -
1592A TYR 3.0 21.1 - - - +
1593A LYS* 4.6 10.3 - - + -
1605A SER 5.1 1.1 - - - +
1606A TYR* 1.3 79.9 - - - +
1608A SER* 1.3 62.4 + - - +
1609A VAL* 4.2 13.2 - - + -
1633A THR 5.8 0.4 - - - +
1634A CYS 3.3 7.4 + - - +
1635A THR* 3.5 27.9 + - - +
1636A LEU* 2.8 32.2 + - - +
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Residues in contact with SER1608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565A ALA* 3.5 12.5 - - - +
1574A VAL* 2.9 35.4 + - - +
1590A LEU 3.7 2.1 - - - +
1591A VAL* 3.6 1.4 - - - -
1592A TYR* 2.8 44.7 + - - +
1607A LYS* 1.3 75.2 + - - +
1609A VAL* 1.3 61.2 - - - +
1610A ILE* 3.9 3.4 - - - -
1636A LEU* 3.6 5.1 - - - +
1638A PHE* 3.9 20.7 - - - -
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Residues in contact with VAL1609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589A GLN* 4.1 30.5 - - + +
1590A LEU 3.9 1.6 - - - -
1591A VAL* 4.2 15.5 - - + +
1607A LYS* 4.2 6.5 - - + -
1608A SER* 1.3 76.5 - - - +
1610A ILE* 1.3 65.5 + - - +
1611A SER* 4.6 5.9 - - - -
1635A THR* 3.9 20.9 - - + -
1636A LEU 2.9 18.6 + - - +
1637A PHE* 4.0 19.3 - - + -
1638A PHE* 2.8 31.0 + - - +
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Residues in contact with ILE1610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550A MET* 3.7 25.8 - - + -
1552A ILE* 4.9 3.1 - - + -
1588A LEU 3.3 0.6 - - - +
1589A GLN* 3.2 9.7 - - - +
1590A LEU* 2.8 61.0 + - + +
1592A TYR* 4.3 21.8 - - + -
1608A SER* 4.6 4.5 - - - -
1609A VAL* 1.3 75.2 - - - +
1611A SER* 1.3 63.4 + - - +
1612A PHE* 3.6 38.4 - - + -
1638A PHE* 3.9 19.5 - - + +
1640A TRP* 4.7 11.0 - - + -
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Residues in contact with SER1611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1587A VAL* 3.4 26.5 - - - +
1588A LEU 3.5 3.6 - - - -
1589A GLN* 6.0 0.4 - - - -
1609A VAL* 4.6 7.9 - - - -
1610A ILE* 1.3 76.5 - - - +
1612A PHE* 1.3 60.8 + - - +
1613A VAL* 3.7 9.1 + - - +
1627A ILE* 6.3 0.7 - - - -
1638A PHE 2.8 19.5 + - - -
1639A SER* 3.4 4.6 - - - -
1640A TRP 3.1 24.2 + - - -
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Residues in contact with PHE1612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529A LEU* 3.7 26.0 - - + -
1532A LEU* 3.7 25.6 - - + -
1552A ILE* 4.0 18.4 - - + -
1581A LEU* 4.9 0.4 - - + -
1586A GLN 3.6 2.8 - - - +
1587A VAL* 3.6 8.5 - - - -
1588A LEU* 2.8 59.2 + - + +
1590A LEU* 4.1 17.3 - - + -
1610A ILE* 3.6 22.0 - - + -
1611A SER* 1.3 71.6 - - - +
1613A VAL* 1.3 61.5 + - - +
1640A TRP* 3.5 40.6 - + + -
1642A THR* 4.4 9.6 - - + -
1645A ALA* 4.0 11.7 - - + -
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Residues in contact with VAL1613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1586A GLN* 4.4 17.9 - - + +
1587A VAL* 4.9 10.1 - - + -
1611A SER* 4.0 18.6 - - - +
1612A PHE* 1.3 80.0 - - - +
1614A CYS* 1.3 71.1 + - - +
1639A SER* 4.4 6.1 - - - +
1640A TRP 2.8 10.4 + - - +
1641A HIS* 3.3 35.9 - - + +
1642A THR* 3.0 29.0 + - - +
1645A ALA* 4.5 3.6 - - - -
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Residues in contact with CYS1614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1586A GLN* 4.3 20.9 + - - +
1613A VAL* 1.3 79.5 - - - +
1615A ARG* 1.3 60.2 + - - +
1616A PRO* 3.5 18.3 - - - +
1641A HIS* 5.0 0.7 + - - -
1642A THR 3.5 6.7 - - - -
1645A ALA 3.9 7.4 + - - +
1646A CYS* 2.0 53.6 - - + -
1647A GLU* 4.7 4.7 - - - +
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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