Contacts of the strand formed by residues 1548 - 1551 (chain F) in PDB entry 6C3P
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 VAL1548 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1375F GLY 3.2 3.4 - - - -
1377F CYS* 4.2 6.1 - - - -
1542F ILE* 4.0 33.9 - - + +
1545F ALA* 5.1 0.4 - - + +
1547F LEU* 1.3 75.8 - - - +
1549F ILE* 1.3 63.8 + - - +
1550F VAL* 4.1 19.2 + - + -
1559F PHE* 3.0 7.1 - - - +
1560F ASP 2.6 35.5 + - - +
1562F PRO* 3.6 36.6 - - + -
1565F LEU* 3.9 13.6 - - + +
1573F PHE* 4.6 13.2 - - + -
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Residues in contact with ILE1549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366F ALA* 5.4 5.8 - - + -
1368F ILE* 4.9 12.8 - - + -
1374F ILE* 3.8 23.1 - - + -
1375F GLY 2.4 17.5 + - - +
1376F ILE* 3.2 36.3 - - + +
1377F CYS* 2.8 32.7 + - - +
1387F PHE* 6.1 0.4 - - + -
1547F LEU* 5.1 4.5 - - + -
1548F VAL* 1.3 78.2 - - - +
1550F VAL* 1.3 61.8 + - - +
1551F LEU* 4.7 2.2 - - + -
1556F ILE* 3.7 33.4 - - + -
1559F PHE* 3.7 21.5 - - + -
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Residues in contact with VAL1550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377F CYS* 3.8 16.6 - - - +
1378F GLY* 5.2 0.7 - - - -
1548F VAL* 4.1 11.4 + - + +
1549F ILE* 1.3 77.9 - - - +
1551F LEU* 1.3 68.0 + - - +
1552F LYS* 4.9 2.2 - - + +
1556F ILE* 3.0 9.6 - - - +
1557F LEU* 2.8 50.8 + - + +
1558F GLU 5.4 0.7 - - - +
1559F PHE* 4.8 0.8 - - - +
1565F LEU* 5.0 4.7 - - + -
1571F SER* 4.4 10.8 - - - +
1572F VAL* 5.5 4.5 - - + -
1573F PHE* 4.0 26.2 - - + +
1576F PHE* 4.6 18.8 - - + -
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Residues in contact with LEU1551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361F LEU* 4.4 13.2 - - + -
1364F VAL* 5.5 0.9 - - + -
1376F ILE* 4.1 19.1 - - + -
1377F CYS 3.4 9.1 + - - +
1378F GLY* 4.1 7.3 - - - -
1379F ARG* 3.9 6.8 + - - -
1382F SER* 2.9 32.3 + - - +
1383F GLY 4.2 5.6 - - - +
1384F LYS* 3.7 39.7 - - + +
1387F PHE* 5.0 8.5 - - + -
1549F ILE* 4.7 1.3 - - + -
1550F VAL* 1.3 77.0 - - - +
1552F LYS* 1.3 61.4 + - - +
1555F ALA* 3.3 28.0 - - - +
1556F ILE* 3.6 19.3 - - + -
1576F PHE* 6.0 0.2 - - - -
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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