Contacts of the helix formed by residues 142 - 154 (chain 9) in PDB entry 6FF7
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 LEU 142 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409 LEU* 3.2 10.4 + - + +
1419 ASP* 1.3 73.0 - - - +
1439 HIS* 1.3 66.1 + - - +
1449 ASP 3.3 2.2 - - - -
1459 CYS* 3.2 14.5 + - + +
1469 TYR* 2.9 20.5 + - - +
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Residues in contact with HIS 143 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419 ASP* 3.6 3.3 - - + -
1429 LEU* 1.3 77.7 - - - +
1449 ASP* 1.3 56.2 + - - +
1469 TYR* 2.7 29.8 + - - +
1479 LEU* 2.9 11.8 + - - +
1609 TYR* 6.3 2.0 - - - -
92h LYS* 5.4 12.8 - - + -
93h ASP 5.6 6.1 - - - +
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Residues in contact with ASP 144 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419 ASP* 4.9 7.9 + - + +
1429 LEU 3.3 1.3 - - - +
1439 HIS* 1.3 78.4 - - - +
1459 CYS* 1.3 57.7 + - - +
1479 LEU* 3.1 12.2 + - - +
1489 LYS* 3.0 25.9 + - - +
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Residues in contact with CYS 145 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419 ASP 5.3 0.6 + - - +
1429 LEU* 3.2 18.1 + - + +
1449 ASP* 1.3 75.5 - - - +
1469 TYR* 1.3 60.8 + - - +
1489 LYS* 3.8 9.2 - - - +
1499 TYR* 2.9 28.8 + - - +
1899 LEU* 5.4 13.0 - - + -
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Residues in contact with TYR 146 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429 LEU 2.9 11.7 + - - +
1439 HIS* 2.7 22.9 + - - +
1459 CYS* 1.3 69.6 - - - +
1479 LEU* 1.3 61.9 + - - +
1499 TYR* 3.2 7.5 + - - +
1509 ILE* 2.9 23.0 + - - +
1599 ASP 5.9 0.2 - - - -
1609 TYR* 4.8 15.7 - - + +
1639 TYR* 4.6 21.3 - - + -
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Residues in contact with LEU 147 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439 HIS 2.9 8.7 + - - +
1449 ASP* 3.1 13.5 - - - +
1469 TYR* 1.3 72.2 - - - +
1489 LYS* 1.3 68.2 + - - +
1509 ILE* 2.8 19.7 + - - +
1519 ASN* 3.0 11.1 + - - +
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Residues in contact with LYS 148 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1449 ASP 3.0 9.0 + - - +
1459 CYS* 3.9 11.0 - - - +
1479 LEU* 1.3 78.6 - - - +
1499 TYR* 1.3 56.7 + - - +
1519 ASN* 3.1 13.2 + - - +
1529 LEU* 2.9 26.0 + - - +
1859 TYR* 5.8 8.7 - - + -
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Residues in contact with TYR 149 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459 CYS 2.9 20.6 + - - +
1469 TYR* 3.3 8.7 - - - +
1479 LEU 2.9 0.2 + - - -
1489 LYS* 1.3 74.7 - - - +
1509 ILE* 1.3 61.2 + - - +
1529 LEU* 2.8 23.7 + - - +
1539 LYS* 2.9 16.7 + - - +
1639 TYR* 5.6 7.0 - - + -
1859 TYR* 6.0 2.9 - - - -
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Residues in contact with ILE 150 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469 TYR 2.9 11.8 + - - +
1479 LEU* 2.8 12.6 + - - +
1499 TYR* 1.3 74.4 - - - +
1519 ASN* 1.3 63.4 + - - +
1539 LYS* 3.4 3.4 + - - +
1549 ALA* 3.2 19.4 + - - -
1559 SER 3.6 23.4 + - - +
1569 GLU* 5.6 2.5 - - - -
1589 LEU* 5.7 11.2 - - + +
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Residues in contact with ASN 151 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479 LEU 3.0 11.0 + - - +
1489 LYS* 3.2 16.8 - - - +
1509 ILE* 1.3 77.8 - - - +
1529 LEU* 1.3 59.5 + - - +
1549 ALA* 4.0 7.9 + - - +
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Residues in contact with LEU 152 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489 LYS 2.9 10.2 + - - +
1499 TYR* 2.8 14.5 + - - +
1519 ASN* 1.3 76.1 - - - +
1539 LYS* 1.3 58.3 + - - +
1549 ALA* 3.2 6.7 + - - +
1819 GLU* 4.5 34.2 - - + +
1829 TYR* 5.3 2.7 - - - +
1859 TYR* 5.0 9.4 - - + -
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Residues in contact with LYS 153 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499 TYR 2.9 12.5 + - - +
1509 ILE* 4.4 3.8 - - - +
1529 LEU* 1.3 75.0 - - + +
1549 ALA* 1.3 72.0 + - - +
1559 SER* 3.3 10.9 + - - +
1589 LEU* 5.9 7.0 - - + -
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Residues in contact with ALA 154 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509 ILE 3.2 9.4 + - - -
1519 ASN* 4.0 6.3 + - - +
1529 LEU 3.2 6.3 - - - +
1539 LYS* 1.3 81.5 - - - +
1559 SER* 1.3 61.9 + - - +
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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