Contacts of the strand formed by residues 1550 - 1556 (chain A) in PDB entry 2VK7
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 LEU1550 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469A ILE* 3.9 22.9 - - + -
1471A ILE* 4.1 17.3 - - + -
1481A VAL* 4.5 12.6 - - + -
1542A VAL* 4.0 17.5 - - + -
1543A VAL 3.5 5.8 - - - +
1544A GLU* 4.2 5.8 - - + -
1548A GLY 3.6 15.0 - - - +
1549A GLN* 1.3 75.9 - - - +
1551A LYS* 1.3 64.6 + - - +
1564A ALA 3.8 0.2 - - - +
1565A THR* 3.3 8.0 - - - +
1566A SER* 2.9 35.5 + - - +
1569A GLY* 3.6 36.1 - - - +
1570A GLY* 3.6 9.2 - - - +
1573A TRP* 4.2 11.0 - - + -
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Residues in contact with LYS1551 (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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1542A VAL* 3.3 5.9 - - - -
1543A VAL* 2.9 40.6 + - + +
1545A MET* 3.8 24.0 - - + -
1549A GLN* 3.5 21.3 + - - -
1550A LEU* 1.3 75.5 - - - +
1552A LEU* 1.3 60.7 + - - +
1553A PHE* 3.9 20.3 + - + -
1563A ILE* 3.8 15.3 - - + +
1564A ALA 3.2 1.3 - - - -
1565A THR* 2.8 26.2 + - - +
1578A GLU* 3.8 13.5 + - - -
1631A TYR* 4.1 5.5 + - - -
1638A TYR* 3.1 35.7 + - - +
1640A PHE* 4.0 10.2 - - + -
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Residues in contact with LEU1552 (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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1483A PRO* 4.6 0.9 - - + -
1495A SER* 4.1 13.2 - - - -
1496A ALA 4.5 7.2 - - - +
1497A VAL* 4.0 13.0 - - + -
1513A PRO* 3.9 25.8 - - + -
1540A CYS* 3.8 26.0 - - + -
1541A GLN 3.7 15.0 - - - +
1542A VAL* 3.8 17.9 - - + -
1551A LYS* 1.3 71.0 - - - +
1553A PHE* 1.3 63.3 + - - +
1554A MET* 3.7 12.0 - - + +
1562A ASN 3.7 0.5 - - - +
1563A ILE* 3.3 4.9 - - - -
1564A ALA* 2.8 37.8 + - + +
1573A TRP* 3.6 27.0 - - + -
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Residues in contact with PHE1553 (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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1540A CYS* 3.1 5.4 - - - +
1541A GLN 2.8 35.3 + - - +
1543A VAL* 3.8 12.3 - - + -
1551A LYS* 4.0 12.1 - - + -
1552A LEU* 1.3 75.1 - - - +
1554A MET* 1.3 57.5 + - - +
1561A LEU* 3.7 25.4 - - + -
1562A ASN 3.5 5.4 - - - -
1563A ILE* 4.1 9.6 - - + -
1590A LEU* 3.7 18.9 - - + +
1592A VAL* 3.7 21.8 - - + -
1607A PHE* 3.8 17.3 - + - -
1640A PHE* 3.6 44.4 - + - -
1642A TRP* 3.7 27.8 - + - -
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Residues in contact with MET1554 (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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1495A SER* 3.7 24.7 - - - +
1513A PRO* 3.9 15.3 - - - -
1537A LEU* 3.7 28.0 - - + -
1539A GLU 3.6 3.6 - - - -
1540A CYS* 3.7 10.3 - - + -
1552A LEU* 3.7 9.9 - - + +
1553A PHE* 1.3 77.9 - - - +
1555A ARG* 1.3 65.6 + - - +
1556A ASN* 2.9 22.2 + - - -
1561A LEU* 4.2 1.4 - - - +
1562A ASN* 2.9 22.9 + - + +
1564A ALA* 3.6 33.9 - - + +
1577A VAL* 3.8 22.2 - - + -
1585A GLU* 4.4 1.4 - - - +
1590A LEU* 4.1 8.9 - - - +
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Residues in contact with ARG1555 (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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1537A LEU* 3.7 1.6 - - - -
1538A THR* 2.9 41.0 + - - +
1539A GLU* 2.7 55.5 + - + +
1554A MET* 1.3 73.7 - - - +
1556A ASN* 1.3 64.9 + - - +
1585A GLU* 3.3 14.8 - - - +
1587A TYR* 3.2 59.3 + - + -
1588A CYS 3.5 23.3 - - - +
1589A GLN* 3.9 2.7 - - - +
1590A LEU* 4.2 5.1 - - + +
1615A ARG* 3.4 4.8 - - - +
1655A TYR* 3.0 21.0 + - - -
2693A FSI 3.1 31.6 + - - -
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Residues in contact with ASN1556 (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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1536A GLN 3.6 18.6 - - - +
1537A LEU* 4.0 4.3 - - + -
1538A THR* 5.1 0.7 - - - -
1554A MET 2.9 22.4 + - - -
1555A ARG* 1.3 75.5 - - - +
1557A LEU* 1.3 62.0 + - - +
1558A SER* 2.7 41.2 + - - -
1559A GLY 4.8 0.6 + - - -
1560A TYR 2.9 20.8 + - - +
1561A LEU* 4.2 0.4 - - - +
1562A ASN* 3.3 29.7 + - - +
1585A GLU* 2.9 23.4 + - - +
1587A TYR* 3.2 19.7 + - - +
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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