Contacts of the helix formed by residues 159 - 169 (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 ASP 159 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1469 TYR* 5.9 0.7 - - - -
1579 LYS 3.9 2.6 + - - +
1589 LEU* 1.3 73.6 - - - +
1609 TYR* 1.3 57.5 + - - +
1619 ILE* 3.1 8.3 - - + +
1629 THR* 2.9 14.8 + - - +
1639 TYR* 2.7 34.9 + - - +
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Residues in contact with TYR 160 (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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1439 HIS* 6.3 1.8 - - - -
1469 TYR* 4.8 15.4 - - + +
1599 ASP* 1.3 73.1 - - - +
1619 ILE* 1.3 57.5 + - - +
1639 TYR* 3.2 8.6 + - - +
1649 LEU* 2.9 27.7 + - - +
3169 ARG* 6.1 5.4 - - + -
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Residues in contact with ILE 161 (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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1599 ASP* 3.1 5.9 - - + +
1609 TYR* 1.3 76.9 - - - +
1629 THR* 1.3 60.6 + - - +
1649 LEU* 3.3 8.6 + - - +
1659 SER* 2.9 26.5 + - - -
3169 ARG* 6.5 1.1 - - + -
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Residues in contact with THR 162 (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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1579 LYS 5.3 2.0 - - - -
1589 LEU* 4.7 6.7 - - - -
1599 ASP* 2.9 26.0 + - - +
1619 ILE* 1.3 75.3 - - - +
1639 TYR* 1.3 60.6 + - - +
1659 SER* 3.3 11.0 - - - -
1669 ILE* 2.9 24.6 + - - +
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Residues in contact with TYR 163 (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* 4.6 19.3 - - + -
1499 TYR* 5.6 6.5 - - + -
1589 LEU* 5.4 7.1 - - + +
1599 ASP 2.7 11.3 + - - +
1609 TYR* 3.3 13.7 - - - +
1629 THR* 1.3 75.3 - - - +
1649 LEU* 1.3 59.9 + - - +
1669 ILE* 2.9 23.8 + - - +
1679 PHE* 2.9 13.7 + - - +
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Residues in contact with LEU 164 (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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1609 TYR 2.9 12.8 + - - +
1619 ILE* 3.3 11.4 + - - +
1639 TYR* 1.3 75.6 - - - +
1659 SER* 1.3 63.6 + - - +
1679 PHE* 3.1 10.0 + - - +
1689 ASP* 2.9 23.0 + - - +
3139 ASP* 5.2 15.7 - - + -
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Residues in contact with SER 165 (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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1619 ILE 2.9 14.5 + - - -
1629 THR* 3.3 15.0 - - - -
1649 LEU* 1.3 76.2 - - - +
1669 ILE* 1.3 62.3 + - - +
1689 ASP* 3.5 19.5 - - - +
1699 GLN* 4.0 2.6 + - - +
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Residues in contact with ILE 166 (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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1629 THR 2.9 12.1 + - - +
1639 TYR* 2.9 17.1 + - - +
1659 SER* 1.3 74.6 - - - +
1679 PHE* 1.3 63.6 + - - +
1699 GLN* 3.1 24.6 + - - +
1749 PRO* 5.0 16.4 - - + -
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Residues in contact with PHE 167 (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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1639 TYR 2.9 11.3 + - - +
1649 LEU* 3.1 13.2 + - - +
1669 ILE* 1.3 76.0 - - - +
1689 ASP* 1.3 53.0 + - - +
1709 LEU* 2.8 37.5 + - - +
1719 PHE 4.1 0.7 + - - -
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Residues in contact with ASP 168 (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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1649 LEU 2.9 11.9 + - - +
1659 SER* 3.5 16.4 - - - +
1669 ILE 3.2 0.4 - - - -
1679 PHE* 1.3 75.4 - - - +
1699 GLN* 1.3 63.1 + - - +
1719 PHE* 2.7 26.2 + - + +
1729 ASP* 3.9 2.3 + - - +
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Residues in contact with GLN 169 (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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1659 SER 4.0 2.9 + - - +
1669 ILE* 3.1 17.9 + - - +
1679 PHE 2.9 0.2 + - - -
1689 ASP* 1.3 77.2 - - - +
1709 LEU* 1.3 54.9 + - - +
1729 ASP* 3.2 29.5 + - - +
1739 ILE* 6.5 1.1 - - - -
1749 PRO 6.3 0.7 - - - -
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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